Extract histogram features
This example shows how to extract histogram features from tissue image.
Histogram features give a more detailed view than summary features (Extract summary features) by computing a histogram of each image channel and returning bin-counts for each Visium spot.
In addition to feature_name and channels we can specify the following features_kwargs:
bins- number of bins of the histogram, default is 10.
v_range- range on which values are binned, default is the whole image range.
See also
See Extract image features for general usage of
squidpy.im.calculate_image_features().
import squidpy as sq
Lets load the fluorescence Visium dataset and calculate bin-counts (3 bins) of channels 0 and 1.
# get spatial dataset including high-resolution tissue image
img = sq.datasets.visium_fluo_image_crop()
adata = sq.datasets.visium_fluo_adata_crop()
# calculate histogram features and save in key "histogram_features"
sq.im.calculate_image_features(
adata,
img,
features="histogram",
features_kwargs={"histogram": {"bins": 3, "channels": [0, 1]}},
key_added="histogram_features",
)
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44%|####3 | 307/704 [01:12<01:25, 4.62/s]
44%|####3 | 308/704 [01:13<01:25, 4.63/s]
44%|####3 | 309/704 [01:13<01:24, 4.67/s]
44%|####4 | 310/704 [01:13<01:24, 4.68/s]
44%|####4 | 311/704 [01:13<01:24, 4.66/s]
44%|####4 | 312/704 [01:13<01:23, 4.68/s]
44%|####4 | 313/704 [01:14<01:23, 4.68/s]
45%|####4 | 314/704 [01:14<01:23, 4.64/s]
45%|####4 | 315/704 [01:14<01:23, 4.65/s]
45%|####4 | 316/704 [01:14<01:23, 4.62/s]
45%|####5 | 317/704 [01:14<01:23, 4.64/s]
45%|####5 | 318/704 [01:15<01:23, 4.63/s]
45%|####5 | 319/704 [01:15<01:22, 4.66/s]
45%|####5 | 320/704 [01:15<01:22, 4.64/s]
46%|####5 | 321/704 [01:15<01:22, 4.67/s]
46%|####5 | 322/704 [01:16<01:21, 4.68/s]
46%|####5 | 323/704 [01:16<01:21, 4.66/s]
46%|####6 | 324/704 [01:16<01:20, 4.70/s]
46%|####6 | 325/704 [01:16<01:20, 4.72/s]
46%|####6 | 326/704 [01:16<01:20, 4.72/s]
46%|####6 | 327/704 [01:17<01:20, 4.69/s]
47%|####6 | 328/704 [01:17<01:20, 4.68/s]
47%|####6 | 329/704 [01:17<01:19, 4.70/s]
47%|####6 | 330/704 [01:17<01:20, 4.66/s]
47%|####7 | 331/704 [01:17<01:19, 4.68/s]
47%|####7 | 332/704 [01:18<01:20, 4.62/s]
47%|####7 | 333/704 [01:18<01:19, 4.64/s]
47%|####7 | 334/704 [01:18<01:19, 4.65/s]
48%|####7 | 335/704 [01:18<01:19, 4.67/s]
48%|####7 | 336/704 [01:19<01:18, 4.68/s]
48%|####7 | 337/704 [01:19<01:18, 4.66/s]
48%|####8 | 338/704 [01:19<01:18, 4.66/s]
48%|####8 | 339/704 [01:19<01:18, 4.64/s]
48%|####8 | 340/704 [01:19<01:18, 4.62/s]
