Tutorial 2: Design CosMx experiment for 2 kidney sections
Please download according demo data from following link and place it under the demo folder:
google drive: https://drive.google.com/drive/folders/1z1nk0sF_e25LKMyHxJVMtROFjuWet2G_?usp=drive_link
Please also download the checkpoint file for the pathology foundation model and place it under the checkpoints folder
Step 1: Preprocess the H&E image
Make sure the physical size of each pixel is 0.5 micron
[1]:
import sys
sys.path.append('..')
from s2omics.p1_histology_preprocess import histology_preprocess
prefix = '../demo/Tutorial_2_CosMx_FOV_selection_kidney/'
histology_preprocess(prefix, show_image=True)
Image loaded from ../demo/Tutorial_2_CosMx_FOV_selection_kidney/he-raw.jpg
Rescaling image (scale: 1.000)...
305 sec
../demo/Tutorial_2_CosMx_FOV_selection_kidney/he-scaled.jpg
../demo/Tutorial_2_CosMx_FOV_selection_kidney/he.jpg
Preprocessed H&E image saved!
Step 2: Quality control for all superpixels
Superpixels are 8 microns * 8 microns square-shaped pseudo cells
We use our new QC package HistoSweep for this procedure
[2]:
from s2omics.p2_superpixel_quality_control import superpixel_quality_control
save_folder = '../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output'
superpixel_quality_control(prefix, save_folder, show_image=True)
Image loaded from ../demo/Tutorial_2_CosMx_FOV_selection_kidney/he.jpg
0 0
../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/pickle_files/shapes.pickle
[compute_metrics_memory_optimized] Current memory: 0.2311 GB; Peak memory: 4.6564 GB
[compute_low_density_mask] Current memory: 0.0058 GB; Peak memory: 0.3760 GB
Total selected for density filtering: 363189
✅ Entropy map saved as 'glcm_entropy_map_colored.png'
✅ Energy map saved as 'glcm_energy_map_colored.png'
✅ Homogeneity map saved as 'glcm_homogeneity_map_colored.png'
=== GLCM Metric Means ===
homogeneity energy entropy
0 0.386803 0.073254 0.778767
1 0.508877 0.148862 0.657161
2 0.283242 0.034037 0.877141
3 0.856751 0.458045 0.296625
=== Cluster Scores ===
Cluster 0: Score = -0.3187
Cluster 1: Score = 0.0006
Cluster 2: Score = -0.5599
Cluster 3: Score = 1.0182
=== Number of Observations per Cluster ===
Cluster 0: 87256
Cluster 1: 31992
Cluster 2: 130565
Cluster 3: 3230
Total: 253043
✅ Clustered texture map saved as 'cluster_labels_colored.png'
[run_texture_analysis] Current memory: 0.0061 GB; Peak memory: 14.7983 GB
[run_ratio_filtering] Current memory: 0.0058 GB; Peak memory: 0.1400 GB
(6204416,)
✅ Final masks saved in: HistoSweep_output
[generate_final_mask] Current memory: 0.0000 GB; Peak memory: 1.4969 GB
Running successfully!
../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/pickle_files/qc_preserve_indicator.pickle
Step 3: Histology feature extraction
[3]:
from s2omics.p3_feature_extraction import histology_feature_extraction
# down_samp_step: the down-sampling step,
# default = 10 refers to only extract features for superpixels whose row_index and col_index can both be divided by 10 (roughly 1:100 down-sampling rate).
# down_samp_step = 1 means extract features for every superpixel
histology_feature_extraction(prefix, save_folder,
foundation_model='uni',
ckpt_path='../checkpoints/uni/',
device='cuda:0',
batch_size=32,
down_samp_step=10,
num_workers=4)
/data1/msyuan/anaconda3/envs/S2Omics/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
from .autonotebook import tqdm as notebook_tqdm
Histology foundation model loaded!
Foundation model name: uni
Start extracting histology feature embeddings...
