DOI: 10.5281/zenodo.7506942
title: labsyspharm/CRC_atlas_2022

description: Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancerJia-Ren Lin*, Shu Wang*, Shannon Coy*, Yu-An Chen, Clarence Yapp, Madison Tyler, Maulik K. Nariya, Cody N. Heiser, Ken S. Lau, Sandro Santagata†, and Peter K. Sorger†

Associated publication DOI: 10.1016/J.CELL.2022.12.028Learn more: tissue-atlas.org/atlas-datasets/lin-wang-coy-2021/

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VIEW IMAGE DATA ONLINE

Some data is available as narrated data explorations (with text and audio narration) for anonymous on-line browsing using MINERVA software (Rashid et al., 2022), which allows users to pan and zoom through the images without requiring any software installation.

To view the Minerva stories, please visit tissue-atlas.org/atlas-datasets/lin-wang-coy-2021/#data-explorations.

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ACCESS THE DATA

The dataset consists of 47 CRC1 images (2.1 TB) and CRC2-17 images (4.4 TB). All full resolution images, derived image data (e.g., segmentation masks), and cell count tables have been released via the NCI-sponsored repository for Human Tumor Atlas Network (HTAN; humantumoratlas.org/explore).

The dataset is also available through Amazon Web Services S3 in the following bucket: s3://lin-2021-crc-atlas/data/


The list of S3 objects in the bucket can be accessed at https://lin-2021-crc-atlas.s3.amazonaws.com/

For instructions on how to access primary image data through AWS, see "Access Laboratory of Systems Pharmacology Datasets on AWS," DOI: 10.5281/zenodo.10223573. 

 

LIST OF ALL FILES:

The tables below inventory the dataset, which includes:



CRC1 images and image metadataCRC2-17 images and image metadataSpatial features tablesSingle-cell sequencing data and GeoMX count tables


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CRC1 Images

The following table contains summary biospecimen and file metadata for all 47 sections.




Section
Internal_Biospecimen_ID
Method
Thickness (μm)
Size (GB)
Image Filename
Metadata Filename