48%|####8 | 341/704 [01:20<01:19, 4.57/s]
49%|####8 | 342/704 [01:20<01:18, 4.58/s]
49%|####8 | 343/704 [01:20<01:18, 4.59/s]
49%|####8 | 344/704 [01:20<01:18, 4.58/s]
49%|####9 | 345/704 [01:21<01:18, 4.58/s]
49%|####9 | 346/704 [01:21<01:18, 4.55/s]
49%|####9 | 347/704 [01:21<01:18, 4.56/s]
49%|####9 | 348/704 [01:21<01:18, 4.53/s]
50%|####9 | 349/704 [01:21<01:18, 4.53/s]
50%|####9 | 350/704 [01:22<01:18, 4.53/s]
50%|####9 | 351/704 [01:22<01:18, 4.51/s]
50%|##### | 352/704 [01:22<01:17, 4.54/s]
50%|##### | 353/704 [01:22<01:17, 4.54/s]
50%|##### | 354/704 [01:22<01:16, 4.55/s]
50%|##### | 355/704 [01:23<01:16, 4.54/s]
51%|##### | 356/704 [01:23<01:16, 4.54/s]
51%|##### | 357/704 [01:23<01:16, 4.53/s]
51%|##### | 358/704 [01:23<01:16, 4.54/s]
51%|##### | 359/704 [01:24<01:16, 4.51/s]
51%|#####1 | 360/704 [01:24<01:16, 4.49/s]
51%|#####1 | 361/704 [01:24<01:16, 4.48/s]
51%|#####1 | 362/704 [01:24<01:16, 4.50/s]
52%|#####1 | 363/704 [01:24<01:15, 4.50/s]
52%|#####1 | 364/704 [01:25<01:15, 4.50/s]
52%|#####1 | 365/704 [01:25<01:15, 4.51/s]
52%|#####1 | 366/704 [01:25<01:15, 4.50/s]
52%|#####2 | 367/704 [01:25<01:14, 4.49/s]
52%|#####2 | 368/704 [01:26<01:14, 4.51/s]
52%|#####2 | 369/704 [01:26<01:14, 4.51/s]
53%|#####2 | 370/704 [01:26<01:13, 4.53/s]
53%|#####2 | 371/704 [01:26<01:13, 4.55/s]
53%|#####2 | 372/704 [01:26<01:13, 4.51/s]
53%|#####2 | 373/704 [01:27<01:16, 4.30/s]
53%|#####3 | 374/704 [01:27<01:28, 3.73/s]
53%|#####3 | 375/704 [01:27<01:37, 3.38/s]
53%|#####3 | 376/704 [01:28<01:33, 3.50/s]
54%|#####3 | 377/704 [01:28<01:29, 3.66/s]
54%|#####3 | 378/704 [01:28<01:26, 3.75/s]
54%|#####3 | 379/704 [01:28<01:23, 3.88/s]
54%|#####3 | 380/704 [01:29<01:24, 3.84/s]
54%|#####4 | 381/704 [01:29<01:23, 3.89/s]
54%|#####4 | 382/704 [01:29<01:19, 4.06/s]
54%|#####4 | 383/704 [01:29<01:16, 4.19/s]
55%|#####4 | 384/704 [01:30<01:19, 4.03/s]
55%|#####4 | 385/704 [01:30<01:19, 4.01/s]
55%|#####4 | 386/704 [01:30<01:17, 4.11/s]
55%|#####4 | 387/704 [01:30<01:15, 4.18/s]
55%|#####5 | 388/704 [01:31<01:15, 4.20/s]
55%|#####5 | 389/704 [01:31<01:13, 4.26/s]
55%|#####5 | 390/704 [01:31<01:12, 4.31/s]
56%|#####5 | 391/704 [01:31<01:13, 4.28/s]
56%|#####5 | 392/704 [01:32<01:11, 4.34/s]
56%|#####5 | 393/704 [01:32<01:10, 4.43/s]
56%|#####5 | 394/704 [01:32<01:11, 4.32/s]
56%|#####6 | 395/704 [01:32<01:10, 4.36/s]
56%|#####6 | 396/704 [01:32<01:09, 4.41/s]
56%|#####6 | 397/704 [01:33<01:09, 4.41/s]
57%|#####6 | 398/704 [01:33<01:08, 4.44/s]
57%|#####6 | 399/704 [01:33<01:08, 4.47/s]
57%|#####6 | 400/704 [01:33<01:08, 4.43/s]
57%|#####6 | 401/704 [01:34<01:08, 4.43/s]
