Analyze Visium fluorescence data

This tutorial shows how to apply Squidpy image analysis features for the analysis of Visium data.

For a tutorial using Visium data that includes the graph analysis functions, have a look at Analyze Visium H&E data. The dataset used here consists of a Visium slide of a coronal section of the mouse brain. The original dataset is publicly available at the 10x genomics dataset portal . Here, we provide a pre-processed dataset, with pre-annotated clusters, in anndata.AnnData format and the tissue image in squidpy.im.ImageContainer format.

A couple of notes on pre-processing:

• The pre-processing pipeline is the same as the one shown in the original Scanpy tutorial .

• The cluster annotation was performed using several resources, such as the Allen Brain Atlas , the Mouse Brain gene expression atlas from the Linnarson lab and this recent pre-print [Villacampa et al., 2020].

See also

See Analyze Visium H&E data for additional analysis examples.

Import packages & data

To run the notebook locally, create a conda environment as conda env create -f environment.yml using this environment.yml.

import scanpy as sc
import anndata as ad
import squidpy as sq

import pandas as pd

import matplotlib.pyplot as plt

sc.logging.print_header()
print(f"squidpy=={sq.__version__}")

# load the pre-processed dataset
img = sq.datasets.visium_fluo_image_crop()
adata = sq.datasets.visium_fluo_adata_crop()

Out:

scanpy==1.9.1 anndata==0.8.0 umap==0.5.3 numpy==1.22.4 scipy==1.8.1 pandas==1.4.2 scikit-learn==1.1.1 statsmodels==0.13.2 python-igraph==0.9.11 pynndescent==0.5.7
squidpy==1.2.2

First, let’s visualize the cluster annotation in the spatial context with squidpy.pl.spatial_scatter().

As you can see, this dataset is a smaller crop of the whole brain section. We provide this crop to make the execution time of this tutorial a bit shorter.

sq.pl.spatial_scatter(adata, color="cluster")

The fluorescence image provided with this dataset has three channels: DAPI (specific to DNA), anti-NEUN (specific to neurons), anti-GFAP (specific to Glial cells). We can directly visualize the channels with the method squidpy.im.ImageContainer.show().

img.show(channelwise=True)

Visium datasets contain high-resolution images of the tissue. Using the function squidpy.im.calculate_image_features() you can calculate image features for each Visium spot and create a obs x features matrix in adata that can then be analyzed together with the obs x gene gene expression matrix.

By extracting image features we are aiming to get both similar and complementary information to the gene expression values. Similar information is for example present in the case of a tissue with two different cell types whose morphology is different. Such cell type information is then contained in both the gene expression values and the tissue image features. Complementary or additional information is present in the fact that we can use a nucleus segmentation to count cells and add features summarizing the immediate spatial neighborhood of a spot.

Squidpy contains several feature extractors and a flexible pipeline of calculating features of different scales and sizes. There are several detailed examples of how to use squidpy.im.calculate_image_features(). Extract image features provides a good starting point for learning more.

Here, we will extract summary, histogram, segmentation, and texture features. To provide more context and allow the calculation of multi-scale features, we will additionally calculate summary and histogram features at different crop sizes and scales.

Image segmentation

To calculate segmentation features, we first need to segment the tissue image using squidpy.im.segment(). But even before that, it’s best practice to pre-process the image by e.g. smoothing it using in squidpy.im.process(). We will then use the DAPI channel of the fluorescence image (channel_id s= 0). Please refer to Cell-segmentation for fluorescence images for more details on how to calculate a segmented image.

sq.im.process(
    img=img,
    layer="image",
    method="smooth",
)

sq.im.segment(img=img, layer="image_smooth", method="watershed", channel=0, chunks=1000)

# plot the resulting segmentation
fig, ax = plt.subplots(1, 2)
img_crop = img.crop_corner(2000, 2000, size=500)
img_crop.show(layer="image", channel=0, ax=ax[0])
img_crop.show(
    layer="segmented_watershed",
    channel=0,
    ax=ax[1],
)

The result of squidpy.im.segment() is saved in img['segmented_watershed'] by default. It is a label image where each segmented object is annotated with a different integer number.

Segmentation features

We can now use the segmentation to calculate segmentation features. These include morphological features of the segmented objects and channel-wise image intensities beneath the segmentation mask. In particular, we can count the segmented objects within each Visium spot to get an approximation of the number of cells. In addition, we can calculate the mean intensity of each fluorescence channel within the segmented objects. Depending on the fluorescence channels, this can give us e.g., an estimation of the cell type. For more details on how the segmentation features, you can have a look at the docs of squidpy.im.calculate_image_features() or the example at Extract segmentation features.

# define image layer to use for segmentation
features_kwargs = {"segmentation": {"label_layer": "segmented_watershed"}}
# calculate segmentation features
sq.im.calculate_image_features(
    adata,
    img,
    features="segmentation",
    layer="image",
    key_added="features_segmentation",
    n_jobs=1,
    features_kwargs=features_kwargs,
)
# plot results and compare with gene-space clustering
sq.pl.spatial_scatter(
    sq.pl.extract(adata, "features_segmentation"),
    color=[
        "segmentation_label",
        "cluster",
        "segmentation_ch-0_mean_intensity_mean",
        "segmentation_ch-1_mean_intensity_mean",
    ],
    frameon=False,
    ncols=2,
)