1
WD-76845-001
H&E
5
12.2
WD-76845-001.ome.tif
WD-76845-001-metadata.csv


2
WD-76845-002
t-CyCIF
5
88
WD-76845-002.ome.tif
WD-76845-002-metadata.csv


6
WD-76845-006
H&E
5
11
WD-76845-006.ome.tif
WD-76845-006-metadata.csv


7
WD-76845-007
t-CyCIF
5
80.2
WD-76845-007.ome.tif
WD-76845-007-metadata.csv


13
WD-76845-013
H&E
5
11.9
WD-76845-013.ome.tif
WD-76845-013-metadata.csv


14
WD-76845-014
t-CyCIF
5
72.4
WD-76845-014.ome.tif
WD-76845-014-metadata.csv


19
WD-76845-019
H&E
5
12.7
WD-76845-019.ome.tif
WD-76845-019-metadata.csv


20
WD-76845-020
t-CyCIF
5
83.6
WD-76845-020.ome.tif
WD-76845-020-metadata.csv


24
WD-76845-024
H&E
5
11
WD-76845-024.ome.tif
WD-76845-024-metadata.csv


25
WD-76845-025
t-CyCIF
5
83.6
WD-76845-025.ome.tif
WD-76845-025-metadata.csv


28
WD-76845-028
H&E
5
10.1
WD-76845-028.ome.tif
WD-76845-028-metadata.csv


29
WD-76845-029
t-CyCIF
5
74.4
WD-76845-029.ome.tif
WD-76845-029-metadata.csv


33
WD-76845-033
H&E
5
11.8
WD-76845-033.ome.tif
WD-76845-033-metadata.csv


34
WD-76845-034
t-CyCIF
5
82.2
WD-76845-034.ome.tif
WD-76845-034-metadata.csv


38
WD-76845-038
H&E
5
11.3
WD-76845-038.ome.tif
WD-76845-038-metadata.csv


39
WD-76845-039
t-CyCIF
5
80.2
WD-76845-039.ome.tif
WD-76845-039-metadata.csv


43
WD-76845-043
H&E
5
11
WD-76845-043.ome.tif
WD-76845-043-metadata.csv


44
WD-76845-044
t-CyCIF
5
76.6
WD-76845-044.ome.tif
WD-76845-044-metadata.csv


48
WD-76845-048
H&E
5
11.2
WD-76845-048.ome.tif
WD-76845-048-metadata.csv


49
WD-76845-049
t-CyCIF
5
76.6
WD-76845-049.ome.tif
WD-76845-049-metadata.csv


50
WD-76845-050
t-CyCIF
5
80.2
WD-76845-050.ome.tif
WD-76845-050-metadata.csv


51
WD-76845-051
t-CyCIF
5
76.6
WD-76845-051.ome.tif
WD-76845-051-metadata.csv


52
WD-76845-052
t-CyCIF
5
80.2
WD-76845-052.ome.tif
WD-76845-052-metadata.csv


53
WD-76845-053
H&E
5
10.5
WD-76845-053.ome.tif
WD-76845-053-metadata.csv


54
WD-76845-054
t-CyCIF
5
74.5
WD-76845-054.ome.tif
WD-76845-054-metadata.csv


58
WD-76845-058
H&E
5
10.5
WD-76845-058.ome.tif
WD-76845-058-metadata.csv


59
WD-76845-059
t-CyCIF
5
80.2
WD-76845-059.ome.tif
WD-76845-059-metadata.csv


63
WD-76845-063
H&E
5
10.5
WD-76845-063.ome.tif
WD-76845-063-metadata.csv


64
WD-76845-064
t-CyCIF
5
74.4
WD-76845-064.ome.tif
WD-76845-064-metadata.csv


68
WD-76845-068
H&E
5
10.1
WD-76845-068.ome.tif
WD-76845-068-metadata.csv


69
WD-76845-069
t-CyCIF
5
69.5
WD-76845-069.ome.tif
WD-76845-069-metadata.csv


73
WD-76845-073
H&E
5
9.1
WD-76845-073.ome.tif
WD-76845-073-metadata.csv


74
WD-76845-074
t-CyCIF
5
69.5
WD-76845-074.ome.tif
WD-76845-074-metadata.csv


77
WD-76845-077
H&E
5
10.5
WD-76845-077.ome.tif
WD-76845-077-metadata.csv


78
WD-76845-078
t-CyCIF
5
69.5
WD-76845-078.ome.tif
WD-76845-078-metadata.csv


83
WD-76845-083
H&E
5
9.6
WD-76845-083.ome.tif
WD-76845-083-metadata.csv


84
WD-76845-084
t-CyCIF
5
69.5
WD-76845-084.ome.tif
WD-76845-084-metadata.csv


85
WD-76845-085
H&E
4
10.6
WD-76845-085.ome.tif
WD-76845-085-metadata.csv


86
WD-76845-086
t-CyCIF
4
72.4
WD-76845-086.ome.tif
WD-76845-086-metadata.csv


90
WD-76845-090
H&E
4
9.9
WD-76845-090.ome.tif
WD-76845-090-metadata.csv


91
WD-76845-091
t-CyCIF
4
72.4
WD-76845-091.ome.tif
WD-76845-091-metadata.csv


96
WD-76845-096
H&E
4
10.6
WD-76845-096.ome.tif
WD-76845-096-metadata.csv


97
WD-76845-097
t-CyCIF
4
74.5
WD-76845-097.ome.tif
WD-76845-097-metadata.csv


101
WD-76845-101
H&E
4
10.5
WD-76845-101.ome.tif
WD-76845-101-metadata.csv


102
WD-76845-102
t-CyCIF
4
72.4
WD-76845-102.ome.tif
WD-76845-102-metadata.csv


105
WD-76845-105
H&E
4
9.6
WD-76845-105.ome.tif
WD-76845-105-metadata.csv


106
WD-76845-106
t-CyCIF
4
69.5
WD-76845-106.ome.tif
WD-76845-106-metadata.csv




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CRC2-17 Images

Files CRC02 to CRC17 derive from additional patients from the Brigham and Women’s Hospital.