Image loaded from ../demo/Tutorial_2_CosMx_FOV_selection_kidney/he.jpg
../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/pickle_files/num_patches.pickle
0%| | 0/1946 [00:00<?, ?it/s]
Batch 0:
Shape of patches: torch.Size([32, 3, 224, 224])
Shape of positions[0]: torch.Size([32])
Content of positions[0][:10]: tensor([0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
Content of positions[1][:10]: tensor([ 0, 160, 320, 480, 640, 800, 960, 1120, 1280, 1440])
Shape of feature_emb: torch.Size([32, 197, 1024])
Shape of patch_emb: torch.Size([32, 1024, 14, 14])
100%|█████████▉| 1945/1946 [25:13<00:00, 1.28it/s]
Part 0 patch number: 62244
100%|██████████| 1946/1946 [25:15<00:00, 1.28it/s]
../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/pickle_files/uni_embeddings_downsamp_10_part_0.pickle
Step 4: Histology segmentation
[4]:
from s2omics.single_section.p4_get_histology_segmentation import get_histology_segmentation
get_histology_segmentation(prefix, save_folder,
foundation_model='uni',
down_samp_step=10,
clustering_method='kmeans',
n_clusters=20)
Pickle loaded from ../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/pickle_files/shapes.pickle
Pickle loaded from ../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/pickle_files/qc_preserve_indicator.pickle
Loading histology feature embeddings...
Pickle loaded from ../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/pickle_files/uni_embeddings_downsamp_10_part_0.pickle
Sucessfully loaded and normalized all histology feature embeddings!
Start segmenting the histology image, clustering method: kmeans
../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/pickle_files/cluster_image.pickle
../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/pickle_files/linkage_matrix.pickle
Segmentation image is stored at: ../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/image_files/cluster_image_num_clusters_20.jpg
Step 5: Merge over-clusters
[5]:
from s2omics.single_section.p5_merge_over_clusters import merge_over_clusters
merge_over_clusters(prefix, save_folder,
target_n_clusters=15)
Pickle loaded from ../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/pickle_files/shapes.pickle
Pickle loaded from ../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/pickle_files/qc_preserve_indicator.pickle
Pickle loaded from ../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/pickle_files/cluster_image.pickle
Merging over-clusters...
Pickle loaded from ../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/pickle_files/linkage_matrix.pickle
../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/pickle_files/adjusted_cluster_image.pickle
Combined the original 20 clusters into 15 clusters.
Adjusted segmentation image is stored at: ../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/image_files/adjusted_cluster_image_num_clusters_15.jpg
Step 6: Select best ROI for CosMx experiment
[6]:
from s2omics.single_section.p6_roi_selection_rectangle import roi_selection_for_single_section
# fusion_weights: the weight of three scores, default=[0.33,0.33,0.33], the sum of three weights should be equal to 1 (if not they will be normalized)
# positive_prior, negative_prior: prior information about interested and not-interested histology clusters, default = [],[]
# prior_preference: the larger this parameter is, S2Omics will focus more on those interested histology clusters, default= 1
roi_selection_for_single_section(prefix, save_folder,
down_samp_step=10,
roi_size=[5.0, 5.0],
rotation_seg=1,
num_roi=2, #0 refers to automatiacally determine the number of ROI
fusion_weights=[0.33,0.33,0.33],
emphasize_clusters=[], discard_clusters=[],
prior_preference=1)
Image loaded from ../demo/Tutorial_2_CosMx_FOV_selection_kidney/he.jpg
Pickle loaded from ../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/pickle_files/shapes.pickle
Pickle loaded from ../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/pickle_files/qc_preserve_indicator.pickle
Pickle loaded from ../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/pickle_files/adjusted_cluster_image.pickle
Sampling ROI candidates...
100%|██████████| 1600/1600 [00:00<00:00, 3325.19it/s]
Current best ROI: [[[51, 80], [113, 80], [113, 142], [51, 142]]]
roi score: 0.7310565501632443
scale score: 0.555703635936308
valid score: 0.8170274285105769
balance score: 0.8605439252241127
Current number of ROIs is 1.
100%|██████████| 1600/1600 [00:00<00:00, 2381.33it/s]
Current best ROI: [[[134, 167], [196, 167], [196, 229], [134, 229]], [[70, 38], [132, 38], [132, 100], [70, 100]]]
roi score: 0.7769145672056587
scale score: 0.6372115988605451
valid score: 0.9166627250569562
balance score: 0.8028354660177291
Current number of ROIs is 2.