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 34%|###3      | 236/704 [01:02<01:48,  4.31/s]
 34%|###3      | 237/704 [01:03<01:51,  4.20/s]
 34%|###3      | 238/704 [01:03<01:51,  4.16/s]
 34%|###3      | 239/704 [01:03<01:50,  4.21/s]
 34%|###4      | 240/704 [01:03<01:50,  4.21/s]
 34%|###4      | 241/704 [01:03<01:48,  4.26/s]
 34%|###4      | 242/704 [01:04<01:50,  4.19/s]
 35%|###4      | 243/704 [01:04<01:50,  4.19/s]
 35%|###4      | 244/704 [01:04<01:48,  4.23/s]
 35%|###4      | 245/704 [01:04<01:48,  4.25/s]
 35%|###4      | 246/704 [01:05<01:48,  4.24/s]
 35%|###5      | 247/704 [01:05<01:47,  4.27/s]
 35%|###5      | 248/704 [01:05<01:46,  4.27/s]
 35%|###5      | 249/704 [01:05<01:46,  4.27/s]
 36%|###5      | 250/704 [01:06<01:46,  4.28/s]
 36%|###5      | 251/704 [01:06<01:45,  4.29/s]
 36%|###5      | 252/704 [01:06<01:45,  4.29/s]
 36%|###5      | 253/704 [01:06<01:43,  4.35/s]
 36%|###6      | 254/704 [01:06<01:43,  4.35/s]
 36%|###6      | 255/704 [01:07<01:44,  4.28/s]
 36%|###6      | 256/704 [01:07<01:44,  4.30/s]
 37%|###6      | 257/704 [01:07<01:44,  4.28/s]
 37%|###6      | 258/704 [01:07<01:44,  4.25/s]
 37%|###6      | 259/704 [01:08<01:45,  4.23/s]
 37%|###6      | 260/704 [01:08<01:46,  4.16/s]
 37%|###7      | 261/704 [01:08<01:48,  4.07/s]
 37%|###7      | 262/704 [01:08<01:45,  4.17/s]
 37%|###7      | 263/704 [01:09<01:44,  4.22/s]
 38%|###7      | 264/704 [01:09<01:45,  4.17/s]
 38%|###7      | 265/704 [01:09<01:45,  4.17/s]
 38%|###7      | 266/704 [01:09<01:47,  4.08/s]
 38%|###7      | 267/704 [01:10<01:46,  4.11/s]
 38%|###8      | 268/704 [01:10<01:43,  4.20/s]
 38%|###8      | 269/704 [01:10<01:41,  4.27/s]
 38%|###8      | 270/704 [01:10<01:41,  4.29/s]
 38%|###8      | 271/704 [01:11<01:41,  4.27/s]
 39%|###8      | 272/704 [01:11<01:41,  4.24/s]
 39%|###8      | 273/704 [01:11<01:41,  4.24/s]
 39%|###8      | 274/704 [01:11<01:44,  4.13/s]
 39%|###9      | 275/704 [01:12<01:43,  4.14/s]
 39%|###9      | 276/704 [01:12<01:44,  4.09/s]
 39%|###9      | 277/704 [01:12<01:45,  4.05/s]
 39%|###9      | 278/704 [01:12<01:44,  4.09/s]
 40%|###9      | 279/704 [01:12<01:43,  4.12/s]
 40%|###9      | 280/704 [01:13<01:43,  4.11/s]
 40%|###9      | 281/704 [01:13<01:45,  4.02/s]
 40%|####      | 282/704 [01:13<01:43,  4.07/s]
 40%|####      | 283/704 [01:14<01:46,  3.97/s]
 40%|####      | 284/704 [01:14<01:45,  3.98/s]
 40%|####      | 285/704 [01:14<01:44,  4.01/s]
 41%|####      | 286/704 [01:14<01:44,  4.02/s]
 41%|####      | 287/704 [01:14<01:41,  4.10/s]
 41%|####      | 288/704 [01:15<01:38,  4.23/s]
 41%|####1     | 289/704 [01:15<01:34,  4.37/s]
 41%|####1     | 290/704 [01:15<01:34,  4.40/s]
 41%|####1     | 291/704 [01:15<01:34,  4.37/s]
 41%|####1     | 292/704 [01:16<01:36,  4.26/s]
 42%|####1     | 293/704 [01:16<01:38,  4.18/s]
 42%|####1     | 294/704 [01:16<01:37,  4.21/s]
 42%|####1     | 295/704 [01:16<01:36,  4.22/s]
 42%|####2     | 296/704 [01:17<01:34,  4.30/s]
 42%|####2     | 297/704 [01:17<01:35,  4.28/s]
 42%|####2     | 298/704 [01:17<01:34,  4.30/s]
 42%|####2     | 299/704 [01:17<01:33,  4.32/s]
 43%|####2     | 300/704 [01:17<01:35,  4.23/s]
 43%|####2     | 301/704 [01:18<01:35,  4.21/s]
 43%|####2     | 302/704 [01:18<01:35,  4.21/s]
 43%|####3     | 303/704 [01:18<01:36,  4.17/s]
 43%|####3     | 304/704 [01:18<01:35,  4.18/s]
 43%|####3     | 305/704 [01:19<01:35,  4.17/s]
 43%|####3     | 306/704 [01:19<01:35,  4.16/s]
 44%|####3     | 307/704 [01:19<01:35,  4.15/s]
 44%|####3     | 308/704 [01:19<01:33,  4.23/s]
 44%|####3     | 309/704 [01:20<01:33,  4.24/s]
 44%|####4     | 310/704 [01:20<01:34,  4.19/s]
 44%|####4     | 311/704 [01:20<01:32,  4.24/s]
 44%|####4     | 312/704 [01:20<01:31,  4.29/s]
 44%|####4     | 313/704 [01:21<01:30,  4.30/s]
 45%|####4     | 314/704 [01:21<01:32,  4.21/s]
 45%|####4     | 315/704 [01:21<01:33,  4.17/s]
 45%|####4     | 316/704 [01:21<01:34,  4.12/s]
 45%|####5     | 317/704 [01:22<01:37,  3.96/s]
 45%|####5     | 318/704 [01:22<01:38,  3.90/s]
 45%|####5     | 319/704 [01:22<01:37,  3.94/s]
 45%|####5     | 320/704 [01:22<01:36,  3.96/s]
 46%|####5     | 321/704 [01:23<01:34,  4.06/s]
 46%|####5     | 322/704 [01:23<01:34,  4.04/s]
 46%|####5     | 323/704 [01:23<01:31,  4.17/s]
 46%|####6     | 324/704 [01:23<01:30,  4.21/s]
 46%|####6     | 325/704 [01:24<01:28,  4.26/s]
 46%|####6     | 326/704 [01:24<01:28,  4.28/s]
 46%|####6     | 327/704 [01:24<01:28,  4.28/s]
 47%|####6     | 328/704 [01:24<01:27,  4.32/s]
 47%|####6     | 329/704 [01:24<01:26,  4.35/s]
 47%|####6     | 330/704 [01:25<01:27,  4.29/s]
 47%|####7     | 331/704 [01:25<01:26,  4.31/s]
 47%|####7     | 332/704 [01:25<01:26,  4.32/s]
 47%|####7     | 333/704 [01:25<01:27,  4.23/s]
 47%|####7     | 334/704 [01:26<01:26,  4.27/s]
 48%|####7     | 335/704 [01:26<01:27,  4.22/s]
 48%|####7     | 336/704 [01:26<01:27,  4.23/s]
 48%|####7     | 337/704 [01:26<01:26,  4.24/s]
 48%|####8     | 338/704 [01:27<01:27,  4.21/s]
 48%|####8     | 339/704 [01:27<01:25,  4.28/s]
 48%|####8     | 340/704 [01:27<01:25,  4.27/s]
 48%|####8     | 341/704 [01:27<01:23,  4.33/s]
 49%|####8     | 342/704 [01:27<01:23,  4.35/s]
 49%|####8     | 343/704 [01:28<01:23,  4.33/s]
 49%|####8     | 344/704 [01:28<01:24,  4.26/s]
 49%|####9     | 345/704 [01:28<01:23,  4.27/s]
 49%|####9     | 346/704 [01:28<01:24,  4.26/s]
 49%|####9     | 347/704 [01:29<01:22,  4.30/s]
 49%|####9     | 348/704 [01:29<01:23,  4.27/s]
 50%|####9     | 349/704 [01:29<01:22,  4.28/s]
 50%|####9     | 350/704 [01:29<01:24,  4.18/s]
 50%|####9     | 351/704 [01:30<01:31,  3.88/s]
 50%|#####     | 352/704 [01:30<01:28,  3.97/s]
 50%|#####     | 353/704 [01:30<01:28,  3.95/s]
 50%|#####     | 354/704 [01:30<01:27,  4.00/s]
 50%|#####     | 355/704 [01:31<01:25,  4.09/s]
 51%|#####     | 356/704 [01:31<01:24,  4.14/s]
 51%|#####     | 357/704 [01:31<01:22,  4.21/s]
 51%|#####     | 358/704 [01:31<01:21,  4.24/s]
 51%|#####     | 359/704 [01:32<01:20,  4.29/s]
 51%|#####1    | 360/704 [01:32<01:20,  4.30/s]
 51%|#####1    | 361/704 [01:32<01:21,  4.23/s]
 51%|#####1    | 362/704 [01:32<01:21,  4.20/s]
 52%|#####1    | 363/704 [01:33<01:21,  4.16/s]
 52%|#####1    | 364/704 [01:33<01:22,  4.13/s]
 52%|#####1    | 365/704 [01:33<01:22,  4.12/s]
 52%|#####1    | 366/704 [01:33<01:21,  4.17/s]
 52%|#####2    | 367/704 [01:34<01:21,  4.12/s]
 52%|#####2    | 368/704 [01:34<01:20,  4.16/s]
 52%|#####2    | 369/704 [01:34<01:20,  4.17/s]
 53%|#####2    | 370/704 [01:34<01:19,  4.21/s]
 53%|#####2    | 371/704 [01:34<01:20,  4.12/s]
 53%|#####2    | 372/704 [01:35<01:21,  4.09/s]
 53%|#####2    | 373/704 [01:35<01:19,  4.14/s]
 53%|#####3    | 374/704 [01:35<01:19,  4.17/s]
 53%|#####3    | 375/704 [01:35<01:19,  4.15/s]
 53%|#####3    | 376/704 [01:36<01:20,  4.10/s]
 54%|#####3    | 377/704 [01:36<01:22,  3.99/s]
 54%|#####3    | 378/704 [01:36<01:21,  4.01/s]
 54%|#####3    | 379/704 [01:36<01:19,  4.10/s]
 54%|#####3    | 380/704 [01:37<01:17,  4.21/s]
 54%|#####4    | 381/704 [01:37<01:17,  4.19/s]
 54%|#####4    | 382/704 [01:37<01:16,  4.20/s]
 54%|#####4    | 383/704 [01:37<01:15,  4.24/s]
 55%|#####4    | 384/704 [01:38<01:15,  4.27/s]
 55%|#####4    | 385/704 [01:38<01:15,  4.23/s]
 55%|#####4    | 386/704 [01:38<01:17,  4.13/s]
 55%|#####4    | 387/704 [01:38<01:16,  4.14/s]
 55%|#####5    | 388/704 [01:39<01:14,  4.22/s]
 55%|#####5    | 389/704 [01:39<01:14,  4.23/s]
 55%|#####5    | 390/704 [01:39<01:13,  4.26/s]
 56%|#####5    | 391/704 [01:39<01:13,  4.25/s]
 56%|#####5    | 392/704 [01:40<01:14,  4.18/s]
 56%|#####5    | 393/704 [01:40<01:14,  4.20/s]
 56%|#####5    | 394/704 [01:40<01:13,  4.20/s]
 56%|#####6    | 395/704 [01:40<01:13,  4.21/s]
 56%|#####6    | 396/704 [01:40<01:13,  4.20/s]
 56%|#####6    | 397/704 [01:41<01:13,  4.19/s]
 57%|#####6    | 398/704 [01:41<01:13,  4.17/s]
 57%|#####6    | 399/704 [01:41<01:12,  4.18/s]
 57%|#####6    | 400/704 [01:41<01:11,  4.23/s]
 57%|#####6    | 401/704 [01:42<01:11,  4.23/s]
 57%|#####7    | 402/704 [01:42<01:12,  4.19/s]
 57%|#####7    | 403/704 [01:42<01:11,  4.23/s]
 57%|#####7    | 404/704 [01:42<01:10,  4.25/s]
 58%|#####7    | 405/704 [01:43<01:10,  4.24/s]
 58%|#####7    | 406/704 [01:43<01:09,  4.28/s]
 58%|#####7    | 407/704 [01:43<01:08,  4.31/s]
 58%|#####7    | 408/704 [01:43<01:09,  4.26/s]
 58%|#####8    | 409/704 [01:44<01:16,  3.88/s]
 58%|#####8    | 410/704 [01:44<01:24,  3.47/s]
 58%|#####8    | 411/704 [01:44<01:18,  3.72/s]
 59%|#####8    | 412/704 [01:44<01:13,  3.98/s]
 59%|#####8    | 413/704 [01:45<01:08,  4.24/s]
 59%|#####8    | 414/704 [01:45<01:06,  4.39/s]
 59%|#####8    | 415/704 [01:45<01:03,  4.54/s]
 59%|#####9    | 416/704 [01:45<01:02,  4.58/s]
 59%|#####9    | 417/704 [01:45<01:01,  4.64/s]
 59%|#####9    | 418/704 [01:46<01:01,  4.69/s]
 60%|#####9    | 419/704 [01:46<00:59,  4.75/s]
 60%|#####9    | 420/704 [01:46<00:59,  4.76/s]
 60%|#####9    | 421/704 [01:46<00:59,  4.74/s]
 60%|#####9    | 422/704 [01:46<00:59,  4.76/s]
 60%|######    | 423/704 [01:47<00:58,  4.83/s]
 60%|######    | 424/704 [01:47<00:57,  4.88/s]
 60%|######    | 425/704 [01:47<00:58,  4.80/s]
 61%|######    | 426/704 [01:47<00:58,  4.77/s]
 61%|######    | 427/704 [01:48<00:59,  4.67/s]
 61%|######    | 428/704 [01:48<01:01,  4.52/s]
 61%|######    | 429/704 [01:48<01:01,  4.44/s]
 61%|######1   | 430/704 [01:48<01:00,  4.51/s]
 61%|######1   | 431/704 [01:48<01:02,  4.40/s]
 61%|######1   | 432/704 [01:49<01:03,  4.29/s]
 62%|######1   | 433/704 [01:49<01:04,  4.18/s]
 62%|######1   | 434/704 [01:49<01:04,  4.20/s]
 62%|######1   | 435/704 [01:49<01:02,  4.28/s]
 62%|######1   | 436/704 [01:50<01:02,  4.31/s]
 62%|######2   | 437/704 [01:50<01:02,  4.29/s]
 62%|######2   | 438/704 [01:50<01:01,  4.30/s]
 62%|######2   | 439/704 [01:50<01:00,  4.35/s]
 62%|######2   | 440/704 [01:51<00:59,  4.41/s]
 63%|######2   | 441/704 [01:51<00:59,  4.43/s]
 63%|######2   | 442/704 [01:51<00:59,  4.43/s]
 63%|######2   | 443/704 [01:51<00:58,  4.45/s]
 63%|######3   | 444/704 [01:51<00:58,  4.47/s]
 63%|######3   | 445/704 [01:52<00:58,  4.39/s]
 63%|######3   | 446/704 [01:52<00:59,  4.33/s]
 63%|######3   | 447/704 [01:52<00:59,  4.29/s]
 64%|######3   | 448/704 [01:52<00:59,  4.34/s]
 64%|######3   | 449/704 [01:53<00:58,  4.33/s]
 64%|######3   | 450/704 [01:53<00:58,  4.34/s]
 64%|######4   | 451/704 [01:53<00:58,  4.32/s]
 64%|######4   | 452/704 [01:53<00:58,  4.31/s]
 64%|######4   | 453/704 [01:54<00:57,  4.33/s]
 64%|######4   | 454/704 [01:54<00:57,  4.34/s]
 65%|######4   | 455/704 [01:54<00:57,  4.34/s]
 65%|######4   | 456/704 [01:54<00:57,  4.34/s]
 65%|######4   | 457/704 [01:54<00:56,  4.35/s]
 65%|######5   | 458/704 [01:55<00:55,  4.40/s]
 65%|######5   | 459/704 [01:55<00:57,  4.29/s]
 65%|######5   | 460/704 [01:55<00:55,  4.40/s]
 65%|######5   | 461/704 [01:55<00:53,  4.52/s]
 66%|######5   | 462/704 [01:56<00:53,  4.54/s]
 66%|######5   | 463/704 [01:56<00:52,  4.57/s]
 66%|######5   | 464/704 [01:56<00:52,  4.57/s]
 66%|######6   | 465/704 [01:56<00:51,  4.63/s]
 66%|######6   | 466/704 [01:56<00:52,  4.53/s]
 66%|######6   | 467/704 [01:57<00:51,  4.57/s]
 66%|######6   | 468/704 [01:57<00:52,  4.47/s]
 67%|######6   | 469/704 [01:57<00:54,  4.32/s]
 67%|######6   | 470/704 [01:57<00:54,  4.31/s]
 67%|######6   | 471/704 [01:58<00:54,  4.28/s]
 67%|######7   | 472/704 [01:58<01:00,  3.86/s]
 67%|######7   | 473/704 [01:58<00:58,  3.96/s]
 67%|######7   | 474/704 [01:58<00:55,  4.11/s]
 67%|######7   | 475/704 [01:59<00:53,  4.26/s]
 68%|######7   | 476/704 [01:59<00:52,  4.35/s]
 68%|######7   | 477/704 [01:59<00:52,  4.36/s]
 68%|######7   | 478/704 [01:59<00:50,  4.45/s]
 68%|######8   | 479/704 [01:59<00:49,  4.52/s]
 68%|######8   | 480/704 [02:00<00:49,  4.49/s]
 68%|######8   | 481/704 [02:00<00:49,  4.54/s]
 68%|######8   | 482/704 [02:00<00:49,  4.53/s]
 69%|######8   | 483/704 [02:00<00:49,  4.51/s]
 69%|######8   | 484/704 [02:01<00:48,  4.52/s]
 69%|######8   | 485/704 [02:01<00:49,  4.43/s]
 69%|######9   | 486/704 [02:01<00:50,  4.36/s]
 69%|######9   | 487/704 [02:01<00:49,  4.35/s]
 69%|######9   | 488/704 [02:01<00:48,  4.44/s]
 69%|######9   | 489/704 [02:02<00:48,  4.42/s]
 70%|######9   | 490/704 [02:02<00:51,  4.18/s]
 70%|######9   | 491/704 [02:02<00:50,  4.18/s]
 70%|######9   | 492/704 [02:02<00:51,  4.13/s]
 70%|#######   | 493/704 [02:03<00:51,  4.13/s]
 70%|#######   | 494/704 [02:03<00:50,  4.13/s]
 70%|#######   | 495/704 [02:03<00:50,  4.14/s]
 70%|#######   | 496/704 [02:03<00:50,  4.11/s]
 71%|#######   | 497/704 [02:04<00:49,  4.18/s]
 71%|#######   | 498/704 [02:04<00:48,  4.21/s]
 71%|#######   | 499/704 [02:04<00:49,  4.12/s]
 71%|#######1  | 500/704 [02:04<00:49,  4.12/s]
 71%|#######1  | 501/704 [02:05<00:49,  4.10/s]
 71%|#######1  | 502/704 [02:05<00:49,  4.11/s]
 71%|#######1  | 503/704 [02:05<00:48,  4.13/s]
 72%|#######1  | 504/704 [02:05<00:50,  3.98/s]
 72%|#######1  | 505/704 [02:06<00:51,  3.90/s]
 72%|#######1  | 506/704 [02:06<00:51,  3.87/s]
 72%|#######2  | 507/704 [02:06<00:52,  3.76/s]
 72%|#######2  | 508/704 [02:07<00:52,  3.70/s]
 72%|#######2  | 509/704 [02:07<00:51,  3.75/s]
 72%|#######2  | 510/704 [02:07<00:52,  3.70/s]
 73%|#######2  | 511/704 [02:07<00:52,  3.66/s]
 73%|#######2  | 512/704 [02:08<00:53,  3.56/s]
 73%|#######2  | 513/704 [02:08<00:53,  3.56/s]
 73%|#######3  | 514/704 [02:08<00:52,  3.59/s]
 73%|#######3  | 515/704 [02:08<00:51,  3.69/s]
 73%|#######3  | 516/704 [02:09<00:51,  3.66/s]
 73%|#######3  | 517/704 [02:09<00:52,  3.57/s]
 74%|#######3  | 518/704 [02:09<00:50,  3.71/s]
 74%|#######3  | 519/704 [02:09<00:48,  3.79/s]
 74%|#######3  | 520/704 [02:10<00:48,  3.82/s]
 74%|#######4  | 521/704 [02:10<00:48,  3.75/s]
 74%|#######4  | 522/704 [02:10<00:49,  3.71/s]
 74%|#######4  | 523/704 [02:11<00:47,  3.77/s]
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Above, we made use of squidpy.pl.extract(), a method to extract all features in a given adata.obsm[‘{key}’] and temporarily save them to anndata.AnnData.obs. Such method is particularly useful for plotting purpose, as shown above.

The number of cells per Visium spot provides an interesting view of the data that can enhance the characterization of gene-space clusters. We can see that the cell-rich pyramidal layer of the Hippocampus has more cells than the surrounding areas (upper left). This fine-grained view of the Hippocampus is not visible in the gene clusters where the Hippocampus is one cluster only.

The per-channel intensities plotted in the second row show us that the areas labeled with Cortex_1 and Cortex_3 have a higher intensity of channel 1, anti-NEUN (lower left). This means that these areas have more neurons that the remaining areas in this crop. In addition, cluster Fiber_tracts and lateral ventricles seems to be enriched with Glial cells, seen by the larger mean intensities of channel 2, anti-GFAP, in these areas (lower right).

Extract and cluster features

Now we will calculate summary, histogram, and texture features. These features provide a useful compressed summary of the tissue image. For more information on these features, refer to:

• Extract summary features.

• Extract histogram features.

• Extract texture features.

# define different feature calculation combinations
params = {
    # all features, corresponding only to tissue underneath spot
    "features_orig": {
        "features": ["summary", "texture", "histogram"],
        "scale": 1.0,
        "mask_circle": True,
    },
    # summary and histogram features with a bit more context, original resolution
    "features_context": {"features": ["summary", "histogram"], "scale": 1.0},
    # summary and histogram features with more context and at lower resolution
    "features_lowres": {"features": ["summary", "histogram"], "scale": 0.25},
}

for feature_name, cur_params in params.items():
    # features will be saved in `adata.obsm[feature_name]`
    sq.im.calculate_image_features(adata, img, layer="image", key_added=feature_name, n_jobs=1, **cur_params)

# combine features in one dataframe
adata.obsm["features"] = pd.concat([adata.obsm[f] for f in params.keys()], axis="columns")

# make sure that we have no duplicated feature names in the combined table
adata.obsm["features"].columns = ad.utils.make_index_unique(adata.obsm["features"].columns)

Out:

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 12%|#1        | 84/704 [00:31<03:07,  3.31/s]
 12%|#2        | 85/704 [00:32<03:06,  3.31/s]
 12%|#2        | 86/704 [00:32<03:06,  3.31/s]
 12%|#2        | 87/704 [00:32<03:06,  3.30/s]
 12%|#2        | 88/704 [00:33<03:04,  3.34/s]
 13%|#2        | 89/704 [00:33<03:03,  3.35/s]
 13%|#2        | 90/704 [00:33<03:02,  3.37/s]
 13%|#2        | 91/704 [00:34<03:01,  3.38/s]
 13%|#3        | 92/704 [00:34<03:00,  3.39/s]
 13%|#3        | 93/704 [00:34<02:59,  3.41/s]
 13%|#3        | 94/704 [00:34<03:00,  3.37/s]
 13%|#3        | 95/704 [00:35<03:00,  3.37/s]
 14%|#3        | 96/704 [00:35<03:02,  3.34/s]
 14%|#3        | 97/704 [00:35<03:01,  3.34/s]
 14%|#3        | 98/704 [00:36<03:05,  3.26/s]
 14%|#4        | 99/704 [00:36<03:13,  3.13/s]
 14%|#4        | 100/704 [00:36<03:14,  3.10/s]
 14%|#4        | 101/704 [00:37<03:10,  3.17/s]
 14%|#4        | 102/704 [00:37<03:11,  3.14/s]
 15%|#4        | 103/704 [00:37<03:12,  3.12/s]
 15%|#4        | 104/704 [00:38<03:10,  3.15/s]
 15%|#4        | 105/704 [00:38<03:07,  3.19/s]
 15%|#5        | 106/704 [00:38<03:02,  3.28/s]
 15%|#5        | 107/704 [00:38<02:58,  3.34/s]
 15%|#5        | 108/704 [00:39<02:56,  3.37/s]
 15%|#5        | 109/704 [00:39<02:56,  3.36/s]
 16%|#5        | 110/704 [00:39<02:55,  3.38/s]
 16%|#5        | 111/704 [00:40<02:55,  3.37/s]
 16%|#5        | 112/704 [00:40<02:55,  3.37/s]
 16%|#6        | 113/704 [00:40<02:55,  3.37/s]
 16%|#6        | 114/704 [00:41<02:55,  3.35/s]
 16%|#6        | 115/704 [00:41<02:56,  3.33/s]
 16%|#6        | 116/704 [00:41<02:56,  3.32/s]
 17%|#6        | 117/704 [00:41<02:56,  3.33/s]
 17%|#6        | 118/704 [00:42<02:55,  3.34/s]
 17%|#6        | 119/704 [00:42<02:55,  3.33/s]
 17%|#7        | 120/704 [00:42<02:54,  3.35/s]
 17%|#7        | 121/704 [00:43<02:53,  3.36/s]
 17%|#7        | 122/704 [00:43<02:52,  3.37/s]
 17%|#7        | 123/704 [00:43<02:52,  3.38/s]
 18%|#7        | 124/704 [00:44<02:53,  3.33/s]
 18%|#7        | 125/704 [00:44<02:53,  3.33/s]
 18%|#7        | 126/704 [00:44<02:53,  3.34/s]
 18%|#8        | 127/704 [00:44<02:51,  3.37/s]
 18%|#8        | 128/704 [00:45<02:50,  3.38/s]
 18%|#8        | 129/704 [00:45<02:53,  3.31/s]
 18%|#8        | 130/704 [00:45<02:53,  3.32/s]
 19%|#8        | 131/704 [00:46<02:53,  3.31/s]
 19%|#8        | 132/704 [00:46<02:52,  3.32/s]
 19%|#8        | 133/704 [00:46<02:51,  3.34/s]
 19%|#9        | 134/704 [00:47<02:50,  3.34/s]
 19%|#9        | 135/704 [00:47<02:51,  3.31/s]
 19%|#9        | 136/704 [00:47<02:51,  3.32/s]
 19%|#9        | 137/704 [00:47<02:52,  3.29/s]
 20%|#9        | 138/704 [00:48<02:53,  3.27/s]
 20%|#9        | 139/704 [00:48<02:54,  3.24/s]
 20%|#9        | 140/704 [00:48<02:53,  3.24/s]
 20%|##        | 141/704 [00:49<02:50,  3.30/s]
 20%|##        | 142/704 [00:49<02:49,  3.32/s]
 20%|##        | 143/704 [00:49<02:48,  3.32/s]
 20%|##        | 144/704 [00:50<02:53,  3.23/s]
 21%|##        | 145/704 [00:50<02:51,  3.26/s]
 21%|##        | 146/704 [00:50<02:52,  3.24/s]
 21%|##        | 147/704 [00:51<02:52,  3.23/s]
 21%|##1       | 148/704 [00:51<02:50,  3.26/s]
 21%|##1       | 149/704 [00:51<02:48,  3.28/s]
 21%|##1       | 150/704 [00:51<02:50,  3.25/s]
 21%|##1       | 151/704 [00:52<02:50,  3.24/s]
 22%|##1       | 152/704 [00:52<02:48,  3.28/s]
 22%|##1       | 153/704 [00:52<02:45,  3.33/s]
 22%|##1       | 154/704 [00:53<02:42,  3.38/s]
 22%|##2       | 155/704 [00:53<02:42,  3.38/s]
 22%|##2       | 156/704 [00:53<02:46,  3.30/s]
 22%|##2       | 157/704 [00:54<02:46,  3.28/s]
 22%|##2       | 158/704 [00:54<02:57,  3.08/s]
 23%|##2       | 159/704 [00:54<03:03,  2.97/s]
 23%|##2       | 160/704 [00:55<02:59,  3.04/s]
 23%|##2       | 161/704 [00:55<02:52,  3.14/s]
 23%|##3       | 162/704 [00:55<02:48,  3.22/s]
 23%|##3       | 163/704 [00:55<02:49,  3.20/s]
 23%|##3       | 164/704 [00:56<02:55,  3.07/s]
 23%|##3       | 165/704 [00:56<02:51,  3.14/s]
 24%|##3       | 166/704 [00:56<02:48,  3.20/s]
 24%|##3       | 167/704 [00:57<02:44,  3.26/s]
 24%|##3       | 168/704 [00:57<02:42,  3.30/s]
 24%|##4       | 169/704 [00:57<02:40,  3.34/s]
 24%|##4       | 170/704 [00:58<02:39,  3.35/s]
 24%|##4       | 171/704 [00:58<02:38,  3.36/s]
 24%|##4       | 172/704 [00:58<02:37,  3.38/s]
 25%|##4       | 173/704 [00:58<02:36,  3.38/s]
 25%|##4       | 174/704 [00:59<02:35,  3.40/s]
 25%|##4       | 175/704 [00:59<02:36,  3.39/s]
 25%|##5       | 176/704 [00:59<02:36,  3.38/s]
 25%|##5       | 177/704 [01:00<02:36,  3.37/s]
 25%|##5       | 178/704 [01:00<02:35,  3.38/s]
 25%|##5       | 179/704 [01:00<02:36,  3.36/s]
 26%|##5       | 180/704 [01:01<02:38,  3.32/s]
 26%|##5       | 181/704 [01:01<02:38,  3.29/s]
 26%|##5       | 182/704 [01:01<02:39,  3.28/s]
 26%|##5       | 183/704 [01:02<02:38,  3.28/s]
 26%|##6       | 184/704 [01:02<02:37,  3.31/s]
 26%|##6       | 185/704 [01:02<02:36,  3.32/s]
 26%|##6       | 186/704 [01:02<02:35,  3.34/s]
 27%|##6       | 187/704 [01:03<02:34,  3.35/s]
 27%|##6       | 188/704 [01:03<02:34,  3.35/s]
 27%|##6       | 189/704 [01:03<02:33,  3.35/s]
 27%|##6       | 190/704 [01:04<02:33,  3.36/s]
 27%|##7       | 191/704 [01:04<02:35,  3.31/s]
 27%|##7       | 192/704 [01:04<02:34,  3.31/s]
 27%|##7       | 193/704 [01:05<02:35,  3.29/s]
 28%|##7       | 194/704 [01:05<02:33,  3.32/s]
 28%|##7       | 195/704 [01:05<02:32,  3.33/s]
 28%|##7       | 196/704 [01:05<02:31,  3.35/s]
 28%|##7       | 197/704 [01:06<02:31,  3.34/s]
 28%|##8       | 198/704 [01:06<02:33,  3.29/s]
 28%|##8       | 199/704 [01:06<02:36,  3.24/s]
 28%|##8       | 200/704 [01:07<02:35,  3.24/s]
 29%|##8       | 201/704 [01:07<02:34,  3.25/s]
 29%|##8       | 202/704 [01:07<02:31,  3.30/s]
 29%|##8       | 203/704 [01:08<02:30,  3.33/s]
 29%|##8       | 204/704 [01:08<02:27,  3.39/s]
 29%|##9       | 205/704 [01:08<02:29,  3.35/s]
 29%|##9       | 206/704 [01:08<02:31,  3.29/s]
 29%|##9       | 207/704 [01:09<02:33,  3.24/s]
 30%|##9       | 208/704 [01:09<02:36,  3.17/s]
 30%|##9       | 209/704 [01:09<02:33,  3.21/s]
 30%|##9       | 210/704 [01:10<02:31,  3.26/s]
 30%|##9       | 211/704 [01:10<02:35,  3.17/s]
 30%|###       | 212/704 [01:10<02:39,  3.09/s]
 30%|###       | 213/704 [01:11<02:35,  3.16/s]
 30%|###       | 214/704 [01:11<02:33,  3.19/s]
 31%|###       | 215/704 [01:11<02:35,  3.14/s]
 31%|###       | 216/704 [01:12<02:35,  3.14/s]
 31%|###       | 217/704 [01:12<02:35,  3.12/s]
 31%|###       | 218/704 [01:12<02:37,  3.09/s]
 31%|###1      | 219/704 [01:13<02:36,  3.10/s]
 31%|###1      | 220/704 [01:13<02:31,  3.21/s]
 31%|###1      | 221/704 [01:13<02:27,  3.28/s]
 32%|###1      | 222/704 [01:13<02:29,  3.22/s]
 32%|###1      | 223/704 [01:14<02:27,  3.27/s]
 32%|###1      | 224/704 [01:14<02:32,  3.15/s]
 32%|###1      | 225/704 [01:14<02:33,  3.13/s]
 32%|###2      | 226/704 [01:15<02:28,  3.22/s]
 32%|###2      | 227/704 [01:15<02:25,  3.28/s]
 32%|###2      | 228/704 [01:15<02:26,  3.24/s]
 33%|###2      | 229/704 [01:16<02:26,  3.23/s]
 33%|###2      | 230/704 [01:16<02:25,  3.25/s]
 33%|###2      | 231/704 [01:16<02:24,  3.27/s]
 33%|###2      | 232/704 [01:17<02:23,  3.28/s]
 33%|###3      | 233/704 [01:17<02:22,  3.31/s]
 33%|###3      | 234/704 [01:17<02:22,  3.31/s]
 33%|###3      | 235/704 [01:17<02:20,  3.33/s]
 34%|###3      | 236/704 [01:18<02:19,  3.35/s]
 34%|###3      | 237/704 [01:18<02:20,  3.33/s]
 34%|###3      | 238/704 [01:18<02:19,  3.34/s]
 34%|###3      | 239/704 [01:19<02:18,  3.36/s]
 34%|###4      | 240/704 [01:19<02:17,  3.36/s]
 34%|###4      | 241/704 [01:19<02:17,  3.37/s]
 34%|###4      | 242/704 [01:20<02:17,  3.36/s]
 35%|###4      | 243/704 [01:20<02:19,  3.31/s]
 35%|###4      | 244/704 [01:20<02:20,  3.28/s]
 35%|###4      | 245/704 [01:20<02:20,  3.27/s]
 35%|###4      | 246/704 [01:21<02:20,  3.26/s]
 35%|###5      | 247/704 [01:21<02:24,  3.16/s]
 35%|###5      | 248/704 [01:21<02:27,  3.10/s]
 35%|###5      | 249/704 [01:22<02:25,  3.12/s]
 36%|###5      | 250/704 [01:22<02:22,  3.18/s]
 36%|###5      | 251/704 [01:22<02:23,  3.15/s]
 36%|###5      | 252/704 [01:23<02:21,  3.19/s]
 36%|###5      | 253/704 [01:23<02:17,  3.28/s]
 36%|###6      | 254/704 [01:23<02:16,  3.29/s]
 36%|###6      | 255/704 [01:24<02:14,  3.33/s]
 36%|###6      | 256/704 [01:24<02:19,  3.21/s]
 37%|###6      | 257/704 [01:24<02:21,  3.16/s]
 37%|###6      | 258/704 [01:25<02:18,  3.21/s]
 37%|###6      | 259/704 [01:25<02:17,  3.24/s]
 37%|###6      | 260/704 [01:25<02:18,  3.21/s]
 37%|###7      | 261/704 [01:26<02:20,  3.16/s]
 37%|###7      | 262/704 [01:26<02:21,  3.12/s]
 37%|###7      | 263/704 [01:26<02:18,  3.19/s]
 38%|###7      | 264/704 [01:26<02:16,  3.22/s]
 38%|###7      | 265/704 [01:27<02:14,  3.27/s]
 38%|###7      | 266/704 [01:27<02:15,  3.23/s]
 38%|###7      | 267/704 [01:27<02:13,  3.27/s]
 38%|###8      | 268/704 [01:28<02:11,  3.32/s]
 38%|###8      | 269/704 [01:28<02:10,  3.33/s]
 38%|###8      | 270/704 [01:28<02:08,  3.38/s]
 38%|###8      | 271/704 [01:29<02:09,  3.35/s]
 39%|###8      | 272/704 [01:29<02:13,  3.25/s]
 39%|###8      | 273/704 [01:29<02:14,  3.20/s]
 39%|###8      | 274/704 [01:30<02:15,  3.17/s]
 39%|###9      | 275/704 [01:30<02:14,  3.18/s]
 39%|###9      | 276/704 [01:30<02:14,  3.19/s]
 39%|###9      | 277/704 [01:30<02:14,  3.18/s]
 39%|###9      | 278/704 [01:31<02:11,  3.23/s]
 40%|###9      | 279/704 [01:31<02:12,  3.22/s]
 40%|###9      | 280/704 [01:31<02:10,  3.24/s]
 40%|###9      | 281/704 [01:32<02:09,  3.28/s]
 40%|####      | 282/704 [01:32<02:07,  3.30/s]
 40%|####      | 283/704 [01:32<02:07,  3.31/s]
 40%|####      | 284/704 [01:33<02:06,  3.31/s]
 40%|####      | 285/704 [01:33<02:09,  3.24/s]
 41%|####      | 286/704 [01:33<02:07,  3.27/s]
 41%|####      | 287/704 [01:33<02:05,  3.31/s]
 41%|####      | 288/704 [01:34<02:05,  3.31/s]
 41%|####1     | 289/704 [01:34<02:06,  3.27/s]
 41%|####1     | 290/704 [01:34<02:07,  3.26/s]
 41%|####1     | 291/704 [01:35<02:05,  3.29/s]
 41%|####1     | 292/704 [01:35<02:03,  3.33/s]
 42%|####1     | 293/704 [01:35<02:03,  3.34/s]
 42%|####1     | 294/704 [01:36<02:02,  3.34/s]
 42%|####1     | 295/704 [01:36<02:02,  3.34/s]
 42%|####2     | 296/704 [01:36<02:03,  3.31/s]
 42%|####2     | 297/704 [01:36<02:03,  3.30/s]
 42%|####2     | 298/704 [01:37<02:02,  3.32/s]
 42%|####2     | 299/704 [01:37<02:02,  3.30/s]
 43%|####2     | 300/704 [01:37<02:03,  3.28/s]
 43%|####2     | 301/704 [01:38<02:02,  3.29/s]
 43%|####2     | 302/704 [01:38<02:02,  3.28/s]
 43%|####3     | 303/704 [01:38<02:03,  3.26/s]
 43%|####3     | 304/704 [01:39<02:02,  3.26/s]
 43%|####3     | 305/704 [01:39<02:01,  3.28/s]
 43%|####3     | 306/704 [01:39<02:00,  3.30/s]
 44%|####3     | 307/704 [01:40<02:00,  3.29/s]
 44%|####3     | 308/704 [01:40<02:00,  3.28/s]
 44%|####3     | 309/704 [01:40<02:00,  3.27/s]
 44%|####4     | 310/704 [01:41<02:07,  3.09/s]
 44%|####4     | 311/704 [01:41<02:05,  3.14/s]
 44%|####4     | 312/704 [01:41<02:04,  3.15/s]
 44%|####4     | 313/704 [01:41<02:06,  3.08/s]
 45%|####4     | 314/704 [01:42<02:11,  2.97/s]
 45%|####4     | 315/704 [01:42<02:09,  3.00/s]
 45%|####4     | 316/704 [01:42<02:07,  3.05/s]
 45%|####5     | 317/704 [01:43<02:06,  3.05/s]
 45%|####5     | 318/704 [01:43<02:05,  3.07/s]
 45%|####5     | 319/704 [01:43<02:05,  3.06/s]
 45%|####5     | 320/704 [01:44<02:02,  3.15/s]
 46%|####5     | 321/704 [01:44<02:01,  3.15/s]
 46%|####5     | 322/704 [01:44<02:02,  3.13/s]
 46%|####5     | 323/704 [01:45<02:00,  3.16/s]
 46%|####6     | 324/704 [01:45<01:59,  3.18/s]
 46%|####6     | 325/704 [01:45<01:57,  3.23/s]
 46%|####6     | 326/704 [01:46<01:58,  3.18/s]
 46%|####6     | 327/704 [01:46<01:59,  3.15/s]
 47%|####6     | 328/704 [01:46<01:58,  3.16/s]
 47%|####6     | 329/704 [01:47<01:56,  3.21/s]
 47%|####6     | 330/704 [01:47<01:54,  3.26/s]
 47%|####7     | 331/704 [01:47<01:52,  3.31/s]
 47%|####7     | 332/704 [01:47<01:50,  3.37/s]
 47%|####7     | 333/704 [01:48<01:49,  3.38/s]
 47%|####7     | 334/704 [01:48<01:49,  3.38/s]
 48%|####7     | 335/704 [01:48<01:49,  3.38/s]
 48%|####7     | 336/704 [01:49<01:49,  3.37/s]
 48%|####7     | 337/704 [01:49<01:49,  3.34/s]
 48%|####8     | 338/704 [01:49<01:49,  3.35/s]
 48%|####8     | 339/704 [01:50<01:49,  3.34/s]
 48%|####8     | 340/704 [01:50<01:51,  3.28/s]
 48%|####8     | 341/704 [01:50<01:50,  3.29/s]
 49%|####8     | 342/704 [01:50<01:51,  3.24/s]
 49%|####8     | 343/704 [01:51<01:49,  3.29/s]
 49%|####8     | 344/704 [01:51<01:49,  3.29/s]
 49%|####9     | 345/704 [01:51<01:48,  3.32/s]
 49%|####9     | 346/704 [01:52<01:47,  3.34/s]
 49%|####9     | 347/704 [01:52<01:46,  3.35/s]
 49%|####9     | 348/704 [01:52<01:45,  3.36/s]
 50%|####9     | 349/704 [01:53<01:51,  3.19/s]
 50%|####9     | 350/704 [01:53<01:52,  3.16/s]
 50%|####9     | 351/704 [01:53<01:51,  3.16/s]
 50%|#####     | 352/704 [01:54<01:57,  2.99/s]
 50%|#####     | 353/704 [01:54<01:58,  2.96/s]
 50%|#####     | 354/704 [01:54<01:55,  3.03/s]
 50%|#####     | 355/704 [01:55<01:54,  3.04/s]
 51%|#####     | 356/704 [01:55<01:55,  3.02/s]
 51%|#####     | 357/704 [01:55<01:58,  2.92/s]
 51%|#####     | 358/704 [01:56<02:09,  2.67/s]
 51%|#####     | 359/704 [01:56<02:19,  2.48/s]
 51%|#####1    | 360/704 [01:57<02:15,  2.54/s]
 51%|#####1    | 361/704 [01:57<02:08,  2.66/s]
 51%|#####1    | 362/704 [01:57<02:00,  2.85/s]
 52%|#####1    | 363/704 [01:58<01:54,  2.97/s]
 52%|#####1    | 364/704 [01:58<01:50,  3.08/s]
 52%|#####1    | 365/704 [01:58<01:48,  3.14/s]
 52%|#####1    | 366/704 [01:58<01:46,  3.17/s]
 52%|#####2    | 367/704 [01:59<01:49,  3.07/s]
 52%|#####2    | 368/704 [01:59<01:48,  3.10/s]
 52%|#####2    | 369/704 [01:59<01:46,  3.14/s]
 53%|#####2    | 370/704 [02:00<01:43,  3.22/s]
 53%|#####2    | 371/704 [02:00<01:41,  3.27/s]
 53%|#####2    | 372/704 [02:00<01:39,  3.32/s]
 53%|#####2    | 373/704 [02:01<01:38,  3.37/s]
 53%|#####3    | 374/704 [02:01<01:36,  3.42/s]
 53%|#####3    | 375/704 [02:01<01:34,  3.48/s]
 53%|#####3    | 376/704 [02:01<01:32,  3.54/s]
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 94%|#########4| 664/704 [03:31<00:12,  3.25/s]
 94%|#########4| 665/704 [03:31<00:12,  3.18/s]
 95%|#########4| 666/704 [03:31<00:11,  3.19/s]
 95%|#########4| 667/704 [03:32<00:11,  3.15/s]
 95%|#########4| 668/704 [03:32<00:11,  3.15/s]
 95%|#########5| 669/704 [03:32<00:10,  3.21/s]
 95%|#########5| 670/704 [03:32<00:10,  3.26/s]
 95%|#########5| 671/704 [03:33<00:10,  3.28/s]
 95%|#########5| 672/704 [03:33<00:09,  3.26/s]
 96%|#########5| 673/704 [03:33<00:09,  3.30/s]
 96%|#########5| 674/704 [03:34<00:09,  3.32/s]
 96%|#########5| 675/704 [03:34<00:08,  3.34/s]
 96%|#########6| 676/704 [03:34<00:08,  3.36/s]
 96%|#########6| 677/704 [03:35<00:08,  3.33/s]
 96%|#########6| 678/704 [03:35<00:07,  3.29/s]
 96%|#########6| 679/704 [03:35<00:07,  3.28/s]
 97%|#########6| 680/704 [03:36<00:07,  3.31/s]
 97%|#########6| 681/704 [03:36<00:06,  3.32/s]
 97%|#########6| 682/704 [03:36<00:06,  3.32/s]
 97%|#########7| 683/704 [03:36<00:06,  3.29/s]
 97%|#########7| 684/704 [03:37<00:06,  3.30/s]
 97%|#########7| 685/704 [03:37<00:05,  3.28/s]
 97%|#########7| 686/704 [03:37<00:05,  3.30/s]
 98%|#########7| 687/704 [03:38<00:05,  3.31/s]
 98%|#########7| 688/704 [03:38<00:04,  3.32/s]
 98%|#########7| 689/704 [03:38<00:04,  3.33/s]
 98%|#########8| 690/704 [03:39<00:04,  3.33/s]
 98%|#########8| 691/704 [03:39<00:03,  3.33/s]
 98%|#########8| 692/704 [03:39<00:03,  3.33/s]
 98%|#########8| 693/704 [03:39<00:03,  3.33/s]
 99%|#########8| 694/704 [03:40<00:02,  3.35/s]
 99%|#########8| 695/704 [03:40<00:02,  3.36/s]
 99%|#########8| 696/704 [03:40<00:02,  3.36/s]
 99%|#########9| 697/704 [03:41<00:02,  3.35/s]
 99%|#########9| 698/704 [03:41<00:01,  3.33/s]
 99%|#########9| 699/704 [03:41<00:01,  3.28/s]
 99%|#########9| 700/704 [03:42<00:01,  3.19/s]
100%|#########9| 701/704 [03:42<00:00,  3.17/s]
100%|#########9| 702/704 [03:42<00:00,  3.18/s]
100%|#########9| 703/704 [03:43<00:00,  3.17/s]
100%|##########| 704/704 [03:43<00:00,  3.13/s]
100%|##########| 704/704 [03:43<00:00,  3.15/s]