H&E




Patient
Data filename
Metadata filename
File size (GB)




CRC02
data/CRC02-HE.ome.tif
-
17.2


CRC03
data/CRC03-HE.ome.tif
-
12.9


CRC04
data/CRC04-HE.ome.tif
-
15.5


CRC05
data/CRC05-HE.ome.tif
-
12.8


CRC06
data/CRC06-HE.ome.tif
-
16.2


CRC07
data/CRC07-HE.ome.tif
-
10.9


CRC08
data/CRC08-HE.ome.tif
-
18.0


CRC09
data/CRC09-HE.ome.tif
-
12.6


CRC10
data/CRC10-HE.ome.tif
-
19.5


CRC11
data/CRC11-HE.ome.tif
-
13.6


CRC12
data/CRC12-HE.ome.tif
-
15.0


CRC13
data/CRC13-HE.ome.tif
-
7.5


CRC14
data/CRC14-HE.ome.tif
-
13.2


CRC15
data/CRC15-HE.ome.tif
-
12.6


CRC16
data/CRC16-HE.ome.tif
-
15.4


CRC17
data/CRC17-HE.ome.tif
-
16.5




Main CyCIF panel




Patient
Data filename
Metadata filename
File size (GB)




CRC02
data/CRC02.ome.tif
metadata/CRC202105 HTAN channel metadata.csv
93.4


CRC03
data/CRC03.ome.tif
metadata/CRC202105 HTAN channel metadata.csv
72.6


CRC04
data/CRC04.ome.tif
metadata/CRC202105 HTAN channel metadata.csv
70.6


CRC05
data/CRC05.ome.tif
metadata/CRC202105 HTAN channel metadata.csv
54.7


CRC06
data/CRC06.ome.tif
metadata/CRC202105 HTAN channel metadata.csv
74.5


CRC07
data/CRC07.ome.tif
metadata/CRC202105 HTAN channel metadata.csv
61.2


CRC08
data/CRC08.ome.tif
metadata/CRC202105 HTAN channel metadata.csv
86.2


CRC09
data/CRC09.ome.tif
metadata/CRC202105 HTAN channel metadata.csv
68.1


CRC10
data/CRC10.ome.tif
metadata/CRC202105 HTAN channel metadata.csv
62.5


CRC11
data/CRC11.ome.tif
metadata/CRC202105 HTAN channel metadata.csv
59.6


CRC12
data/CRC12.ome.tif
metadata/CRC202105 HTAN channel metadata.csv
76.7


CRC13
data/CRC13.ome.tif
metadata/CRC202105 HTAN channel metadata.csv
49.6


CRC14
data/CRC14.ome.tif
metadata/CRC202105 HTAN channel metadata.csv
75.5


CRC15
data/CRC15.ome.tif
metadata/CRC202105 HTAN channel metadata.csv
75.1


CRC16
data/CRC16.ome.tif
metadata/CRC202105 HTAN channel metadata.csv
81.7


CRC17
data/CRC17.ome.tif
metadata/CRC202105 HTAN channel metadata.csv
79.6




Immune-focused CyCIF panel




Patient
Data filename
Metadata filename
File size (GB)




CRC02
data/73-8/TNPCRC_01.ome.tif
metadata/73-8-channel-metadata.csv
111.2


CRC03
data/73-8/TNPCRC_02.ome.tif
metadata/73-8-channel-metadata.csv
70.1


CRC04
data/73-8/TNPCRC_03.ome.tif
metadata/73-8-channel-metadata.csv
100.3


CRC05
data/73-8/TNPCRC_04.ome.tif
metadata/73-8-channel-metadata.csv
81.9


CRC06
data/73-8/TNPCRC_05.ome.tif
metadata/73-8-channel-metadata.csv
118.3


CRC07
data/73-8/TNPCRC_06.ome.tif
metadata/73-8-channel-metadata.csv
65.8


CRC08
data/73-8/TNPCRC_08.ome.tif
metadata/73-8-channel-metadata.csv
75.1


CRC09
data/73-8/TNPCRC_09.ome.tif
metadata/73-8-channel-metadata.csv
81.0


CRC10
data/73-8/TNPCRC_10.ome.tif
metadata/73-8-channel-metadata.csv
103.0


CRC11
data/73-8/TNPCRC_11.ome.tif
metadata/73-8-channel-metadata.csv
84.3


CRC12
data/73-8/TNPCRC_12.ome.tif
metadata/73-8-channel-metadata.csv
52.4


CRC13
data/73-8/TNPCRC_13.ome.tif
metadata/73-8-channel-metadata.csv
78.5


CRC14
data/73-8/TNPCRC_14.ome.tif
metadata/73-8-channel-metadata.csv
86.5


CRC15
data/73-8/TNPCRC_15.ome.tif
metadata/73-8-channel-metadata.csv
86.0


CRC16
data/73-8/TNPCRC_16.ome.tif
metadata/73-8-channel-metadata.csv
105.8


CRC17
data/73-8/TNPCRC_17.ome.tif
metadata/73-8-channel-metadata.csv
137.5




Tumor-focused CyCIF panel




Patient
Data filename
Metadata filename
File size (GB)