Find the best 2 ROI(s) with:
ROI score: 0.7769145672056587
Scale score: 0.6372115988605451
Coverage score: 0.9166627250569562
Balance score: 0.8028354660177291
../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/roi_selection_detailed_output/rectangle_roi_size_5.0_5.0/prior_preference_1/best_roi.pickle
Best ROI on histology segmentation image is stored at ../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/main_output/best_roi_on_histology_segmentations.jpg
Best ROI on H&E image is stored at ../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/main_output/best_roi_on_he.jpg
Step 6: Select best FOV for CosMx experiment
[7]:
from s2omics.single_section.p6_roi_selection_rectangle import roi_selection_for_single_section
# fusion_weights: the weight of three scores, default=[0.33,0.33,0.33], the sum of three weights should be equal to 1 (if not they will be normalized)
# positive_prior, negative_prior: prior information about interested and not-interested histology clusters, default = [],[]
# prior_preference: the larger this parameter is, S2Omics will focus more on those interested histology clusters, default= 1
roi_selection_for_single_section(prefix, save_folder,
down_samp_step=10,
roi_size=[0.5, 0.5],
rotation_seg=1,
num_roi=20, #0 refers to automatiacally determine the number of ROI
fusion_weights=[0.33,0.33,0.33],
emphasize_clusters=[], discard_clusters=[],
prior_preference=1)
Image loaded from ../demo/Tutorial_2_CosMx_FOV_selection_kidney/he.jpg
Pickle loaded from ../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/pickle_files/shapes.pickle
Pickle loaded from ../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/pickle_files/qc_preserve_indicator.pickle
Pickle loaded from ../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/pickle_files/adjusted_cluster_image.pickle
Sampling ROI candidates...
100%|██████████| 161500/161500 [00:38<00:00, 4152.68it/s]
Current best ROI: [[[90, 79], [96, 79], [96, 85], [90, 85]]]
roi score: 0.7633475484886637
scale score: 0.5009155502694107
valid score: 1.0801234497346435
balance score: 0.822108307320585
Current number of ROIs is 1.
100%|██████████| 161500/161500 [00:50<00:00, 3201.47it/s]
Current best ROI: [[[124, 187], [130, 187], [130, 193], [124, 193]], [[149, 22], [155, 22], [155, 28], [149, 28]]]
roi score: 0.787598960569605
scale score: 0.5019400870502737
valid score: 1.1118053386771947
balance score: 0.8754568922558981
Current number of ROIs is 2.
100%|██████████| 161500/161500 [00:42<00:00, 3823.26it/s]
Current best ROI: [[[124, 187], [130, 187], [130, 193], [124, 193]], [[149, 22], [155, 22], [155, 28], [149, 28]], [[82, 130], [88, 130], [88, 136], [82, 136]]]
roi score: 0.812938278953803
scale score: 0.5029428094598825
valid score: 1.1180339887498947
balance score: 0.955430522380051
Current number of ROIs is 3.
100%|██████████| 161500/161500 [00:52<00:00, 3054.13it/s]
Current best ROI: [[[124, 187], [130, 187], [130, 193], [124, 193]], [[149, 22], [155, 22], [155, 28], [149, 28]], [[55, 142], [61, 142], [61, 148], [55, 148]], [[163, 183], [169, 183], [169, 189], [163, 189]]]
roi score: 0.8125264573239902
scale score: 0.5039019132026529
valid score: 1.114924013354971
balance score: 0.9548194500023122
Current number of ROIs is 4.
100%|██████████| 161500/161500 [00:44<00:00, 3602.87it/s]
Current best ROI: [[[124, 187], [130, 187], [130, 193], [124, 193]], [[149, 22], [155, 22], [155, 28], [149, 28]], [[55, 142], [61, 142], [61, 148], [55, 148]], [[163, 183], [169, 183], [169, 189], [163, 189]], [[98, 86], [104, 86], [104, 92], [98, 92]]]
roi score: 0.8192685651529936
scale score: 0.5049481752012746
valid score: 1.122992035194868
balance score: 0.9697401824895223
Current number of ROIs is 5.
100%|██████████| 161500/161500 [00:55<00:00, 2919.34it/s]
Current best ROI: [[[124, 187], [130, 187], [130, 193], [124, 193]], [[149, 22], [155, 22], [155, 28], [149, 28]], [[55, 142], [61, 142], [61, 148], [55, 148]], [[163, 183], [169, 183], [169, 189], [163, 189]], [[99, 87], [105, 87], [105, 93], [99, 93]], [[165, 193], [171, 193], [171, 199], [165, 199]]]
roi score: 0.8189404034709604
scale score: 0.5059508024050038
valid score: 1.1242281302693367
balance score: 0.9655931082325341
Current number of ROIs is 6.