  0%|          | 0/704 [00:00<?, ?/s]
  0%|          | 1/704 [00:05<1:04:55,  5.54s/]
  0%|          | 2/704 [00:05<28:32,  2.44s/]
  0%|          | 3/704 [00:06<16:44,  1.43s/]
  1%|          | 4/704 [00:06<11:12,  1.04/s]
  1%|          | 5/704 [00:06<08:05,  1.44/s]
  1%|          | 6/704 [00:06<06:14,  1.86/s]
  1%|          | 7/704 [00:06<05:06,  2.27/s]
  1%|1         | 8/704 [00:07<04:22,  2.65/s]
  1%|1         | 9/704 [00:07<03:52,  2.99/s]
  1%|1         | 10/704 [00:07<03:31,  3.29/s]
  2%|1         | 11/704 [00:07<03:16,  3.53/s]
  2%|1         | 12/704 [00:08<03:04,  3.76/s]
  2%|1         | 13/704 [00:08<02:56,  3.92/s]
  2%|1         | 14/704 [00:08<02:55,  3.93/s]
  2%|2         | 15/704 [00:08<02:48,  4.09/s]
  2%|2         | 16/704 [00:09<02:44,  4.18/s]
  2%|2         | 17/704 [00:09<02:43,  4.21/s]
  3%|2         | 18/704 [00:09<02:45,  4.14/s]
  3%|2         | 19/704 [00:09<02:43,  4.18/s]
  3%|2         | 20/704 [00:10<02:46,  4.11/s]
  3%|2         | 21/704 [00:10<02:43,  4.18/s]
  3%|3         | 22/704 [00:10<02:39,  4.27/s]
  3%|3         | 23/704 [00:10<02:38,  4.30/s]
  3%|3         | 24/704 [00:10<02:35,  4.36/s]
  4%|3         | 25/704 [00:11<02:33,  4.42/s]
  4%|3         | 26/704 [00:11<02:31,  4.47/s]
  4%|3         | 27/704 [00:11<02:32,  4.43/s]
  4%|3         | 28/704 [00:11<02:32,  4.42/s]
  4%|4         | 29/704 [00:12<02:32,  4.42/s]
  4%|4         | 30/704 [00:12<02:36,  4.32/s]
  4%|4         | 31/704 [00:12<02:35,  4.32/s]
  5%|4         | 32/704 [00:12<02:35,  4.33/s]
  5%|4         | 33/704 [00:13<02:35,  4.31/s]
  5%|4         | 34/704 [00:13<02:34,  4.33/s]
  5%|4         | 35/704 [00:13<02:35,  4.31/s]
  5%|5         | 36/704 [00:13<02:40,  4.16/s]
  5%|5         | 37/704 [00:13<02:39,  4.17/s]
  5%|5         | 38/704 [00:14<02:39,  4.17/s]
  6%|5         | 39/704 [00:14<02:39,  4.17/s]
  6%|5         | 40/704 [00:14<02:36,  4.23/s]
  6%|5         | 41/704 [00:14<02:36,  4.24/s]
  6%|5         | 42/704 [00:15<02:40,  4.14/s]
  6%|6         | 43/704 [00:15<02:37,  4.19/s]
  6%|6         | 44/704 [00:15<02:34,  4.27/s]
  6%|6         | 45/704 [00:15<02:31,  4.34/s]
  7%|6         | 46/704 [00:16<02:29,  4.41/s]
  7%|6         | 47/704 [00:16<02:27,  4.47/s]
  7%|6         | 48/704 [00:16<02:27,  4.44/s]
  7%|6         | 49/704 [00:16<02:29,  4.38/s]
  7%|7         | 50/704 [00:17<02:34,  4.23/s]
  7%|7         | 51/704 [00:17<02:32,  4.27/s]
  7%|7         | 52/704 [00:17<02:34,  4.22/s]
  8%|7         | 53/704 [00:17<02:37,  4.13/s]
  8%|7         | 54/704 [00:17<02:33,  4.23/s]
  8%|7         | 55/704 [00:18<02:32,  4.26/s]
  8%|7         | 56/704 [00:18<02:30,  4.31/s]
  8%|8         | 57/704 [00:18<02:33,  4.20/s]
  8%|8         | 58/704 [00:18<02:32,  4.23/s]
  8%|8         | 59/704 [00:19<02:30,  4.28/s]
  9%|8         | 60/704 [00:19<02:28,  4.33/s]
  9%|8         | 61/704 [00:19<02:33,  4.20/s]
  9%|8         | 62/704 [00:19<02:38,  4.06/s]
  9%|8         | 63/704 [00:20<02:35,  4.13/s]
  9%|9         | 64/704 [00:20<02:33,  4.18/s]
  9%|9         | 65/704 [00:20<02:35,  4.10/s]
  9%|9         | 66/704 [00:20<02:34,  4.13/s]
 10%|9         | 67/704 [00:21<02:37,  4.05/s]
 10%|9         | 68/704 [00:21<02:37,  4.05/s]
 10%|9         | 69/704 [00:21<02:39,  3.98/s]
 10%|9         | 70/704 [00:21<02:42,  3.91/s]
 10%|#         | 71/704 [00:22<02:37,  4.03/s]
 10%|#         | 72/704 [00:22<02:39,  3.97/s]
 10%|#         | 73/704 [00:22<02:40,  3.94/s]
 11%|#         | 74/704 [00:22<02:41,  3.90/s]
 11%|#         | 75/704 [00:23<02:36,  4.02/s]
 11%|#         | 76/704 [00:23<02:36,  4.01/s]
 11%|#         | 77/704 [00:23<02:31,  4.13/s]
 11%|#1        | 78/704 [00:23<02:30,  4.16/s]
 11%|#1        | 79/704 [00:24<02:34,  4.03/s]
 11%|#1        | 80/704 [00:24<02:31,  4.12/s]
 12%|#1        | 81/704 [00:24<02:28,  4.18/s]
 12%|#1        | 82/704 [00:24<02:27,  4.21/s]
 12%|#1        | 83/704 [00:25<02:27,  4.20/s]
 12%|#1        | 84/704 [00:25<02:28,  4.17/s]
 12%|#2        | 85/704 [00:25<02:34,  4.00/s]
 12%|#2        | 86/704 [00:25<02:32,  4.05/s]
 12%|#2        | 87/704 [00:26<02:34,  3.99/s]
 12%|#2        | 88/704 [00:26<02:30,  4.08/s]
 13%|#2        | 89/704 [00:26<02:33,  4.00/s]
 13%|#2        | 90/704 [00:26<02:31,  4.06/s]
 13%|#2        | 91/704 [00:26<02:28,  4.14/s]
 13%|#3        | 92/704 [00:27<02:27,  4.14/s]
 13%|#3        | 93/704 [00:27<02:29,  4.10/s]
 13%|#3        | 94/704 [00:27<02:29,  4.08/s]
 13%|#3        | 95/704 [00:27<02:28,  4.11/s]
 14%|#3        | 96/704 [00:28<02:28,  4.11/s]
 14%|#3        | 97/704 [00:28<02:23,  4.22/s]
 14%|#3        | 98/704 [00:28<02:22,  4.26/s]
 14%|#4        | 99/704 [00:28<02:27,  4.09/s]
 14%|#4        | 100/704 [00:29<02:24,  4.18/s]
 14%|#4        | 101/704 [00:29<02:21,  4.25/s]
 14%|#4        | 102/704 [00:29<02:23,  4.18/s]
 15%|#4        | 103/704 [00:29<02:22,  4.23/s]
 15%|#4        | 104/704 [00:30<02:22,  4.20/s]
 15%|#4        | 105/704 [00:30<02:18,  4.31/s]
 15%|#5        | 106/704 [00:30<02:19,  4.29/s]
 15%|#5        | 107/704 [00:30<02:19,  4.28/s]
 15%|#5        | 108/704 [00:31<02:16,  4.37/s]
 15%|#5        | 109/704 [00:31<02:13,  4.45/s]
 16%|#5        | 110/704 [00:31<02:12,  4.47/s]
 16%|#5        | 111/704 [00:31<02:13,  4.44/s]
 16%|#5        | 112/704 [00:31<02:12,  4.47/s]
 16%|#6        | 113/704 [00:32<02:14,  4.41/s]
 16%|#6        | 114/704 [00:32<02:15,  4.35/s]
 16%|#6        | 115/704 [00:32<02:15,  4.33/s]
 16%|#6        | 116/704 [00:32<02:16,  4.32/s]
 17%|#6        | 117/704 [00:33<02:15,  4.32/s]
 17%|#6        | 118/704 [00:33<02:13,  4.39/s]
 17%|#6        | 119/704 [00:33<02:14,  4.36/s]
 17%|#7        | 120/704 [00:33<02:13,  4.37/s]
 17%|#7        | 121/704 [00:33<02:14,  4.35/s]
 17%|#7        | 122/704 [00:34<02:13,  4.36/s]
 17%|#7        | 123/704 [00:34<02:14,  4.32/s]
 18%|#7        | 124/704 [00:34<02:14,  4.30/s]
 18%|#7        | 125/704 [00:34<02:15,  4.29/s]
 18%|#7        | 126/704 [00:35<02:13,  4.32/s]
 18%|#8        | 127/704 [00:35<02:13,  4.31/s]
 18%|#8        | 128/704 [00:35<02:12,  4.34/s]
 18%|#8        | 129/704 [00:35<02:12,  4.34/s]
 18%|#8        | 130/704 [00:36<02:11,  4.37/s]
 19%|#8        | 131/704 [00:36<02:10,  4.39/s]
 19%|#8        | 132/704 [00:36<02:10,  4.40/s]
 19%|#8        | 133/704 [00:36<02:09,  4.42/s]
 19%|#9        | 134/704 [00:36<02:09,  4.40/s]
 19%|#9        | 135/704 [00:37<02:09,  4.38/s]
 19%|#9        | 136/704 [00:37<02:09,  4.39/s]
 19%|#9        | 137/704 [00:37<02:09,  4.38/s]
 20%|#9        | 138/704 [00:37<02:09,  4.36/s]
 20%|#9        | 139/704 [00:38<02:09,  4.36/s]
 20%|#9        | 140/704 [00:38<02:11,  4.28/s]
 20%|##        | 141/704 [00:38<02:11,  4.27/s]
 20%|##        | 142/704 [00:38<02:11,  4.29/s]
 20%|##        | 143/704 [00:39<02:10,  4.31/s]
 20%|##        | 144/704 [00:39<02:09,  4.34/s]
 21%|##        | 145/704 [00:39<02:08,  4.33/s]
 21%|##        | 146/704 [00:39<02:09,  4.31/s]
 21%|##        | 147/704 [00:39<02:09,  4.29/s]
 21%|##1       | 148/704 [00:40<02:19,  3.98/s]
 21%|##1       | 149/704 [00:40<02:25,  3.80/s]
 21%|##1       | 150/704 [00:40<02:19,  3.97/s]
 21%|##1       | 151/704 [00:41<02:18,  4.00/s]
 22%|##1       | 152/704 [00:41<02:20,  3.94/s]
 22%|##1       | 153/704 [00:41<02:17,  3.99/s]
 22%|##1       | 154/704 [00:41<02:22,  3.86/s]
 22%|##2       | 155/704 [00:42<02:24,  3.81/s]
 22%|##2       | 156/704 [00:42<02:33,  3.58/s]
 22%|##2       | 157/704 [00:42<02:39,  3.42/s]
 22%|##2       | 158/704 [00:43<02:38,  3.45/s]
 23%|##2       | 159/704 [00:43<02:27,  3.70/s]
 23%|##2       | 160/704 [00:43<02:19,  3.90/s]
 23%|##2       | 161/704 [00:43<02:16,  3.97/s]
 23%|##3       | 162/704 [00:43<02:12,  4.08/s]
 23%|##3       | 163/704 [00:44<02:10,  4.16/s]
 23%|##3       | 164/704 [00:44<02:10,  4.13/s]
 23%|##3       | 165/704 [00:44<02:09,  4.18/s]
 24%|##3       | 166/704 [00:44<02:10,  4.12/s]
 24%|##3       | 167/704 [00:45<02:07,  4.22/s]
 24%|##3       | 168/704 [00:45<02:04,  4.30/s]
 24%|##4       | 169/704 [00:45<02:14,  3.98/s]
 24%|##4       | 170/704 [00:45<02:13,  4.01/s]
 24%|##4       | 171/704 [00:46<02:09,  4.12/s]
 24%|##4       | 172/704 [00:46<02:05,  4.22/s]
 25%|##4       | 173/704 [00:46<02:04,  4.27/s]
 25%|##4       | 174/704 [00:46<02:01,  4.37/s]
 25%|##4       | 175/704 [00:47<02:00,  4.40/s]
 25%|##5       | 176/704 [00:47<02:00,  4.39/s]
 25%|##5       | 177/704 [00:47<02:01,  4.34/s]
 25%|##5       | 178/704 [00:47<02:02,  4.29/s]
 25%|##5       | 179/704 [00:47<02:05,  4.20/s]
 26%|##5       | 180/704 [00:48<02:02,  4.27/s]
 26%|##5       | 181/704 [00:48<02:02,  4.28/s]
 26%|##5       | 182/704 [00:48<02:01,  4.28/s]
 26%|##5       | 183/704 [00:48<02:04,  4.19/s]
 26%|##6       | 184/704 [00:49<02:01,  4.27/s]
 26%|##6       | 185/704 [00:49<01:58,  4.37/s]
 26%|##6       | 186/704 [00:49<01:56,  4.45/s]
 27%|##6       | 187/704 [00:49<01:54,  4.51/s]
 27%|##6       | 188/704 [00:49<01:54,  4.51/s]
 27%|##6       | 189/704 [00:50<01:54,  4.50/s]
 27%|##6       | 190/704 [00:50<01:55,  4.44/s]
 27%|##7       | 191/704 [00:50<01:56,  4.42/s]
 27%|##7       | 192/704 [00:50<02:00,  4.26/s]
 27%|##7       | 193/704 [00:51<01:59,  4.28/s]
 28%|##7       | 194/704 [00:51<02:01,  4.19/s]
 28%|##7       | 195/704 [00:51<02:03,  4.11/s]
 28%|##7       | 196/704 [00:51<02:03,  4.11/s]
 28%|##7       | 197/704 [00:52<02:05,  4.04/s]
 28%|##8       | 198/704 [00:52<02:04,  4.05/s]
 28%|##8       | 199/704 [00:52<02:04,  4.05/s]
 28%|##8       | 200/704 [00:52<02:03,  4.08/s]
 29%|##8       | 201/704 [00:53<02:05,  4.02/s]
 29%|##8       | 202/704 [00:53<02:03,  4.08/s]
 29%|##8       | 203/704 [00:53<02:00,  4.15/s]
 29%|##8       | 204/704 [00:53<01:56,  4.28/s]
 29%|##9       | 205/704 [00:54<01:55,  4.31/s]
 29%|##9       | 206/704 [00:54<01:56,  4.29/s]
 29%|##9       | 207/704 [00:54<01:54,  4.33/s]
 30%|##9       | 208/704 [00:54<01:53,  4.36/s]
 30%|##9       | 209/704 [00:54<01:52,  4.40/s]
 30%|##9       | 210/704 [00:55<01:54,  4.31/s]
 30%|##9       | 211/704 [00:55<01:52,  4.38/s]
 30%|###       | 212/704 [00:55<01:51,  4.42/s]
 30%|###       | 213/704 [00:55<01:50,  4.44/s]
 30%|###       | 214/704 [00:56<01:51,  4.38/s]
 31%|###       | 215/704 [00:56<01:51,  4.37/s]
 31%|###       | 216/704 [00:56<02:01,  4.03/s]
 31%|###       | 217/704 [00:56<02:12,  3.67/s]
 31%|###       | 218/704 [00:57<02:12,  3.66/s]
 31%|###1      | 219/704 [00:57<02:04,  3.89/s]
 31%|###1      | 220/704 [00:57<01:58,  4.07/s]
 31%|###1      | 221/704 [00:57<01:58,  4.09/s]
 32%|###1      | 222/704 [00:58<01:56,  4.15/s]
 32%|###1      | 223/704 [00:58<01:55,  4.16/s]
 32%|###1      | 224/704 [00:58<01:53,  4.25/s]
 32%|###1      | 225/704 [00:58<01:49,  4.38/s]
 32%|###2      | 226/704 [00:59<01:47,  4.44/s]
 32%|###2      | 227/704 [00:59<01:48,  4.42/s]
 32%|###2      | 228/704 [00:59<01:47,  4.44/s]
 33%|###2      | 229/704 [00:59<01:47,  4.41/s]
 33%|###2      | 230/704 [00:59<01:48,  4.35/s]
 33%|###2      | 231/704 [01:00<01:48,  4.34/s]
 33%|###2      | 232/704 [01:00<01:48,  4.33/s]
 33%|###3      | 233/704 [01:00<01:48,  4.36/s]
 33%|###3      | 234/704 [01:00<01:46,  4.41/s]
 33%|###3      | 235/704 [01:01<01:45,  4.44/s]
 34%|###3      | 236/704 [01:01<01:44,  4.48/s]
 34%|###3      | 237/704 [01:01<01:43,  4.50/s]
 34%|###3      | 238/704 [01:01<01:43,  4.50/s]
 34%|###3      | 239/704 [01:01<01:43,  4.51/s]
 34%|###4      | 240/704 [01:02<01:42,  4.51/s]
 34%|###4      | 241/704 [01:02<01:43,  4.48/s]
 34%|###4      | 242/704 [01:02<01:42,  4.50/s]
 35%|###4      | 243/704 [01:02<01:41,  4.56/s]
 35%|###4      | 244/704 [01:03<01:40,  4.56/s]
 35%|###4      | 245/704 [01:03<01:40,  4.58/s]
 35%|###4      | 246/704 [01:03<01:39,  4.60/s]
 35%|###5      | 247/704 [01:03<01:39,  4.60/s]
 35%|###5      | 248/704 [01:03<01:39,  4.60/s]
 35%|###5      | 249/704 [01:04<01:39,  4.58/s]
 36%|###5      | 250/704 [01:04<01:39,  4.54/s]
 36%|###5      | 251/704 [01:04<01:40,  4.53/s]
 36%|###5      | 252/704 [01:04<01:39,  4.53/s]
 36%|###5      | 253/704 [01:05<01:39,  4.52/s]
 36%|###6      | 254/704 [01:05<01:40,  4.49/s]
 36%|###6      | 255/704 [01:05<01:40,  4.47/s]
 36%|###6      | 256/704 [01:05<01:41,  4.44/s]
 37%|###6      | 257/704 [01:05<01:43,  4.30/s]
 37%|###6      | 258/704 [01:06<01:44,  4.29/s]
 37%|###6      | 259/704 [01:06<01:42,  4.33/s]
 37%|###6      | 260/704 [01:06<01:45,  4.23/s]
 37%|###7      | 261/704 [01:06<01:44,  4.26/s]
 37%|###7      | 262/704 [01:07<01:42,  4.32/s]
 37%|###7      | 263/704 [01:07<01:40,  4.37/s]
 38%|###7      | 264/704 [01:07<01:40,  4.38/s]
 38%|###7      | 265/704 [01:07<01:39,  4.42/s]
 38%|###7      | 266/704 [01:08<01:38,  4.45/s]
 38%|###7      | 267/704 [01:08<01:37,  4.49/s]
 38%|###8      | 268/704 [01:08<01:37,  4.47/s]
 38%|###8      | 269/704 [01:08<01:36,  4.50/s]
 38%|###8      | 270/704 [01:08<01:36,  4.51/s]
 38%|###8      | 271/704 [01:09<01:36,  4.51/s]
 39%|###8      | 272/704 [01:09<01:35,  4.52/s]
 39%|###8      | 273/704 [01:09<01:35,  4.51/s]
 39%|###8      | 274/704 [01:09<01:36,  4.48/s]
 39%|###9      | 275/704 [01:10<01:36,  4.46/s]
 39%|###9      | 276/704 [01:10<01:36,  4.43/s]
 39%|###9      | 277/704 [01:10<01:37,  4.39/s]
 39%|###9      | 278/704 [01:10<01:36,  4.41/s]
 40%|###9      | 279/704 [01:10<01:36,  4.40/s]
 40%|###9      | 280/704 [01:11<01:36,  4.41/s]
 40%|###9      | 281/704 [01:11<01:35,  4.43/s]
 40%|####      | 282/704 [01:11<01:34,  4.48/s]