57%|#####7 | 402/704 [01:34<01:07, 4.47/s]
57%|#####7 | 403/704 [01:34<01:06, 4.54/s]
57%|#####7 | 404/704 [01:34<01:05, 4.57/s]
58%|#####7 | 405/704 [01:34<01:05, 4.56/s]
58%|#####7 | 406/704 [01:35<01:05, 4.56/s]
58%|#####7 | 407/704 [01:35<01:05, 4.56/s]
58%|#####7 | 408/704 [01:35<01:04, 4.58/s]
58%|#####8 | 409/704 [01:35<01:04, 4.58/s]
58%|#####8 | 410/704 [01:36<01:04, 4.59/s]
58%|#####8 | 411/704 [01:36<01:04, 4.56/s]
59%|#####8 | 412/704 [01:36<01:03, 4.57/s]
59%|#####8 | 413/704 [01:36<01:03, 4.59/s]
59%|#####8 | 414/704 [01:36<01:02, 4.62/s]
59%|#####8 | 415/704 [01:37<01:02, 4.63/s]
59%|#####9 | 416/704 [01:37<01:03, 4.56/s]
59%|#####9 | 417/704 [01:37<01:01, 4.64/s]
59%|#####9 | 418/704 [01:37<01:02, 4.55/s]
60%|#####9 | 419/704 [01:37<01:01, 4.60/s]
60%|#####9 | 420/704 [01:38<01:00, 4.66/s]
60%|#####9 | 421/704 [01:38<01:01, 4.62/s]
60%|#####9 | 422/704 [01:38<01:01, 4.55/s]
60%|###### | 423/704 [01:38<01:03, 4.45/s]
60%|###### | 424/704 [01:39<01:03, 4.43/s]
60%|###### | 425/704 [01:39<01:03, 4.42/s]
61%|###### | 426/704 [01:39<01:02, 4.42/s]
61%|###### | 427/704 [01:39<01:03, 4.37/s]
61%|###### | 428/704 [01:40<01:02, 4.39/s]
61%|###### | 429/704 [01:40<01:02, 4.42/s]
61%|######1 | 430/704 [01:40<01:01, 4.48/s]
61%|######1 | 431/704 [01:40<01:00, 4.51/s]
61%|######1 | 432/704 [01:40<01:00, 4.52/s]
62%|######1 | 433/704 [01:41<01:00, 4.51/s]
62%|######1 | 434/704 [01:41<01:00, 4.48/s]
62%|######1 | 435/704 [01:41<00:59, 4.50/s]
62%|######1 | 436/704 [01:41<00:59, 4.48/s]
62%|######2 | 437/704 [01:42<00:59, 4.50/s]
62%|######2 | 438/704 [01:42<00:58, 4.55/s]
62%|######2 | 439/704 [01:42<00:57, 4.60/s]
62%|######2 | 440/704 [01:42<00:57, 4.55/s]
63%|######2 | 441/704 [01:42<00:57, 4.58/s]
63%|######2 | 442/704 [01:43<00:56, 4.60/s]
63%|######2 | 443/704 [01:43<00:56, 4.61/s]
63%|######3 | 444/704 [01:43<00:56, 4.59/s]
63%|######3 | 445/704 [01:43<00:56, 4.56/s]
63%|######3 | 446/704 [01:43<00:56, 4.56/s]
63%|######3 | 447/704 [01:44<00:56, 4.53/s]
64%|######3 | 448/704 [01:44<00:56, 4.51/s]
64%|######3 | 449/704 [01:44<00:56, 4.50/s]
64%|######3 | 450/704 [01:44<00:56, 4.53/s]
64%|######4 | 451/704 [01:45<00:56, 4.52/s]
64%|######4 | 452/704 [01:45<00:55, 4.50/s]
64%|######4 | 453/704 [01:45<00:55, 4.50/s]
64%|######4 | 454/704 [01:45<00:55, 4.50/s]
65%|######4 | 455/704 [01:45<00:55, 4.49/s]
65%|######4 | 456/704 [01:46<00:55, 4.51/s]
65%|######4 | 457/704 [01:46<00:54, 4.50/s]
65%|######5 | 458/704 [01:46<00:54, 4.49/s]
65%|######5 | 459/704 [01:46<00:55, 4.45/s]
65%|######5 | 460/704 [01:47<00:56, 4.31/s]
65%|######5 | 461/704 [01:47<00:55, 4.34/s]