100%|██████████| 161500/161500 [00:45<00:00, 3535.31it/s]
Current best ROI: [[[124, 187], [130, 187], [130, 193], [124, 193]], [[149, 22], [155, 22], [155, 28], [149, 28]], [[55, 142], [61, 142], [61, 148], [55, 148]], [[163, 183], [169, 183], [169, 189], [163, 189]], [[99, 87], [105, 87], [105, 93], [99, 93]], [[165, 193], [171, 193], [171, 199], [165, 199]], [[114, 78], [120, 78], [120, 84], [114, 84]]]
roi score: 0.8210495413616404
scale score: 0.506844408296478
valid score: 1.116257920926766
balance score: 0.9782928406968969
Current number of ROIs is 7.
100%|██████████| 161500/161500 [00:57<00:00, 2808.42it/s]
Current best ROI: [[[124, 187], [130, 187], [130, 193], [124, 193]], [[149, 22], [155, 22], [155, 28], [149, 28]], [[55, 142], [61, 142], [61, 148], [55, 148]], [[163, 183], [169, 183], [169, 189], [163, 189]], [[99, 87], [105, 87], [105, 93], [99, 93]], [[165, 193], [171, 193], [171, 199], [165, 199]], [[66, 164], [72, 164], [72, 170], [66, 170]], [[105, 221], [111, 221], [111, 227], [105, 227]]]
roi score: 0.8207920254957598
scale score: 0.5079994917493161
valid score: 1.1288514320120056
balance score: 0.9642714735213632
Current number of ROIs is 8.
100%|██████████| 161500/161500 [00:54<00:00, 2970.21it/s]
Current best ROI: [[[124, 187], [130, 187], [130, 193], [124, 193]], [[149, 22], [155, 22], [155, 28], [149, 28]], [[55, 142], [61, 142], [61, 148], [55, 148]], [[163, 183], [169, 183], [169, 189], [163, 189]], [[99, 87], [105, 87], [105, 93], [99, 93]], [[165, 193], [171, 193], [171, 199], [165, 199]], [[66, 164], [72, 164], [72, 170], [66, 170]], [[105, 221], [111, 221], [111, 227], [105, 227]], [[137, 30], [143, 30], [143, 36], [137, 36]]]
roi score: 0.8241116396047302
scale score: 0.5090673233929748
valid score: 1.133115447465063
balance score: 0.9703061032238947
Current number of ROIs is 9.
100%|██████████| 161500/161500 [00:59<00:00, 2712.19it/s]
Current best ROI: [[[124, 187], [130, 187], [130, 193], [124, 193]], [[149, 22], [155, 22], [155, 28], [149, 28]], [[55, 142], [61, 142], [61, 148], [55, 148]], [[163, 183], [169, 183], [169, 189], [163, 189]], [[99, 87], [105, 87], [105, 93], [99, 93]], [[165, 193], [171, 193], [171, 199], [165, 199]], [[66, 164], [72, 164], [72, 170], [66, 170]], [[105, 221], [111, 221], [111, 227], [105, 227]], [[172, 213], [178, 213], [178, 219], [172, 219]], [[152, 48], [158, 48], [158, 54], [152, 54]]]
roi score: 0.8248393594492931
scale score: 0.5100479124609589
valid score: 1.131616346451197
balance score: 0.9722947532787561
Current number of ROIs is 10.
100%|██████████| 161500/161500 [00:51<00:00, 3133.87it/s]
Current best ROI: [[[124, 187], [130, 187], [130, 193], [124, 193]], [[149, 22], [155, 22], [155, 28], [149, 28]], [[55, 142], [61, 142], [61, 148], [55, 148]], [[163, 183], [169, 183], [169, 189], [163, 189]], [[99, 87], [105, 87], [105, 93], [99, 93]], [[165, 193], [171, 193], [171, 199], [165, 199]], [[66, 164], [72, 164], [72, 170], [66, 170]], [[105, 221], [111, 221], [111, 227], [105, 227]], [[172, 213], [178, 213], [178, 219], [172, 219]], [[152, 48], [158, 48], [158, 54], [152, 54]], [[66, 64], [72, 64], [72, 70], [66, 70]]]
roi score: 0.8271930155786374
scale score: 0.5110720005970698
valid score: 1.1326200964261064
balance score: 0.9778094376503255
Current number of ROIs is 11.