 40%|####      | 283/704 [01:11<01:33,  4.49/s]
 40%|####      | 284/704 [01:12<01:36,  4.35/s]
 40%|####      | 285/704 [01:12<01:45,  3.96/s]
 41%|####      | 286/704 [01:12<01:52,  3.73/s]
 41%|####      | 287/704 [01:12<01:49,  3.79/s]
 41%|####      | 288/704 [01:13<01:46,  3.89/s]
 41%|####1     | 289/704 [01:13<01:43,  4.02/s]
 41%|####1     | 290/704 [01:13<01:40,  4.13/s]
 41%|####1     | 291/704 [01:13<01:38,  4.18/s]
 41%|####1     | 292/704 [01:14<01:36,  4.25/s]
 42%|####1     | 293/704 [01:14<01:34,  4.34/s]
 42%|####1     | 294/704 [01:14<01:33,  4.36/s]
 42%|####1     | 295/704 [01:14<01:33,  4.37/s]
 42%|####2     | 296/704 [01:15<01:35,  4.26/s]
 42%|####2     | 297/704 [01:15<01:41,  4.00/s]
 42%|####2     | 298/704 [01:15<01:42,  3.96/s]
 42%|####2     | 299/704 [01:15<01:40,  4.04/s]
 43%|####2     | 300/704 [01:16<01:37,  4.15/s]
 43%|####2     | 301/704 [01:16<01:35,  4.21/s]
 43%|####2     | 302/704 [01:16<01:32,  4.33/s]
 43%|####3     | 303/704 [01:16<01:31,  4.40/s]
 43%|####3     | 304/704 [01:16<01:31,  4.39/s]
 43%|####3     | 305/704 [01:17<01:31,  4.36/s]
 43%|####3     | 306/704 [01:17<01:31,  4.35/s]
 44%|####3     | 307/704 [01:17<01:30,  4.37/s]
 44%|####3     | 308/704 [01:17<01:31,  4.33/s]
 44%|####3     | 309/704 [01:18<01:31,  4.34/s]
 44%|####4     | 310/704 [01:18<01:33,  4.23/s]
 44%|####4     | 311/704 [01:18<01:30,  4.32/s]
 44%|####4     | 312/704 [01:18<01:32,  4.25/s]
 44%|####4     | 313/704 [01:19<01:31,  4.30/s]
 45%|####4     | 314/704 [01:19<01:32,  4.21/s]
 45%|####4     | 315/704 [01:19<01:30,  4.28/s]
 45%|####4     | 316/704 [01:19<01:29,  4.33/s]
 45%|####5     | 317/704 [01:19<01:29,  4.32/s]
 45%|####5     | 318/704 [01:20<01:28,  4.35/s]
 45%|####5     | 319/704 [01:20<01:27,  4.39/s]
 45%|####5     | 320/704 [01:20<01:27,  4.41/s]
 46%|####5     | 321/704 [01:20<01:26,  4.44/s]
 46%|####5     | 322/704 [01:21<01:26,  4.44/s]
 46%|####5     | 323/704 [01:21<01:26,  4.42/s]
 46%|####6     | 324/704 [01:21<01:28,  4.31/s]
 46%|####6     | 325/704 [01:21<01:31,  4.13/s]
 46%|####6     | 326/704 [01:22<01:35,  3.94/s]
 46%|####6     | 327/704 [01:22<01:37,  3.87/s]
 47%|####6     | 328/704 [01:22<01:40,  3.75/s]
 47%|####6     | 329/704 [01:22<01:38,  3.79/s]
 47%|####6     | 330/704 [01:23<01:38,  3.81/s]
 47%|####7     | 331/704 [01:23<01:34,  3.95/s]
 47%|####7     | 332/704 [01:23<01:30,  4.12/s]
 47%|####7     | 333/704 [01:23<01:26,  4.27/s]
 47%|####7     | 334/704 [01:24<01:28,  4.18/s]
 48%|####7     | 335/704 [01:24<01:31,  4.05/s]
 48%|####7     | 336/704 [01:24<01:35,  3.85/s]
 48%|####7     | 337/704 [01:24<01:34,  3.87/s]
 48%|####8     | 338/704 [01:25<01:30,  4.05/s]
 48%|####8     | 339/704 [01:25<01:26,  4.20/s]
 48%|####8     | 340/704 [01:25<01:29,  4.09/s]
 48%|####8     | 341/704 [01:25<01:26,  4.18/s]
 49%|####8     | 342/704 [01:26<01:25,  4.25/s]
 49%|####8     | 343/704 [01:26<01:23,  4.31/s]
 49%|####8     | 344/704 [01:26<01:22,  4.39/s]
 49%|####9     | 345/704 [01:26<01:20,  4.46/s]
 49%|####9     | 346/704 [01:26<01:21,  4.40/s]
 49%|####9     | 347/704 [01:27<01:20,  4.41/s]
 49%|####9     | 348/704 [01:27<01:20,  4.42/s]
 50%|####9     | 349/704 [01:27<01:19,  4.44/s]
 50%|####9     | 350/704 [01:27<01:19,  4.44/s]
 50%|####9     | 351/704 [01:28<01:18,  4.51/s]
 50%|#####     | 352/704 [01:28<01:18,  4.49/s]
 50%|#####     | 353/704 [01:28<01:17,  4.51/s]
 50%|#####     | 354/704 [01:28<01:16,  4.56/s]
 50%|#####     | 355/704 [01:28<01:16,  4.55/s]
 51%|#####     | 356/704 [01:29<01:16,  4.54/s]
 51%|#####     | 357/704 [01:29<01:16,  4.55/s]
 51%|#####     | 358/704 [01:29<01:16,  4.51/s]
 51%|#####     | 359/704 [01:29<01:16,  4.51/s]
 51%|#####1    | 360/704 [01:30<01:16,  4.53/s]
 51%|#####1    | 361/704 [01:30<01:15,  4.55/s]
 51%|#####1    | 362/704 [01:30<01:16,  4.48/s]
 52%|#####1    | 363/704 [01:30<01:16,  4.45/s]
 52%|#####1    | 364/704 [01:30<01:16,  4.43/s]
 52%|#####1    | 365/704 [01:31<01:16,  4.46/s]
 52%|#####1    | 366/704 [01:31<01:15,  4.48/s]
 52%|#####2    | 367/704 [01:31<01:14,  4.50/s]
 52%|#####2    | 368/704 [01:31<01:14,  4.53/s]
 52%|#####2    | 369/704 [01:32<01:13,  4.57/s]
 53%|#####2    | 370/704 [01:32<01:14,  4.49/s]
 53%|#####2    | 371/704 [01:32<01:14,  4.48/s]
 53%|#####2    | 372/704 [01:32<01:16,  4.35/s]
 53%|#####2    | 373/704 [01:32<01:15,  4.36/s]
 53%|#####3    | 374/704 [01:33<01:15,  4.37/s]
 53%|#####3    | 375/704 [01:33<01:14,  4.41/s]
 53%|#####3    | 376/704 [01:33<01:15,  4.33/s]
 54%|#####3    | 377/704 [01:33<01:15,  4.36/s]
 54%|#####3    | 378/704 [01:34<01:14,  4.40/s]
 54%|#####3    | 379/704 [01:34<01:13,  4.41/s]
 54%|#####3    | 380/704 [01:34<01:14,  4.37/s]
 54%|#####4    | 381/704 [01:34<01:13,  4.39/s]
 54%|#####4    | 382/704 [01:35<01:14,  4.30/s]
 54%|#####4    | 383/704 [01:35<01:14,  4.32/s]
 55%|#####4    | 384/704 [01:35<01:12,  4.40/s]
 55%|#####4    | 385/704 [01:35<01:11,  4.47/s]
 55%|#####4    | 386/704 [01:35<01:10,  4.49/s]
 55%|#####4    | 387/704 [01:36<01:10,  4.47/s]
 55%|#####5    | 388/704 [01:36<01:11,  4.44/s]
 55%|#####5    | 389/704 [01:36<01:10,  4.49/s]
 55%|#####5    | 390/704 [01:36<01:16,  4.11/s]
 56%|#####5    | 391/704 [01:37<01:18,  3.98/s]
 56%|#####5    | 392/704 [01:37<01:18,  3.95/s]
 56%|#####5    | 393/704 [01:37<01:15,  4.10/s]
 56%|#####5    | 394/704 [01:37<01:13,  4.24/s]
 56%|#####6    | 395/704 [01:38<01:11,  4.35/s]
 56%|#####6    | 396/704 [01:38<01:09,  4.43/s]
 56%|#####6    | 397/704 [01:38<01:08,  4.51/s]
 57%|#####6    | 398/704 [01:38<01:07,  4.52/s]
 57%|#####6    | 399/704 [01:38<01:06,  4.56/s]
 57%|#####6    | 400/704 [01:39<01:08,  4.46/s]
 57%|#####6    | 401/704 [01:39<01:09,  4.34/s]
 57%|#####7    | 402/704 [01:39<01:08,  4.38/s]
 57%|#####7    | 403/704 [01:39<01:07,  4.43/s]
 57%|#####7    | 404/704 [01:40<01:08,  4.35/s]
 58%|#####7    | 405/704 [01:40<01:08,  4.35/s]
 58%|#####7    | 406/704 [01:40<01:09,  4.28/s]
 58%|#####7    | 407/704 [01:40<01:08,  4.32/s]
 58%|#####7    | 408/704 [01:41<01:07,  4.37/s]
 58%|#####8    | 409/704 [01:41<01:06,  4.44/s]
 58%|#####8    | 410/704 [01:41<01:08,  4.31/s]
 58%|#####8    | 411/704 [01:41<01:09,  4.20/s]
 59%|#####8    | 412/704 [01:41<01:08,  4.27/s]
 59%|#####8    | 413/704 [01:42<01:06,  4.36/s]
 59%|#####8    | 414/704 [01:42<01:05,  4.41/s]
 59%|#####8    | 415/704 [01:42<01:04,  4.47/s]
 59%|#####9    | 416/704 [01:42<01:04,  4.47/s]
 59%|#####9    | 417/704 [01:43<01:03,  4.54/s]
 59%|#####9    | 418/704 [01:43<01:02,  4.55/s]
 60%|#####9    | 419/704 [01:43<01:02,  4.55/s]
 60%|#####9    | 420/704 [01:43<01:02,  4.58/s]
 60%|#####9    | 421/704 [01:43<01:01,  4.58/s]
 60%|#####9    | 422/704 [01:44<01:01,  4.59/s]
 60%|######    | 423/704 [01:44<01:01,  4.59/s]
 60%|######    | 424/704 [01:44<01:01,  4.57/s]
 60%|######    | 425/704 [01:44<01:01,  4.55/s]
 61%|######    | 426/704 [01:45<01:01,  4.55/s]
 61%|######    | 427/704 [01:45<01:01,  4.50/s]
 61%|######    | 428/704 [01:45<01:01,  4.50/s]
 61%|######    | 429/704 [01:45<01:00,  4.52/s]
 61%|######1   | 430/704 [01:45<01:00,  4.54/s]
 61%|######1   | 431/704 [01:46<01:00,  4.53/s]
 61%|######1   | 432/704 [01:46<01:00,  4.52/s]
 62%|######1   | 433/704 [01:46<01:00,  4.47/s]
 62%|######1   | 434/704 [01:46<01:00,  4.47/s]
 62%|######1   | 435/704 [01:47<00:59,  4.48/s]
 62%|######1   | 436/704 [01:47<01:00,  4.43/s]
 62%|######2   | 437/704 [01:47<01:00,  4.45/s]
 62%|######2   | 438/704 [01:47<00:59,  4.47/s]
 62%|######2   | 439/704 [01:47<00:59,  4.47/s]
 62%|######2   | 440/704 [01:48<00:58,  4.48/s]
 63%|######2   | 441/704 [01:48<00:58,  4.48/s]
 63%|######2   | 442/704 [01:48<00:59,  4.44/s]
 63%|######2   | 443/704 [01:48<00:58,  4.44/s]
 63%|######3   | 444/704 [01:49<00:58,  4.43/s]
 63%|######3   | 445/704 [01:49<00:58,  4.44/s]
 63%|######3   | 446/704 [01:49<00:58,  4.45/s]
 63%|######3   | 447/704 [01:49<00:57,  4.48/s]
 64%|######3   | 448/704 [01:49<00:57,  4.43/s]
 64%|######3   | 449/704 [01:50<00:58,  4.37/s]
 64%|######3   | 450/704 [01:50<00:57,  4.42/s]
 64%|######4   | 451/704 [01:50<00:57,  4.44/s]
 64%|######4   | 452/704 [01:50<00:57,  4.36/s]
 64%|######4   | 453/704 [01:51<00:56,  4.42/s]
 64%|######4   | 454/704 [01:51<00:56,  4.43/s]
 65%|######4   | 455/704 [01:51<00:56,  4.37/s]
 65%|######4   | 456/704 [01:51<00:56,  4.38/s]
 65%|######4   | 457/704 [01:52<00:55,  4.42/s]
 65%|######5   | 458/704 [01:52<00:55,  4.42/s]
 65%|######5   | 459/704 [01:52<00:55,  4.45/s]
 65%|######5   | 460/704 [01:52<00:54,  4.44/s]
 65%|######5   | 461/704 [01:52<00:54,  4.43/s]
 66%|######5   | 462/704 [01:53<00:54,  4.42/s]
 66%|######5   | 463/704 [01:53<00:54,  4.42/s]
 66%|######5   | 464/704 [01:53<00:53,  4.47/s]
 66%|######6   | 465/704 [01:53<00:53,  4.47/s]
 66%|######6   | 466/704 [01:54<00:53,  4.46/s]
 66%|######6   | 467/704 [01:54<00:53,  4.45/s]
 66%|######6   | 468/704 [01:54<00:53,  4.45/s]
 67%|######6   | 469/704 [01:54<00:51,  4.54/s]
 67%|######6   | 470/704 [01:54<00:51,  4.57/s]
 67%|######6   | 471/704 [01:55<00:50,  4.62/s]
 67%|######7   | 472/704 [01:55<00:50,  4.60/s]
 67%|######7   | 473/704 [01:55<00:50,  4.60/s]
 67%|######7   | 474/704 [01:55<00:50,  4.59/s]
 67%|######7   | 475/704 [01:55<00:49,  4.61/s]
 68%|######7   | 476/704 [01:56<00:49,  4.61/s]
 68%|######7   | 477/704 [01:56<00:49,  4.62/s]
 68%|######7   | 478/704 [01:56<00:48,  4.62/s]
 68%|######8   | 479/704 [01:56<00:48,  4.62/s]
 68%|######8   | 480/704 [01:57<00:48,  4.61/s]
 68%|######8   | 481/704 [01:57<00:48,  4.60/s]
 68%|######8   | 482/704 [01:57<00:48,  4.54/s]
 69%|######8   | 483/704 [01:57<00:48,  4.55/s]
 69%|######8   | 484/704 [01:57<00:48,  4.55/s]
 69%|######8   | 485/704 [01:58<00:48,  4.55/s]
 69%|######9   | 486/704 [01:58<00:47,  4.57/s]
 69%|######9   | 487/704 [01:58<00:47,  4.56/s]
 69%|######9   | 488/704 [01:58<00:47,  4.54/s]
 69%|######9   | 489/704 [01:59<00:47,  4.56/s]
 70%|######9   | 490/704 [01:59<00:47,  4.52/s]
 70%|######9   | 491/704 [01:59<00:47,  4.53/s]
 70%|######9   | 492/704 [01:59<00:47,  4.49/s]
 70%|#######   | 493/704 [01:59<00:46,  4.52/s]
 70%|#######   | 494/704 [02:00<00:46,  4.53/s]
 70%|#######   | 495/704 [02:00<00:45,  4.55/s]
 70%|#######   | 496/704 [02:00<00:45,  4.55/s]
 71%|#######   | 497/704 [02:00<00:45,  4.53/s]
 71%|#######   | 498/704 [02:01<00:45,  4.57/s]
 71%|#######   | 499/704 [02:01<00:45,  4.53/s]
 71%|#######1  | 500/704 [02:01<00:45,  4.51/s]
 71%|#######1  | 501/704 [02:01<00:44,  4.51/s]
 71%|#######1  | 502/704 [02:01<00:44,  4.51/s]
 71%|#######1  | 503/704 [02:02<00:44,  4.48/s]
 72%|#######1  | 504/704 [02:02<00:44,  4.47/s]
 72%|#######1  | 505/704 [02:02<00:44,  4.45/s]
 72%|#######1  | 506/704 [02:02<00:44,  4.45/s]
 72%|#######2  | 507/704 [02:03<00:43,  4.50/s]
 72%|#######2  | 508/704 [02:03<00:43,  4.51/s]
 72%|#######2  | 509/704 [02:03<00:43,  4.50/s]
 72%|#######2  | 510/704 [02:03<00:42,  4.53/s]
 73%|#######2  | 511/704 [02:03<00:42,  4.52/s]
 73%|#######2  | 512/704 [02:04<00:42,  4.55/s]
 73%|#######2  | 513/704 [02:04<00:41,  4.57/s]
 73%|#######3  | 514/704 [02:04<00:41,  4.60/s]
 73%|#######3  | 515/704 [02:04<00:43,  4.38/s]
 73%|#######3  | 516/704 [02:05<00:45,  4.10/s]
 73%|#######3  | 517/704 [02:05<00:48,  3.86/s]
 74%|#######3  | 518/704 [02:05<00:46,  3.96/s]
 74%|#######3  | 519/704 [02:05<00:46,  4.02/s]
 74%|#######3  | 520/704 [02:06<00:44,  4.11/s]
 74%|#######4  | 521/704 [02:06<00:43,  4.16/s]
 74%|#######4  | 522/704 [02:06<00:44,  4.11/s]
 74%|#######4  | 523/704 [02:06<00:44,  4.11/s]
 74%|#######4  | 524/704 [02:07<00:43,  4.10/s]
 75%|#######4  | 525/704 [02:07<00:43,  4.08/s]
 75%|#######4  | 526/704 [02:07<00:43,  4.09/s]
 75%|#######4  | 527/704 [02:07<00:43,  4.11/s]
 75%|#######5  | 528/704 [02:08<00:42,  4.11/s]
 75%|#######5  | 529/704 [02:08<00:41,  4.20/s]
 75%|#######5  | 530/704 [02:08<00:40,  4.25/s]
 75%|#######5  | 531/704 [02:08<00:41,  4.21/s]
 76%|#######5  | 532/704 [02:08<00:40,  4.29/s]
 76%|#######5  | 533/704 [02:09<00:39,  4.37/s]
 76%|#######5  | 534/704 [02:09<00:37,  4.50/s]
 76%|#######5  | 535/704 [02:09<00:36,  4.57/s]
 76%|#######6  | 536/704 [02:09<00:36,  4.63/s]
 76%|#######6  | 537/704 [02:10<00:36,  4.63/s]
 76%|#######6  | 538/704 [02:10<00:35,  4.61/s]
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 80%|########  | 564/704 [02:16<00:31,  4.39/s]
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 81%|########1 | 571/704 [02:17<00:32,  4.11/s]
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 82%|########1 | 576/704 [02:19<00:29,  4.31/s]
 82%|########1 | 577/704 [02:19<00:29,  4.33/s]
 82%|########2 | 578/704 [02:19<00:28,  4.36/s]
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 83%|########3 | 587/704 [02:21<00:26,  4.36/s]
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 91%|#########1| 641/704 [02:33<00:14,  4.37/s]
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 93%|#########3| 655/704 [02:36<00:10,  4.73/s]
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 94%|#########4| 662/704 [02:38<00:09,  4.53/s]
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 96%|#########6| 676/704 [02:41<00:06,  4.24/s]
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100%|#########9| 702/704 [02:46<00:00,  4.87/s]
100%|#########9| 703/704 [02:47<00:00,  4.87/s]
100%|##########| 704/704 [02:47<00:00,  4.91/s]
100%|##########| 704/704 [02:47<00:00,  4.21/s]