66%|######5 | 462/704 [01:47<00:56, 4.31/s]
66%|######5 | 463/704 [01:47<00:55, 4.33/s]
66%|######5 | 464/704 [01:48<00:54, 4.41/s]
66%|######6 | 465/704 [01:48<00:54, 4.40/s]
66%|######6 | 466/704 [01:48<00:52, 4.54/s]
66%|######6 | 467/704 [01:48<00:52, 4.55/s]
66%|######6 | 468/704 [01:48<00:50, 4.66/s]
67%|######6 | 469/704 [01:49<00:51, 4.58/s]
67%|######6 | 470/704 [01:49<00:50, 4.62/s]
67%|######6 | 471/704 [01:49<00:51, 4.55/s]
67%|######7 | 472/704 [01:49<00:51, 4.46/s]
67%|######7 | 473/704 [01:49<00:50, 4.56/s]
67%|######7 | 474/704 [01:50<00:49, 4.63/s]
67%|######7 | 475/704 [01:50<00:49, 4.63/s]
68%|######7 | 476/704 [01:50<00:49, 4.62/s]
68%|######7 | 477/704 [01:50<00:49, 4.60/s]
68%|######7 | 478/704 [01:51<00:49, 4.59/s]
68%|######8 | 479/704 [01:51<00:49, 4.57/s]
68%|######8 | 480/704 [01:51<00:49, 4.52/s]
68%|######8 | 481/704 [01:51<00:51, 4.32/s]
68%|######8 | 482/704 [01:52<00:51, 4.32/s]
69%|######8 | 483/704 [01:52<00:52, 4.22/s]
69%|######8 | 484/704 [01:52<00:51, 4.27/s]
69%|######8 | 485/704 [01:52<00:51, 4.25/s]
69%|######9 | 486/704 [01:53<00:58, 3.74/s]
69%|######9 | 487/704 [01:53<00:56, 3.82/s]
69%|######9 | 488/704 [01:53<00:54, 3.98/s]
69%|######9 | 489/704 [01:53<00:52, 4.11/s]
70%|######9 | 490/704 [01:53<00:51, 4.13/s]
70%|######9 | 491/704 [01:54<00:50, 4.22/s]
70%|######9 | 492/704 [01:54<00:49, 4.30/s]
70%|####### | 493/704 [01:54<00:48, 4.39/s]
70%|####### | 494/704 [01:54<00:48, 4.33/s]
70%|####### | 495/704 [01:55<00:47, 4.37/s]
70%|####### | 496/704 [01:55<00:49, 4.22/s]
71%|####### | 497/704 [01:55<00:51, 4.05/s]
71%|####### | 498/704 [01:55<00:50, 4.07/s]
71%|####### | 499/704 [01:56<00:50, 4.05/s]
71%|#######1 | 500/704 [01:56<00:51, 3.97/s]
71%|#######1 | 501/704 [01:56<00:51, 3.93/s]
71%|#######1 | 502/704 [01:56<00:50, 3.97/s]
71%|#######1 | 503/704 [01:57<00:48, 4.12/s]
72%|#######1 | 504/704 [01:57<00:47, 4.20/s]
72%|#######1 | 505/704 [01:57<00:46, 4.29/s]
72%|#######1 | 506/704 [01:57<00:45, 4.38/s]
72%|#######2 | 507/704 [01:58<00:44, 4.39/s]
72%|#######2 | 508/704 [01:58<00:50, 3.90/s]
72%|#######2 | 509/704 [01:58<00:53, 3.61/s]
72%|#######2 | 510/704 [01:58<00:52, 3.67/s]
73%|#######2 | 511/704 [01:59<00:52, 3.71/s]
73%|#######2 | 512/704 [01:59<00:50, 3.78/s]
73%|#######2 | 513/704 [01:59<00:51, 3.72/s]
73%|#######3 | 514/704 [01:59<00:50, 3.76/s]
73%|#######3 | 515/704 [02:00<00:49, 3.82/s]
73%|#######3 | 516/704 [02:00<00:48, 3.87/s]
73%|#######3 | 517/704 [02:00<00:47, 3.90/s]
74%|#######3 | 518/704 [02:01<00:51, 3.60/s]
74%|#######3 | 519/704 [02:01<00:47, 3.91/s]
74%|#######3 | 520/704 [02:01<00:45, 4.08/s]
