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  1. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/README.txt +27 -0
  2. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P01_A_FOV1.npz +3 -0
  3. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P02_A_FOV3.npz +3 -0
  4. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P03_A_FOV5.npz +3 -0
  5. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P04_A_FOV7.npz +3 -0
  6. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P05_A_FOV9.npz +3 -0
  7. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P06_A_FOV11.npz +3 -0
  8. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P07_A_FOV13.npz +3 -0
  9. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P08_A_FOV15.npz +3 -0
  10. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P09_A_FOV17.npz +3 -0
  11. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P10_A_FOV19.npz +3 -0
  12. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P11_A_FOV21.npz +3 -0
  13. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P12_A_FOV23.npz +3 -0
  14. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P13_A_FOV25.npz +3 -0
  15. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P14_A_FOV27.npz +3 -0
  16. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P15_A_FOV29.npz +3 -0
  17. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P16_A_FOV31.npz +3 -0
  18. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P17_A_FOV33.npz +3 -0
  19. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P18_A_FOV35.npz +3 -0
  20. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P19_A_FOV37.npz +3 -0
  21. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P20_A_FOV39.npz +3 -0
  22. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P21_A_FOV41.npz +3 -0
  23. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P22_A_FOV43.npz +3 -0
  24. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P23_A_FOV45.npz +3 -0
  25. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P24_A_FOV47.npz +3 -0
  26. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P25_A_FOV49.npz +3 -0
  27. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P26_A_FOV51.npz +3 -0
  28. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P27_A_FOV54.npz +3 -0
  29. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P28_A_FOV55.npz +3 -0
  30. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P29_A_FOV58.npz +3 -0
  31. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P30_A_FOV59.npz +3 -0
  32. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P31_A_FOV61.npz +3 -0
  33. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P32_A_FOV63.npz +3 -0
  34. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P33_A_FOV65.npz +3 -0
  35. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P34_A_FOV67.npz +3 -0
  36. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells/P35_A_FOV69.npz +3 -0
  37. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells2labels/P01_A_FOV1.npz +3 -0
  38. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells2labels/P02_A_FOV3.npz +3 -0
  39. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells2labels/P03_A_FOV5.npz +3 -0
  40. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells2labels/P04_A_FOV7.npz +3 -0
  41. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells2labels/P05_A_FOV9.npz +3 -0
  42. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells2labels/P06_A_FOV11.npz +3 -0
  43. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells2labels/P07_A_FOV13.npz +3 -0
  44. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells2labels/P08_A_FOV15.npz +3 -0
  45. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells2labels/P09_A_FOV17.npz +3 -0
  46. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells2labels/P10_A_FOV19.npz +3 -0
  47. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells2labels/P11_A_FOV21.npz +3 -0
  48. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells2labels/P12_A_FOV23.npz +3 -0
  49. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells2labels/P13_A_FOV25.npz +3 -0
  50. spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/cells2labels/P14_A_FOV27.npz +3 -0
spatial_omics_data/CellSighter Test Dataset CRC Multiplexed Images/README.txt ADDED
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+ CellSighter Test Dataset: CRC Multiplexed Images
2
+ Contributors:
3
+ Yuval Bussi, Yael Amitay, Leeat Keren
4
+ Description:
5
+ This dataset contains multiplexed protein images from colorectal cancer (CRC) patients, used to benchmark the CellSighter algorithm.
6
+ The images were derived from a subset of the publicly available CRC-FFPE-CODEX collection hosted by The Cancer Imaging Archive (TCIA):
7
+ https://www.cancerimagingarchive.net/collection/crc_ffpe-codex_cellneighs/
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+ Original dataset citation:
9
+ Schürch, C. M., Bhate, S., Barlow, G., Phillips, D., Noti, L., Zlobec, I., Chu, P., Black, S., Demeter, J., McIlwain, D., Samusik, N., Goltsev, Y., & Nolan, G. (2020).
10
+ High-dimensional imaging of colorectal carcinoma and other tumors with 50+ markers [Data set]. The Cancer Imaging Archive.
11
+ https://doi.org/10.7937/TCIA.2020.FQN0-0326
12
+ Derived Annotations:
13
+ The images were re-segmented using DeepCell (https://www.deepcell.org/).
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+ Cell type classifications were generated using CellTune (https://celltune.org/).
15
+ These segmentations and classifications are original contributions and do not appear in the TCIA dataset.
16
+ Images, segmentations, and classifications were formatted for use with CellSighter.
17
+ Usage Policy:
18
+ This dataset is shared under the terms of TCIA’s data usage policy.
19
+ It must not be used in any way that could identify individuals.
20
+ Users must cite both the original dataset and this derived dataset appropriately.
21
+ TCIA data usage policy:
22
+ https://www.cancerimagingarchive.net/data-usage-policies-and-restrictions/
23
+ Use Case:
24
+ This dataset was used to evaluate CellSighter, as described in:
25
+ Amitay, Y., Bussi, Y., Feinstein, B. et al.
26
+ CellSighter: a neural network to classify cells in highly multiplexed images.
27
+ Nat Commun 14, 4302 (2023). https://doi.org/10.1038/s41467-023-40066-7
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