  0%|          | 0/704 [00:00<?, ?/s]
  0%|          | 1/704 [00:06<1:12:02,  6.15s/]
  0%|          | 2/704 [00:06<31:08,  2.66s/]
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  1%|          | 4/704 [00:06<11:59,  1.03s/]
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  1%|          | 6/704 [00:07<06:35,  1.77/s]
  1%|          | 7/704 [00:07<05:16,  2.20/s]
  1%|1         | 8/704 [00:07<04:31,  2.56/s]
  1%|1         | 9/704 [00:08<03:59,  2.90/s]
  1%|1         | 10/704 [00:08<03:32,  3.26/s]
  2%|1         | 11/704 [00:08<03:14,  3.56/s]
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  2%|1         | 13/704 [00:08<02:53,  3.99/s]
  2%|1         | 14/704 [00:09<02:46,  4.14/s]
  2%|2         | 15/704 [00:09<02:41,  4.26/s]
  2%|2         | 16/704 [00:09<02:39,  4.31/s]
  2%|2         | 17/704 [00:09<02:37,  4.36/s]
  3%|2         | 18/704 [00:10<02:36,  4.39/s]
  3%|2         | 19/704 [00:10<02:34,  4.42/s]
  3%|2         | 20/704 [00:10<02:34,  4.42/s]
  3%|2         | 21/704 [00:10<02:41,  4.22/s]
  3%|3         | 22/704 [00:10<02:38,  4.31/s]
  3%|3         | 23/704 [00:11<02:39,  4.26/s]
  3%|3         | 24/704 [00:11<02:38,  4.28/s]
  4%|3         | 25/704 [00:11<02:37,  4.31/s]
  4%|3         | 26/704 [00:11<02:40,  4.23/s]
  4%|3         | 27/704 [00:12<02:39,  4.25/s]
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  4%|4         | 29/704 [00:12<02:31,  4.46/s]
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  4%|4         | 31/704 [00:12<02:28,  4.54/s]
  5%|4         | 32/704 [00:13<02:26,  4.60/s]
  5%|4         | 33/704 [00:13<02:24,  4.64/s]
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  5%|5         | 36/704 [00:14<02:23,  4.64/s]
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  6%|6         | 43/704 [00:15<02:22,  4.63/s]
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  7%|6         | 48/704 [00:16<02:22,  4.60/s]
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  7%|7         | 50/704 [00:17<02:19,  4.70/s]
  7%|7         | 51/704 [00:17<02:26,  4.46/s]
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  8%|7         | 55/704 [00:18<02:26,  4.43/s]
  8%|7         | 56/704 [00:18<02:32,  4.24/s]
  8%|8         | 57/704 [00:18<02:32,  4.25/s]
  8%|8         | 58/704 [00:18<02:33,  4.20/s]
  8%|8         | 59/704 [00:19<02:31,  4.27/s]
  9%|8         | 60/704 [00:19<02:29,  4.31/s]
  9%|8         | 61/704 [00:19<02:27,  4.35/s]
  9%|8         | 62/704 [00:19<02:34,  4.16/s]
  9%|8         | 63/704 [00:20<02:38,  4.05/s]
  9%|9         | 64/704 [00:20<02:33,  4.16/s]
  9%|9         | 65/704 [00:20<02:30,  4.24/s]
  9%|9         | 66/704 [00:20<02:35,  4.11/s]
 10%|9         | 67/704 [00:21<02:30,  4.23/s]
 10%|9         | 68/704 [00:21<02:31,  4.18/s]
 10%|9         | 69/704 [00:21<02:29,  4.24/s]
 10%|9         | 70/704 [00:21<02:29,  4.25/s]
 10%|#         | 71/704 [00:22<02:25,  4.34/s]
 10%|#         | 72/704 [00:22<02:27,  4.30/s]
 10%|#         | 73/704 [00:22<02:24,  4.36/s]
 11%|#         | 74/704 [00:22<02:26,  4.31/s]
 11%|#         | 75/704 [00:22<02:23,  4.40/s]
 11%|#         | 76/704 [00:23<02:20,  4.47/s]
 11%|#         | 77/704 [00:23<02:22,  4.41/s]
 11%|#1        | 78/704 [00:23<02:25,  4.31/s]
 11%|#1        | 79/704 [00:23<02:26,  4.27/s]
 11%|#1        | 80/704 [00:24<02:24,  4.31/s]
 12%|#1        | 81/704 [00:24<02:24,  4.32/s]
 12%|#1        | 82/704 [00:24<02:23,  4.33/s]
 12%|#1        | 83/704 [00:24<02:24,  4.30/s]
 12%|#1        | 84/704 [00:25<02:25,  4.27/s]
 12%|#2        | 85/704 [00:25<02:24,  4.28/s]
 12%|#2        | 86/704 [00:25<02:22,  4.35/s]
 12%|#2        | 87/704 [00:25<02:20,  4.39/s]
 12%|#2        | 88/704 [00:25<02:18,  4.44/s]
 13%|#2        | 89/704 [00:26<02:18,  4.45/s]
 13%|#2        | 90/704 [00:26<02:16,  4.49/s]
 13%|#2        | 91/704 [00:26<02:15,  4.53/s]
 13%|#3        | 92/704 [00:26<02:15,  4.51/s]
 13%|#3        | 93/704 [00:27<02:14,  4.55/s]
 13%|#3        | 94/704 [00:27<02:14,  4.54/s]
 13%|#3        | 95/704 [00:27<02:15,  4.49/s]
 14%|#3        | 96/704 [00:27<02:16,  4.45/s]
 14%|#3        | 97/704 [00:27<02:16,  4.44/s]
 14%|#3        | 98/704 [00:28<02:18,  4.37/s]
 14%|#4        | 99/704 [00:28<02:18,  4.38/s]
 14%|#4        | 100/704 [00:28<02:19,  4.33/s]
 14%|#4        | 101/704 [00:28<02:18,  4.36/s]
 14%|#4        | 102/704 [00:29<02:18,  4.35/s]
 15%|#4        | 103/704 [00:29<02:16,  4.40/s]
 15%|#4        | 104/704 [00:29<02:16,  4.39/s]
 15%|#4        | 105/704 [00:29<02:14,  4.44/s]
 15%|#5        | 106/704 [00:30<02:14,  4.43/s]
 15%|#5        | 107/704 [00:30<02:15,  4.39/s]
 15%|#5        | 108/704 [00:30<02:20,  4.24/s]
 15%|#5        | 109/704 [00:30<02:22,  4.16/s]
 16%|#5        | 110/704 [00:30<02:21,  4.20/s]
 16%|#5        | 111/704 [00:31<02:21,  4.20/s]
 16%|#5        | 112/704 [00:31<02:20,  4.20/s]
 16%|#6        | 113/704 [00:31<02:18,  4.25/s]
 16%|#6        | 114/704 [00:31<02:19,  4.23/s]
 16%|#6        | 115/704 [00:32<02:20,  4.18/s]
 16%|#6        | 116/704 [00:32<02:21,  4.17/s]
 17%|#6        | 117/704 [00:32<02:20,  4.18/s]
 17%|#6        | 118/704 [00:32<02:17,  4.25/s]
 17%|#6        | 119/704 [00:33<02:20,  4.17/s]
 17%|#7        | 120/704 [00:33<02:19,  4.19/s]
 17%|#7        | 121/704 [00:33<02:19,  4.19/s]
 17%|#7        | 122/704 [00:33<02:18,  4.19/s]
 17%|#7        | 123/704 [00:34<02:17,  4.21/s]
 18%|#7        | 124/704 [00:34<02:20,  4.14/s]
 18%|#7        | 125/704 [00:34<02:19,  4.16/s]
 18%|#7        | 126/704 [00:34<02:17,  4.20/s]
 18%|#8        | 127/704 [00:35<02:17,  4.20/s]
 18%|#8        | 128/704 [00:35<02:17,  4.18/s]
 18%|#8        | 129/704 [00:35<02:16,  4.23/s]
 18%|#8        | 130/704 [00:35<02:16,  4.20/s]
 19%|#8        | 131/704 [00:35<02:15,  4.24/s]
 19%|#8        | 132/704 [00:36<02:13,  4.29/s]
 19%|#8        | 133/704 [00:36<02:12,  4.32/s]
 19%|#9        | 134/704 [00:36<02:11,  4.33/s]
 19%|#9        | 135/704 [00:36<02:10,  4.35/s]
 19%|#9        | 136/704 [00:37<02:10,  4.36/s]
 19%|#9        | 137/704 [00:37<02:09,  4.39/s]
 20%|#9        | 138/704 [00:37<02:08,  4.41/s]
 20%|#9        | 139/704 [00:37<02:07,  4.44/s]
 20%|#9        | 140/704 [00:38<02:06,  4.45/s]
 20%|##        | 141/704 [00:38<02:07,  4.40/s]
 20%|##        | 142/704 [00:38<02:07,  4.41/s]
 20%|##        | 143/704 [00:38<02:08,  4.38/s]
 20%|##        | 144/704 [00:38<02:07,  4.40/s]
 21%|##        | 145/704 [00:39<02:07,  4.39/s]
 21%|##        | 146/704 [00:39<02:06,  4.41/s]
 21%|##        | 147/704 [00:39<02:05,  4.44/s]
 21%|##1       | 148/704 [00:39<02:05,  4.42/s]
 21%|##1       | 149/704 [00:40<02:05,  4.41/s]
 21%|##1       | 150/704 [00:40<02:03,  4.47/s]
 21%|##1       | 151/704 [00:40<02:02,  4.52/s]
 22%|##1       | 152/704 [00:40<02:02,  4.52/s]
 22%|##1       | 153/704 [00:40<02:00,  4.57/s]
 22%|##1       | 154/704 [00:41<02:02,  4.49/s]
 22%|##2       | 155/704 [00:41<02:01,  4.51/s]
 22%|##2       | 156/704 [00:41<02:01,  4.51/s]
 22%|##2       | 157/704 [00:41<02:01,  4.52/s]
 22%|##2       | 158/704 [00:42<02:01,  4.51/s]
 23%|##2       | 159/704 [00:42<02:03,  4.41/s]
 23%|##2       | 160/704 [00:42<02:03,  4.42/s]
 23%|##2       | 161/704 [00:42<02:04,  4.35/s]
 23%|##3       | 162/704 [00:42<02:06,  4.27/s]
 23%|##3       | 163/704 [00:43<02:06,  4.28/s]
 23%|##3       | 164/704 [00:43<02:06,  4.28/s]
 23%|##3       | 165/704 [00:43<02:04,  4.32/s]
 24%|##3       | 166/704 [00:43<02:04,  4.31/s]
 24%|##3       | 167/704 [00:44<02:05,  4.27/s]
 24%|##3       | 168/704 [00:44<02:05,  4.28/s]
 24%|##4       | 169/704 [00:44<02:04,  4.30/s]
 24%|##4       | 170/704 [00:44<02:04,  4.28/s]
 24%|##4       | 171/704 [00:45<02:02,  4.35/s]
 24%|##4       | 172/704 [00:45<02:01,  4.37/s]
 25%|##4       | 173/704 [00:45<01:59,  4.43/s]
 25%|##4       | 174/704 [00:45<01:59,  4.44/s]
 25%|##4       | 175/704 [00:45<01:57,  4.49/s]
 25%|##5       | 176/704 [00:46<01:56,  4.52/s]
 25%|##5       | 177/704 [00:46<01:55,  4.58/s]
 25%|##5       | 178/704 [00:46<01:54,  4.58/s]
 25%|##5       | 179/704 [00:46<01:54,  4.58/s]
 26%|##5       | 180/704 [00:47<01:53,  4.61/s]
 26%|##5       | 181/704 [00:47<01:53,  4.60/s]
 26%|##5       | 182/704 [00:47<01:53,  4.60/s]
 26%|##5       | 183/704 [00:47<01:54,  4.53/s]
 26%|##6       | 184/704 [00:47<01:54,  4.53/s]
 26%|##6       | 185/704 [00:48<01:54,  4.54/s]
 26%|##6       | 186/704 [00:48<01:53,  4.56/s]
 27%|##6       | 187/704 [00:48<01:53,  4.57/s]
 27%|##6       | 188/704 [00:48<01:52,  4.57/s]
 27%|##6       | 189/704 [00:49<01:51,  4.60/s]
 27%|##6       | 190/704 [00:49<01:51,  4.61/s]
 27%|##7       | 191/704 [00:49<01:50,  4.63/s]
 27%|##7       | 192/704 [00:49<01:50,  4.62/s]
 27%|##7       | 193/704 [00:49<01:51,  4.59/s]
 28%|##7       | 194/704 [00:50<01:51,  4.59/s]
 28%|##7       | 195/704 [00:50<01:52,  4.51/s]
 28%|##7       | 196/704 [00:50<01:52,  4.50/s]
 28%|##7       | 197/704 [00:50<01:52,  4.52/s]
 28%|##8       | 198/704 [00:50<01:52,  4.51/s]
 28%|##8       | 199/704 [00:51<01:53,  4.47/s]
 28%|##8       | 200/704 [00:51<01:52,  4.49/s]
 29%|##8       | 201/704 [00:51<01:51,  4.51/s]
 29%|##8       | 202/704 [00:51<01:50,  4.53/s]
 29%|##8       | 203/704 [00:52<01:52,  4.46/s]
 29%|##8       | 204/704 [00:52<01:55,  4.33/s]
 29%|##9       | 205/704 [00:52<01:53,  4.38/s]
 29%|##9       | 206/704 [00:52<01:52,  4.42/s]
 29%|##9       | 207/704 [00:53<01:51,  4.46/s]
 30%|##9       | 208/704 [00:53<01:50,  4.49/s]
 30%|##9       | 209/704 [00:53<01:49,  4.54/s]
 30%|##9       | 210/704 [00:53<01:49,  4.52/s]
 30%|##9       | 211/704 [00:53<01:48,  4.54/s]
 30%|###       | 212/704 [00:54<01:47,  4.56/s]
 30%|###       | 213/704 [00:54<01:48,  4.54/s]
 30%|###       | 214/704 [00:54<01:48,  4.50/s]
 31%|###       | 215/704 [00:54<01:50,  4.44/s]