100%|██████████| 161500/161500 [01:02<00:00, 2595.75it/s]
Current best ROI: [[[124, 187], [130, 187], [130, 193], [124, 193]], [[149, 22], [155, 22], [155, 28], [149, 28]], [[55, 142], [61, 142], [61, 148], [55, 148]], [[163, 183], [169, 183], [169, 189], [163, 189]], [[99, 87], [105, 87], [105, 93], [99, 93]], [[165, 193], [171, 193], [171, 199], [165, 199]], [[66, 164], [72, 164], [72, 170], [66, 170]], [[105, 221], [111, 221], [111, 227], [105, 227]], [[172, 213], [178, 213], [178, 219], [172, 219]], [[152, 48], [158, 48], [158, 54], [152, 54]], [[59, 121], [65, 121], [65, 127], [59, 127]], [[91, 54], [97, 54], [97, 60], [91, 60]]]
roi score: 0.826932449233488
scale score: 0.5119870648162649
valid score: 1.12833866731055
balance score: 0.9788398514091579
Current number of ROIs is 12.
100%|██████████| 161500/161500 [00:53<00:00, 3044.87it/s]
Current best ROI: [[[124, 187], [130, 187], [130, 193], [124, 193]], [[149, 22], [155, 22], [155, 28], [149, 28]], [[55, 142], [61, 142], [61, 148], [55, 148]], [[163, 183], [169, 183], [169, 189], [163, 189]], [[99, 87], [105, 87], [105, 93], [99, 93]], [[165, 193], [171, 193], [171, 199], [165, 199]], [[66, 164], [72, 164], [72, 170], [66, 170]], [[105, 221], [111, 221], [111, 227], [105, 227]], [[172, 213], [178, 213], [178, 219], [172, 219]], [[152, 48], [158, 48], [158, 54], [152, 54]], [[59, 121], [65, 121], [65, 127], [59, 127]], [[91, 54], [97, 54], [97, 60], [91, 60]], [[153, 184], [159, 184], [159, 190], [153, 190]]]
roi score: 0.8274729859725922
scale score: 0.5129238329990933
valid score: 1.125652707141069
balance score: 0.9813053676353111
Current number of ROIs is 13.
100%|██████████| 161500/161500 [01:05<00:00, 2463.88it/s]
Current best ROI: [[[124, 187], [130, 187], [130, 193], [124, 193]], [[149, 22], [155, 22], [155, 28], [149, 28]], [[55, 142], [61, 142], [61, 148], [55, 148]], [[163, 183], [169, 183], [169, 189], [163, 189]], [[99, 87], [105, 87], [105, 93], [99, 93]], [[165, 193], [171, 193], [171, 199], [165, 199]], [[66, 164], [72, 164], [72, 170], [66, 170]], [[105, 221], [111, 221], [111, 227], [105, 227]], [[172, 213], [178, 213], [178, 219], [172, 219]], [[152, 48], [158, 48], [158, 54], [152, 54]], [[59, 121], [65, 121], [65, 127], [59, 127]], [[91, 54], [97, 54], [97, 60], [91, 60]], [[66, 63], [72, 63], [72, 69], [66, 69]], [[134, 189], [140, 189], [140, 195], [134, 195]]]
roi score: 0.8272412229518037
scale score: 0.5138605104011754
valid score: 1.123345344008138
balance score: 0.9807040536422298
Current number of ROIs is 14.
100%|██████████| 161500/161500 [01:05<00:00, 2472.69it/s]
Current best ROI: [[[124, 187], [130, 187], [130, 193], [124, 193]], [[149, 22], [155, 22], [155, 28], [149, 28]], [[55, 142], [61, 142], [61, 148], [55, 148]], [[163, 183], [169, 183], [169, 189], [163, 189]], [[99, 87], [105, 87], [105, 93], [99, 93]], [[165, 193], [171, 193], [171, 199], [165, 199]], [[66, 164], [72, 164], [72, 170], [66, 170]], [[105, 221], [111, 221], [111, 227], [105, 227]], [[172, 213], [178, 213], [178, 219], [172, 219]], [[152, 48], [158, 48], [158, 54], [152, 54]], [[59, 121], [65, 121], [65, 127], [59, 127]], [[91, 54], [97, 54], [97, 60], [91, 60]], [[66, 63], [72, 63], [72, 69], [66, 69]], [[134, 189], [140, 189], [140, 195], [134, 195]], [[82, 129], [88, 129], [88, 135], [82, 135]]]
roi score: 0.8289222577541624
scale score: 0.5148842089964513
valid score: 1.1246398600506808
balance score: 0.9835996354502596
Current number of ROIs is 15.