74%|#######4 | 521/704 [02:01<00:43, 4.16/s]
74%|#######4 | 522/704 [02:01<00:43, 4.16/s]
74%|#######4 | 523/704 [02:02<00:48, 3.76/s]
74%|#######4 | 524/704 [02:02<00:50, 3.57/s]
75%|#######4 | 525/704 [02:02<00:52, 3.43/s]
75%|#######4 | 526/704 [02:03<00:56, 3.16/s]
75%|#######4 | 527/704 [02:03<00:55, 3.20/s]
75%|#######5 | 528/704 [02:03<00:54, 3.22/s]
75%|#######5 | 529/704 [02:04<00:53, 3.24/s]
75%|#######5 | 530/704 [02:04<00:51, 3.38/s]
75%|#######5 | 531/704 [02:04<00:48, 3.57/s]
76%|#######5 | 532/704 [02:04<00:45, 3.76/s]
76%|#######5 | 533/704 [02:05<00:43, 3.91/s]
76%|#######5 | 534/704 [02:05<00:42, 4.04/s]
76%|#######5 | 535/704 [02:05<00:42, 3.94/s]
76%|#######6 | 536/704 [02:05<00:42, 3.95/s]
76%|#######6 | 537/704 [02:06<00:41, 4.03/s]
76%|#######6 | 538/704 [02:06<00:39, 4.17/s]
77%|#######6 | 539/704 [02:06<00:38, 4.28/s]
77%|#######6 | 540/704 [02:06<00:38, 4.31/s]
77%|#######6 | 541/704 [02:07<00:38, 4.26/s]
77%|#######6 | 542/704 [02:07<00:37, 4.35/s]
77%|#######7 | 543/704 [02:07<00:36, 4.44/s]
77%|#######7 | 544/704 [02:07<00:36, 4.41/s]
77%|#######7 | 545/704 [02:07<00:35, 4.47/s]
78%|#######7 | 546/704 [02:08<00:35, 4.43/s]
78%|#######7 | 547/704 [02:08<00:35, 4.47/s]
78%|#######7 | 548/704 [02:08<00:34, 4.46/s]
78%|#######7 | 549/704 [02:08<00:34, 4.47/s]
78%|#######8 | 550/704 [02:09<00:34, 4.44/s]
78%|#######8 | 551/704 [02:09<00:35, 4.34/s]
78%|#######8 | 552/704 [02:09<00:36, 4.13/s]
79%|#######8 | 553/704 [02:09<00:36, 4.12/s]
79%|#######8 | 554/704 [02:10<00:35, 4.21/s]
79%|#######8 | 555/704 [02:10<00:35, 4.17/s]
79%|#######8 | 556/704 [02:10<00:35, 4.23/s]
79%|#######9 | 557/704 [02:10<00:33, 4.33/s]
79%|#######9 | 558/704 [02:10<00:33, 4.32/s]
79%|#######9 | 559/704 [02:11<00:35, 4.12/s]
80%|#######9 | 560/704 [02:11<00:33, 4.26/s]
80%|#######9 | 561/704 [02:11<00:33, 4.33/s]
80%|#######9 | 562/704 [02:11<00:32, 4.35/s]
80%|#######9 | 563/704 [02:12<00:32, 4.35/s]
80%|######## | 564/704 [02:12<00:31, 4.45/s]
80%|######## | 565/704 [02:12<00:31, 4.45/s]
80%|######## | 566/704 [02:12<00:31, 4.40/s]
81%|######## | 567/704 [02:13<00:30, 4.49/s]
81%|######## | 568/704 [02:13<00:31, 4.33/s]
81%|######## | 569/704 [02:13<00:31, 4.29/s]
81%|######## | 570/704 [02:13<00:30, 4.39/s]
81%|########1 | 571/704 [02:13<00:29, 4.46/s]
81%|########1 | 572/704 [02:14<00:30, 4.28/s]
81%|########1 | 573/704 [02:14<00:29, 4.37/s]
82%|########1 | 574/704 [02:14<00:29, 4.48/s]
82%|########1 | 575/704 [02:14<00:28, 4.53/s]
82%|########1 | 576/704 [02:15<00:27, 4.58/s]
82%|########1 | 577/704 [02:15<00:27, 4.62/s]
82%|########2 | 578/704 [02:15<00:27, 4.61/s]