 31%|###       | 216/704 [00:55<01:49,  4.47/s]
 31%|###       | 217/704 [00:55<01:48,  4.50/s]
 31%|###       | 218/704 [00:55<01:47,  4.53/s]
 31%|###1      | 219/704 [00:55<01:46,  4.55/s]
 31%|###1      | 220/704 [00:55<01:46,  4.53/s]
 31%|###1      | 221/704 [00:56<01:46,  4.56/s]
 32%|###1      | 222/704 [00:56<01:46,  4.54/s]
 32%|###1      | 223/704 [00:56<01:45,  4.57/s]
 32%|###1      | 224/704 [00:56<01:44,  4.61/s]
 32%|###1      | 225/704 [00:56<01:44,  4.56/s]
 32%|###2      | 226/704 [00:57<01:44,  4.58/s]
 32%|###2      | 227/704 [00:57<01:44,  4.58/s]
 32%|###2      | 228/704 [00:57<01:44,  4.55/s]
 33%|###2      | 229/704 [00:57<01:44,  4.53/s]
 33%|###2      | 230/704 [00:58<01:44,  4.52/s]
 33%|###2      | 231/704 [00:58<01:44,  4.53/s]
 33%|###2      | 232/704 [00:58<01:43,  4.57/s]
 33%|###3      | 233/704 [00:58<01:43,  4.55/s]
 33%|###3      | 234/704 [00:58<01:43,  4.54/s]
 33%|###3      | 235/704 [00:59<01:42,  4.57/s]
 34%|###3      | 236/704 [00:59<01:42,  4.58/s]
 34%|###3      | 237/704 [00:59<01:42,  4.53/s]
 34%|###3      | 238/704 [00:59<01:42,  4.53/s]
 34%|###3      | 239/704 [01:00<01:44,  4.47/s]
 34%|###4      | 240/704 [01:00<01:52,  4.11/s]
 34%|###4      | 241/704 [01:00<01:54,  4.04/s]
 34%|###4      | 242/704 [01:00<01:53,  4.07/s]
 35%|###4      | 243/704 [01:01<01:49,  4.22/s]
 35%|###4      | 244/704 [01:01<01:46,  4.30/s]
 35%|###4      | 245/704 [01:01<01:44,  4.38/s]
 35%|###4      | 246/704 [01:01<01:42,  4.48/s]
 35%|###5      | 247/704 [01:01<01:40,  4.54/s]
 35%|###5      | 248/704 [01:02<01:39,  4.59/s]
 35%|###5      | 249/704 [01:02<01:38,  4.62/s]
 36%|###5      | 250/704 [01:02<01:37,  4.66/s]
 36%|###5      | 251/704 [01:02<01:36,  4.68/s]
 36%|###5      | 252/704 [01:02<01:36,  4.69/s]
 36%|###5      | 253/704 [01:03<01:35,  4.71/s]
 36%|###6      | 254/704 [01:03<01:35,  4.71/s]
 36%|###6      | 255/704 [01:03<01:35,  4.72/s]
 36%|###6      | 256/704 [01:03<01:35,  4.68/s]
 37%|###6      | 257/704 [01:04<01:35,  4.66/s]
 37%|###6      | 258/704 [01:04<01:36,  4.64/s]
 37%|###6      | 259/704 [01:04<01:35,  4.64/s]
 37%|###6      | 260/704 [01:04<01:35,  4.64/s]
 37%|###7      | 261/704 [01:04<01:34,  4.67/s]
 37%|###7      | 262/704 [01:05<01:34,  4.66/s]
 37%|###7      | 263/704 [01:05<01:35,  4.63/s]
 38%|###7      | 264/704 [01:05<01:33,  4.68/s]
 38%|###7      | 265/704 [01:05<01:33,  4.72/s]
 38%|###7      | 266/704 [01:05<01:32,  4.71/s]
 38%|###7      | 267/704 [01:06<01:33,  4.69/s]
 38%|###8      | 268/704 [01:06<01:33,  4.66/s]
 38%|###8      | 269/704 [01:06<01:33,  4.67/s]
 38%|###8      | 270/704 [01:06<01:33,  4.67/s]
 38%|###8      | 271/704 [01:07<01:32,  4.68/s]
 39%|###8      | 272/704 [01:07<01:32,  4.67/s]
 39%|###8      | 273/704 [01:07<01:32,  4.68/s]
 39%|###8      | 274/704 [01:07<01:31,  4.68/s]
 39%|###9      | 275/704 [01:07<01:31,  4.69/s]
 39%|###9      | 276/704 [01:08<01:31,  4.70/s]
 39%|###9      | 277/704 [01:08<01:30,  4.71/s]
 39%|###9      | 278/704 [01:08<01:30,  4.72/s]
 40%|###9      | 279/704 [01:08<01:29,  4.72/s]
 40%|###9      | 280/704 [01:08<01:29,  4.72/s]
 40%|###9      | 281/704 [01:09<01:30,  4.67/s]
 40%|####      | 282/704 [01:09<01:30,  4.65/s]
 40%|####      | 283/704 [01:09<01:30,  4.64/s]
 40%|####      | 284/704 [01:09<01:30,  4.62/s]
 40%|####      | 285/704 [01:10<01:31,  4.60/s]
 41%|####      | 286/704 [01:10<01:30,  4.64/s]
 41%|####      | 287/704 [01:10<01:29,  4.63/s]
 41%|####      | 288/704 [01:10<01:29,  4.67/s]
 41%|####1     | 289/704 [01:10<01:27,  4.73/s]
 41%|####1     | 290/704 [01:11<01:27,  4.71/s]
 41%|####1     | 291/704 [01:11<01:27,  4.73/s]
 41%|####1     | 292/704 [01:11<01:27,  4.70/s]
 42%|####1     | 293/704 [01:11<01:27,  4.69/s]
 42%|####1     | 294/704 [01:11<01:27,  4.69/s]
 42%|####1     | 295/704 [01:12<01:27,  4.66/s]
 42%|####2     | 296/704 [01:12<01:27,  4.66/s]
 42%|####2     | 297/704 [01:12<01:27,  4.64/s]
 42%|####2     | 298/704 [01:12<01:27,  4.65/s]
 42%|####2     | 299/704 [01:13<01:27,  4.65/s]
 43%|####2     | 300/704 [01:13<01:26,  4.65/s]
 43%|####2     | 301/704 [01:13<01:26,  4.65/s]
 43%|####2     | 302/704 [01:13<01:26,  4.67/s]
 43%|####3     | 303/704 [01:13<01:26,  4.66/s]
 43%|####3     | 304/704 [01:14<01:25,  4.67/s]
 43%|####3     | 305/704 [01:14<01:25,  4.68/s]
 43%|####3     | 306/704 [01:14<01:24,  4.70/s]
 44%|####3     | 307/704 [01:14<01:24,  4.71/s]
 44%|####3     | 308/704 [01:14<01:23,  4.72/s]
 44%|####3     | 309/704 [01:15<01:23,  4.73/s]
 44%|####4     | 310/704 [01:15<01:23,  4.72/s]
 44%|####4     | 311/704 [01:15<01:23,  4.72/s]
 44%|####4     | 312/704 [01:15<01:23,  4.72/s]
 44%|####4     | 313/704 [01:16<01:22,  4.72/s]
 45%|####4     | 314/704 [01:16<01:22,  4.74/s]
 45%|####4     | 315/704 [01:16<01:21,  4.76/s]
 45%|####4     | 316/704 [01:16<01:21,  4.78/s]
 45%|####5     | 317/704 [01:16<01:21,  4.77/s]
 45%|####5     | 318/704 [01:17<01:22,  4.70/s]
 45%|####5     | 319/704 [01:17<01:22,  4.69/s]
 45%|####5     | 320/704 [01:17<01:22,  4.67/s]
 46%|####5     | 321/704 [01:17<01:22,  4.66/s]
 46%|####5     | 322/704 [01:17<01:22,  4.63/s]
 46%|####5     | 323/704 [01:18<01:22,  4.60/s]
 46%|####6     | 324/704 [01:18<01:22,  4.60/s]
 46%|####6     | 325/704 [01:18<01:21,  4.63/s]
 46%|####6     | 326/704 [01:18<01:21,  4.64/s]
 46%|####6     | 327/704 [01:19<01:24,  4.46/s]
 47%|####6     | 328/704 [01:19<01:26,  4.35/s]
 47%|####6     | 329/704 [01:19<01:27,  4.29/s]
 47%|####6     | 330/704 [01:19<01:30,  4.11/s]
 47%|####7     | 331/704 [01:20<01:32,  4.02/s]
 47%|####7     | 332/704 [01:20<01:33,  3.97/s]
 47%|####7     | 333/704 [01:20<01:30,  4.10/s]
 47%|####7     | 334/704 [01:20<01:28,  4.20/s]
 48%|####7     | 335/704 [01:21<01:26,  4.28/s]
 48%|####7     | 336/704 [01:21<01:24,  4.34/s]
 48%|####7     | 337/704 [01:21<01:24,  4.37/s]
 48%|####8     | 338/704 [01:21<01:23,  4.38/s]
 48%|####8     | 339/704 [01:21<01:23,  4.38/s]
 48%|####8     | 340/704 [01:22<01:23,  4.38/s]
 48%|####8     | 341/704 [01:22<01:23,  4.35/s]
 49%|####8     | 342/704 [01:22<01:23,  4.34/s]
 49%|####8     | 343/704 [01:22<01:23,  4.34/s]
 49%|####8     | 344/704 [01:23<01:22,  4.34/s]
 49%|####9     | 345/704 [01:23<01:22,  4.34/s]
 49%|####9     | 346/704 [01:23<01:23,  4.31/s]
 49%|####9     | 347/704 [01:23<01:22,  4.35/s]
 49%|####9     | 348/704 [01:23<01:21,  4.36/s]
 50%|####9     | 349/704 [01:24<01:20,  4.39/s]
 50%|####9     | 350/704 [01:24<01:21,  4.37/s]
 50%|####9     | 351/704 [01:24<01:21,  4.33/s]
 50%|#####     | 352/704 [01:24<01:21,  4.33/s]
 50%|#####     | 353/704 [01:25<01:20,  4.34/s]
 50%|#####     | 354/704 [01:25<01:20,  4.33/s]
 50%|#####     | 355/704 [01:25<01:20,  4.33/s]
 51%|#####     | 356/704 [01:25<01:20,  4.32/s]
 51%|#####     | 357/704 [01:26<01:19,  4.36/s]
 51%|#####     | 358/704 [01:26<01:19,  4.37/s]
 51%|#####     | 359/704 [01:26<01:19,  4.36/s]
 51%|#####1    | 360/704 [01:26<01:20,  4.28/s]
 51%|#####1    | 361/704 [01:27<01:27,  3.92/s]
 51%|#####1    | 362/704 [01:27<01:30,  3.77/s]
 52%|#####1    | 363/704 [01:27<01:30,  3.78/s]
 52%|#####1    | 364/704 [01:27<01:31,  3.72/s]
 52%|#####1    | 365/704 [01:28<01:30,  3.74/s]
 52%|#####1    | 366/704 [01:28<01:29,  3.80/s]
 52%|#####2    | 367/704 [01:28<01:26,  3.92/s]
 52%|#####2    | 368/704 [01:28<01:24,  3.98/s]
 52%|#####2    | 369/704 [01:29<01:22,  4.08/s]
 53%|#####2    | 370/704 [01:29<01:19,  4.18/s]
 53%|#####2    | 371/704 [01:29<01:18,  4.24/s]
 53%|#####2    | 372/704 [01:29<01:16,  4.32/s]
 53%|#####2    | 373/704 [01:30<01:16,  4.35/s]
 53%|#####3    | 374/704 [01:30<01:15,  4.38/s]
 53%|#####3    | 375/704 [01:30<01:14,  4.41/s]
 53%|#####3    | 376/704 [01:30<01:13,  4.45/s]
 54%|#####3    | 377/704 [01:30<01:12,  4.50/s]
 54%|#####3    | 378/704 [01:31<01:12,  4.51/s]
 54%|#####3    | 379/704 [01:31<01:11,  4.55/s]
 54%|#####3    | 380/704 [01:31<01:10,  4.59/s]
 54%|#####4    | 381/704 [01:31<01:10,  4.61/s]
 54%|#####4    | 382/704 [01:31<01:09,  4.62/s]
 54%|#####4    | 383/704 [01:32<01:09,  4.61/s]
 55%|#####4    | 384/704 [01:32<01:09,  4.59/s]
 55%|#####4    | 385/704 [01:32<01:09,  4.59/s]
 55%|#####4    | 386/704 [01:32<01:10,  4.51/s]
 55%|#####4    | 387/704 [01:33<01:14,  4.28/s]
 55%|#####5    | 388/704 [01:33<01:17,  4.08/s]
 55%|#####5    | 389/704 [01:33<01:19,  3.94/s]
 55%|#####5    | 390/704 [01:33<01:21,  3.83/s]
 56%|#####5    | 391/704 [01:34<01:24,  3.69/s]
 56%|#####5    | 392/704 [01:34<01:20,  3.90/s]
 56%|#####5    | 393/704 [01:34<01:15,  4.11/s]
 56%|#####5    | 394/704 [01:34<01:13,  4.21/s]
 56%|#####6    | 395/704 [01:35<01:14,  4.15/s]
 56%|#####6    | 396/704 [01:35<01:14,  4.16/s]
 56%|#####6    | 397/704 [01:35<01:12,  4.22/s]
 57%|#####6    | 398/704 [01:35<01:11,  4.27/s]
 57%|#####6    | 399/704 [01:36<01:12,  4.22/s]
 57%|#####6    | 400/704 [01:36<01:12,  4.22/s]
 57%|#####6    | 401/704 [01:36<01:12,  4.17/s]
 57%|#####7    | 402/704 [01:36<01:11,  4.24/s]
 57%|#####7    | 403/704 [01:37<01:10,  4.26/s]
 57%|#####7    | 404/704 [01:37<01:11,  4.21/s]
 58%|#####7    | 405/704 [01:37<01:09,  4.29/s]
 58%|#####7    | 406/704 [01:37<01:11,  4.19/s]
 58%|#####7    | 407/704 [01:37<01:09,  4.29/s]
 58%|#####7    | 408/704 [01:38<01:07,  4.38/s]
 58%|#####8    | 409/704 [01:38<01:06,  4.45/s]
 58%|#####8    | 410/704 [01:38<01:05,  4.46/s]
 58%|#####8    | 411/704 [01:38<01:04,  4.52/s]
 59%|#####8    | 412/704 [01:39<01:04,  4.54/s]
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100%|#########9| 701/704 [02:49<00:00,  4.34/s]
100%|#########9| 702/704 [02:49<00:00,  4.26/s]
100%|#########9| 703/704 [02:49<00:00,  4.22/s]
100%|##########| 704/704 [02:49<00:00,  4.19/s]
100%|##########| 704/704 [02:49<00:00,  4.14/s]