100%|██████████| 161500/161500 [01:05<00:00, 2469.73it/s]
Current best ROI: [[[124, 187], [130, 187], [130, 193], [124, 193]], [[149, 22], [155, 22], [155, 28], [149, 28]], [[55, 142], [61, 142], [61, 148], [55, 148]], [[163, 183], [169, 183], [169, 189], [163, 189]], [[99, 87], [105, 87], [105, 93], [99, 93]], [[165, 193], [171, 193], [171, 199], [165, 199]], [[66, 164], [72, 164], [72, 170], [66, 170]], [[105, 221], [111, 221], [111, 227], [105, 227]], [[172, 213], [178, 213], [178, 219], [172, 219]], [[152, 48], [158, 48], [158, 54], [152, 54]], [[59, 121], [65, 121], [65, 127], [59, 127]], [[91, 54], [97, 54], [97, 60], [91, 60]], [[66, 63], [72, 63], [72, 69], [66, 69]], [[134, 189], [140, 189], [140, 195], [134, 195]], [[154, 184], [160, 184], [160, 190], [154, 190]], [[83, 129], [89, 129], [89, 135], [83, 135]]]
roi score: 0.8285770395903097
scale score: 0.5157988980842599
valid score: 1.1219093348196882
balance score: 0.9830158311427499
Current number of ROIs is 16.
100%|██████████| 161500/161500 [00:56<00:00, 2863.71it/s]
Current best ROI: [[[124, 187], [130, 187], [130, 193], [124, 193]], [[149, 22], [155, 22], [155, 28], [149, 28]], [[55, 142], [61, 142], [61, 148], [55, 148]], [[163, 183], [169, 183], [169, 189], [163, 189]], [[99, 87], [105, 87], [105, 93], [99, 93]], [[165, 193], [171, 193], [171, 199], [165, 199]], [[66, 164], [72, 164], [72, 170], [66, 170]], [[105, 221], [111, 221], [111, 227], [105, 227]], [[172, 213], [178, 213], [178, 219], [172, 219]], [[152, 48], [158, 48], [158, 54], [152, 54]], [[59, 121], [65, 121], [65, 127], [59, 127]], [[91, 54], [97, 54], [97, 60], [91, 60]], [[66, 63], [72, 63], [72, 69], [66, 69]], [[134, 189], [140, 189], [140, 195], [134, 195]], [[154, 184], [160, 184], [160, 190], [154, 190]], [[83, 129], [89, 129], [89, 135], [83, 135]], [[110, 83], [116, 83], [116, 89], [110, 89]]]
roi score: 0.8288648028214629
scale score: 0.5167570301718512
valid score: 1.1209531425141812
balance score: 0.983053698685127
Current number of ROIs is 17.
100%|██████████| 161500/161500 [01:06<00:00, 2441.80it/s]
Current best ROI: [[[124, 187], [130, 187], [130, 193], [124, 193]], [[149, 22], [155, 22], [155, 28], [149, 28]], [[55, 142], [61, 142], [61, 148], [55, 148]], [[163, 183], [169, 183], [169, 189], [163, 189]], [[99, 87], [105, 87], [105, 93], [99, 93]], [[165, 193], [171, 193], [171, 199], [165, 199]], [[66, 164], [72, 164], [72, 170], [66, 170]], [[105, 221], [111, 221], [111, 227], [105, 227]], [[172, 213], [178, 213], [178, 219], [172, 219]], [[152, 48], [158, 48], [158, 54], [152, 54]], [[59, 121], [65, 121], [65, 127], [59, 127]], [[91, 54], [97, 54], [97, 60], [91, 60]], [[66, 63], [72, 63], [72, 69], [66, 69]], [[134, 189], [140, 189], [140, 195], [134, 195]], [[154, 184], [160, 184], [160, 190], [154, 190]], [[83, 129], [89, 129], [89, 135], [83, 135]], [[94, 149], [100, 149], [100, 155], [94, 155]], [[189, 25], [195, 25], [195, 31], [189, 31]]]
roi score: 0.828820461009692
scale score: 0.5178021244377278
valid score: 1.1228546073004297
balance score: 0.9792510333348633
Current number of ROIs is 18.