82%|########2 | 579/704 [02:15<00:27, 4.61/s]
82%|########2 | 580/704 [02:15<00:26, 4.63/s]
83%|########2 | 581/704 [02:16<00:26, 4.58/s]
83%|########2 | 582/704 [02:16<00:26, 4.61/s]
83%|########2 | 583/704 [02:16<00:26, 4.62/s]
83%|########2 | 584/704 [02:16<00:25, 4.64/s]
83%|########3 | 585/704 [02:17<00:25, 4.66/s]
83%|########3 | 586/704 [02:17<00:25, 4.64/s]
83%|########3 | 587/704 [02:17<00:25, 4.63/s]
84%|########3 | 588/704 [02:17<00:24, 4.65/s]
84%|########3 | 589/704 [02:17<00:25, 4.47/s]
84%|########3 | 590/704 [02:18<00:25, 4.46/s]
84%|########3 | 591/704 [02:18<00:25, 4.47/s]
84%|########4 | 592/704 [02:18<00:24, 4.50/s]
84%|########4 | 593/704 [02:18<00:24, 4.48/s]
84%|########4 | 594/704 [02:19<00:24, 4.43/s]
85%|########4 | 595/704 [02:19<00:24, 4.47/s]
85%|########4 | 596/704 [02:19<00:23, 4.52/s]
85%|########4 | 597/704 [02:19<00:23, 4.55/s]
85%|########4 | 598/704 [02:19<00:23, 4.58/s]
85%|########5 | 599/704 [02:20<00:22, 4.61/s]
85%|########5 | 600/704 [02:20<00:22, 4.60/s]
85%|########5 | 601/704 [02:20<00:22, 4.61/s]
86%|########5 | 602/704 [02:20<00:22, 4.60/s]
86%|########5 | 603/704 [02:20<00:21, 4.62/s]
86%|########5 | 604/704 [02:21<00:21, 4.61/s]
86%|########5 | 605/704 [02:21<00:21, 4.54/s]
86%|########6 | 606/704 [02:21<00:21, 4.46/s]
86%|########6 | 607/704 [02:21<00:21, 4.42/s]
86%|########6 | 608/704 [02:22<00:21, 4.43/s]
87%|########6 | 609/704 [02:22<00:21, 4.40/s]
87%|########6 | 610/704 [02:22<00:21, 4.42/s]
87%|########6 | 611/704 [02:22<00:21, 4.42/s]
87%|########6 | 612/704 [02:23<00:20, 4.42/s]
87%|########7 | 613/704 [02:23<00:21, 4.29/s]
87%|########7 | 614/704 [02:23<00:21, 4.28/s]
87%|########7 | 615/704 [02:23<00:20, 4.26/s]
88%|########7 | 616/704 [02:23<00:20, 4.28/s]
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100%|##########| 704/704 [02:45<00:00, 3.94/s]
100%|##########| 704/704 [02:45<00:00, 4.24/s]
The result is stored in adata.obsm['histogram_features'].
adata.obsm["histogram_features"].head()
Use squidpy.pl.extract() to plot the histogram features on the tissue image or have a look at
our interactive visualisation tutorial to
learn how to use our interactive napari plugin.
With these features we can e.g. appreciate the detailed distribution of
intensity values of channel 0 (DAPI stain) on the different bins.
sq.pl.spatial_scatter(
sq.pl.extract(adata, "histogram_features"),
color=[None, "histogram_ch-0_bin-0", "histogram_ch-0_bin-1", "histogram_ch-0_bin-2"],
img_cmap="gray",
)
Total running time of the script: ( 2 minutes 58.708 seconds)
Estimated memory usage: 363 MB