CRC02
data/73-9/TNPCRC_01.ome.tif
metadata/73-9-channel-metadata.csv
100.1


CRC03
data/73-9/TNPCRC_02.ome.tif
metadata/73-9-channel-metadata.csv
67.4


CRC04
data/73-9/TNPCRC_03.ome.tif
metadata/73-9-channel-metadata.csv
104.8


CRC05
data/73-9/TNPCRC_04.ome.tif
metadata/73-9-channel-metadata.csv
69.4


CRC06
data/73-9/TNPCRC_05.ome.tif
metadata/73-9-channel-metadata.csv
125.5


CRC07
data/73-9/TNPCRC_06.ome.tif
metadata/73-9-channel-metadata.csv
98.5


CRC08
data/73-9/TNPCRC_08.ome.tif
metadata/73-9-channel-metadata.csv
90.6


CRC09
data/73-9/TNPCRC_09.ome.tif
metadata/73-9-channel-metadata.csv
87.8


CRC10
data/73-9/TNPCRC_10.ome.tif
metadata/73-9-channel-metadata.csv
111.6


CRC11
data/73-9/TNPCRC_11.ome.tif
metadata/73-9-channel-metadata.csv
104.8


CRC12
data/73-9/TNPCRC_12.ome.tif
metadata/73-9-channel-metadata.csv
59.3


CRC13
data/73-9/TNPCRC_13.ome.tif
metadata/73-9-channel-metadata.csv
97.3


CRC14
data/73-9/TNPCRC_14.ome.tif
metadata/73-9-channel-metadata.csv
98.5


CRC15
data/73-9/TNPCRC_15.ome.tif
metadata/73-9-channel-metadata.csv
104.0


CRC16
data/73-9/TNPCRC_16.ome.tif
metadata/73-9-channel-metadata.csv
120.4


CRC17
data/73-9/TNPCRC_17.ome.tif
metadata/73-9-channel-metadata.csv
147.4




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Access Spatial feature tables (main CyCIF panel; CRC1-17)



CRC01-002 (46 MB)

CRC01-007 (45 MB)

CRC01-014 (41 MB)

CRC01-020 (38 MB)

CRC01-025 (39 MB)

CRC01-029 (41 MB)

CRC01-034 (54 MB)

CRC01-039 (45 MB)

CRC01-044 (36 MB)

CRC01-049 (52 MB)

CRC01-050 (49 MB)

CRC01-051 (60 MB)

CRC01-052 (55 MB)

CRC01-054 (49 MB)

CRC01-059 (46 MB)

CRC01-064 (57 MB)

CRC01-069 (48 MB)

CRC01-074 (56 MB)

CRC01-078 (54 MB)

CRC01-084 (56 MB)

CRC01-086 (55 MB)

CRC01-091 (49 MB)

CRC01-097 (55 MB)

CRC01-102 (55 MB)

CRC01-106 (53 MB)

CRC02 (58 MB)

CRC03 (50 MB)

CRC04 (75 MB)

CRC05 (57 MB)

CRC06 (39 MB)

CRC07 (51 MB)

CRC08 (67 MB)

CRC09 (22 MB)

CRC10 (41 MB)

CRC11 (34 MB)

CRC12 (69 MB)

CRC13 (24 MB)

CRC14 (32 MB)

CRC15 (56 MB)

CRC16 (22 MB)

CRC17 (79 MB)


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Single-cell sequencing data & GeoMX count tables

The single-cell sequncing data of this study could be found here:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE166319

The GeoMX data (count tables) could be download from here:

https://github.com/labsyspharm/CRC_atlas_2022/tree/main/GeoMX_data