We can use the extracted image features to compute a new cluster annotation. This could be useful to gain insights in similarities across spots based on image morphology.

For this, we first define a helper function to cluster features.

def cluster_features(features: pd.DataFrame, like=None):
    """
    Calculate leiden clustering of features.

    Specify filter of features using `like`.
    """
    # filter features
    if like is not None:
        features = features.filter(like=like)
    # create temporary adata to calculate the clustering
    adata = ad.AnnData(features)
    # important - feature values are not scaled, so need to scale them before PCA
    sc.pp.scale(adata)
    # calculate leiden clustering
    sc.pp.pca(adata, n_comps=min(10, features.shape[1] - 1))
    sc.pp.neighbors(adata)
    sc.tl.leiden(adata)

    return adata.obs["leiden"]

Then, we calculate feature clusters using different features and compare them to gene clusters:

adata.obs["features_summary_cluster"] = cluster_features(adata.obsm["features"], like="summary")
adata.obs["features_histogram_cluster"] = cluster_features(adata.obsm["features"], like="histogram")
adata.obs["features_texture_cluster"] = cluster_features(adata.obsm["features"], like="texture")

sc.set_figure_params(facecolor="white", figsize=(8, 8))
sq.pl.spatial_scatter(
    adata,
    color=[
        "features_summary_cluster",
        "features_histogram_cluster",
        "features_texture_cluster",
        "cluster",
    ],
    ncols=3,
)

Out:

/Users/giovanni.palla/Projects/squidpy_notebooks/tutorials/tutorial_visium_fluo.py:225: FutureWarning: X.dtype being converted to np.float32 from float64. In the next version of anndata (0.9) conversion will not be automatic. Pass dtype explicitly to avoid this warning. Pass `AnnData(X, dtype=X.dtype, ...)` to get the future behavour.
  adata = ad.AnnData(features)
/Users/giovanni.palla/Projects/squidpy_notebooks/tutorials/tutorial_visium_fluo.py:225: FutureWarning: X.dtype being converted to np.float32 from int64. In the next version of anndata (0.9) conversion will not be automatic. Pass dtype explicitly to avoid this warning. Pass `AnnData(X, dtype=X.dtype, ...)` to get the future behavour.
  adata = ad.AnnData(features)
/Users/giovanni.palla/Projects/squidpy_notebooks/tutorials/tutorial_visium_fluo.py:225: FutureWarning: X.dtype being converted to np.float32 from float64. In the next version of anndata (0.9) conversion will not be automatic. Pass dtype explicitly to avoid this warning. Pass `AnnData(X, dtype=X.dtype, ...)` to get the future behavour.
  adata = ad.AnnData(features)

Like the gene-space clusters (bottom middle), the feature space clusters are also spatially coherent.

The feature clusters of the different feature extractors are quite diverse, but all of them reflect the structure of the Hippocampus by assigning different clusters to the different structural areas. This is a higher level of detail than the gene-space clustering provides with only one cluster for the Hippocampus.

The feature clusters also show the layered structure of the cortex, but again subdividing it in more clusters than the gene-space clustering. It might be possible to re-cluster the gene expression counts with a higher resolution to also get more fine-grained clusters, but nevertheless the image features seem to provide additional supporting information to the gene-space clusters.

Estimated memory usage: 1987 MB