100%|██████████| 161500/161500 [00:58<00:00, 2773.00it/s]
Current best ROI: [[[124, 187], [130, 187], [130, 193], [124, 193]], [[149, 22], [155, 22], [155, 28], [149, 28]], [[55, 142], [61, 142], [61, 148], [55, 148]], [[163, 183], [169, 183], [169, 189], [163, 189]], [[99, 87], [105, 87], [105, 93], [99, 93]], [[165, 193], [171, 193], [171, 199], [165, 199]], [[66, 164], [72, 164], [72, 170], [66, 170]], [[105, 221], [111, 221], [111, 227], [105, 227]], [[172, 213], [178, 213], [178, 219], [172, 219]], [[152, 48], [158, 48], [158, 54], [152, 54]], [[59, 121], [65, 121], [65, 127], [59, 127]], [[91, 54], [97, 54], [97, 60], [91, 60]], [[66, 63], [72, 63], [72, 69], [66, 69]], [[134, 189], [140, 189], [140, 195], [134, 195]], [[154, 184], [160, 184], [160, 190], [154, 190]], [[83, 129], [89, 129], [89, 135], [83, 135]], [[94, 149], [100, 149], [100, 155], [94, 155]], [[189, 25], [195, 25], [195, 31], [189, 31]], [[110, 83], [116, 83], [116, 89], [110, 89]]]
roi score: 0.8295245891307287
scale score: 0.5187599909369824
valid score: 1.1219500567425278
balance score: 0.9807262357841259
Current number of ROIs is 19.
100%|██████████| 161500/161500 [01:08<00:00, 2357.92it/s]
Current best ROI: [[[124, 187], [130, 187], [130, 193], [124, 193]], [[149, 22], [155, 22], [155, 28], [149, 28]], [[55, 142], [61, 142], [61, 148], [55, 148]], [[163, 183], [169, 183], [169, 189], [163, 189]], [[99, 87], [105, 87], [105, 93], [99, 93]], [[165, 193], [171, 193], [171, 199], [165, 199]], [[66, 164], [72, 164], [72, 170], [66, 170]], [[105, 221], [111, 221], [111, 227], [105, 227]], [[172, 213], [178, 213], [178, 219], [172, 219]], [[152, 48], [158, 48], [158, 54], [152, 54]], [[59, 121], [65, 121], [65, 127], [59, 127]], [[91, 54], [97, 54], [97, 60], [91, 60]], [[66, 63], [72, 63], [72, 69], [66, 69]], [[134, 189], [140, 189], [140, 195], [134, 195]], [[154, 184], [160, 184], [160, 190], [154, 190]], [[83, 129], [89, 129], [89, 135], [83, 135]], [[94, 149], [100, 149], [100, 155], [94, 155]], [[189, 25], [195, 25], [195, 31], [189, 31]], [[157, 194], [163, 194], [163, 200], [157, 200]], [[133, 96], [139, 96], [139, 102], [133, 102]]]
roi score: 0.8296018153947646
scale score: 0.5197830140444966
valid score: 1.1229920351948677
balance score: 0.9781609523866314
Current number of ROIs is 20.
Find the best 20 ROI(s) with:
ROI score: 0.8296018153947646
Scale score: 0.5197830140444966
Coverage score: 1.1229920351948677
Balance score: 0.9781609523866314
../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/roi_selection_detailed_output/rectangle_roi_size_0.5_0.5/prior_preference_1/best_roi.pickle
/data1/msyuan/S2Omics/notebooks/../s2omics/single_section/p6_roi_selection_rectangle.py:367: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`). Consider using `matplotlib.pyplot.close()`.
plt.figure(figsize=plt_figsize)
Best ROI on histology segmentation image is stored at ../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/main_output/best_roi_on_histology_segmentations.jpg
/data1/msyuan/S2Omics/notebooks/../s2omics/single_section/p6_roi_selection_rectangle.py:402: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`). Consider using `matplotlib.pyplot.close()`.
plt.figure(figsize=plt_figsize)
Best ROI on H&E image is stored at ../demo/Tutorial_2_CosMx_FOV_selection_kidney/S2Omics_output/main_output/best_roi_on_he.jpg
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