All images at full resolution, derived image data (e.g., segmentation masks), and single-cell tables are stored and can be accessed through Amazon Web Services (AWS) S3.
s3://lin-2023-orion-crc/dataTo browse and download the data use either a graphical file transfer application
that supports S3 such as CyberDuck, or the AWS CLI
tools. A graphical tool may be more convenient but
the CLI tools will likely offer higher download speeds. For users who wish to
perform processing within AWS, note that the bucket is located in the
us-east-1 region so any other resources must be instantiated in this same
region.
Make sure anonymous login is selected, either through using the following server
information: s3://anonymous@lin-2023-orion-crc.s3.amazonaws.com/ or make sure
the anonymous login button is selected.
Review your IAM permissions and add additional in-line policies, as needed. For
example, use: aws s3 ls --no-sign-request s3://lin-2023-crc/data/. If you
continue to experience issues using the CLI, please follow the instructions for
using a GUI above or refer to AWS existing documentation.
Email tissue-atlas(at)hms.harvard.edu with the subject line "Orion-CRC: Data Access" if you stil have issues accessing the above S3 buckets.
Each folder corresponds to a patient sample. The following files are available for each patient and are located on AWS.
| File type | File name pattern | Description |
|---|---|---|
| Orion WSIs | P*_S*.ome.tiff | 19-channel Orion whole-slide-images (WSIs), in pyramidal format |
| H&E images | *-registered.ome.tif | H&E WSIs of the same tissue section of the corresponding Orion WSI |
| Segmentation masks | *-mask.ome.tif | Labeled masks, each object in the mask represents a cell |
| Single-cell tables | P*_S*.csv | Single-cell by feature tables generated by quantifying objects in the labeled mask with the Orion WSIs |
| Marker list | markers.csv | List of all markers/channel names/antibody target names in Orion WSIs |
| Patient | Folder name | File name | File size (GiB) |
|---|---|---|---|
| C1 | CRC01 | P37_S29_A24_C59kX_E15_20220106_014304_946511-zlib.ome.tiff | 105.0 |
| C2 | CRC02 | P37_S30_A24_C59kX_E15_20220106_014319_409148-zlib.ome.tiff | 68.4 |
| C3 | CRC03 | P37_S31_A24_C59kX_E15_20220106_014409_014236-zlib.ome.tiff | 79.8 |
| C4 | CRC04 | P37_S32_A24_C59kX_E15_20220106_014630_553652-zlib.ome.tiff | 89.4 |
| C5 | CRC05 | P37_S33_A24_C59kX_E15_20220107_180446_881530-zlib.ome.tiff | 120.6 |
| C6 | CRC06 | P37_S34_A24_C59kX_E15_20220107_202112_212579-zlib.ome.tiff | 80.8 |
| C7 | CRC07 | P37_S35_A24_C59kX_E15_20220108_012037_490594-zlib.ome.tiff | 84.3 |
| C8 | CRC08 | P37_S57_Full_A24_C59nX_E15_20220224_011032_774034-zlib.ome.tiff | 71.0 |
| C9 | CRC09 | P37_S37_A24_C59kX_E15_20220108_012113_953544-zlib.ome.tiff | 95.3 |
| C10 | CRC10 | P37_S38_A24_C59kX_E15_20220108_012130_664519-zlib.ome.tiff | 63.2 |
| C11 | CRC11 | P37_S43_Full_A24_C59mX_E15_20220128_171510_544056-zlib.ome.tiff | 85.3 |
| C12 | CRC12 | P37_S44_Full_A24_C59mX_E15_20220128_171448_903938-zlib.ome.tiff | 88.8 |
| C13 | CRC13 | P37_S45_Full_A24_C59mX_E15_20220128_171409_633341-zlib.ome.tiff | 96.0 |
| C14 | CRC14 | P37_S46_Full_A24_C59mX_E15_20220128_013821_398547-zlib.ome.tiff | 117.5 |
| C15 | CRC15 | P37_S47_Full_A24_C59mX_E15_20220128_020654_901143-zlib.ome.tiff | 104.5 |
| C16 | CRC16 | P37_S48_Full_A24_C59mX_E15_20220129_015105_865195-zlib.ome.tiff | 140.8 |
| C17 | CRC17 | P37_S49_Full_A24_C59mX_E15_20220129_015121_911264-zlib.ome.tiff | 146.8 |
| C18 | CRC18 | P37_S50_Full_A24_C59mX_E15_20220129_015242_755602-zlib.ome.tiff | 117.3 |
| C19 | CRC19 | P37_S51_Full_A24_C59mX_E15_20220129_015300_669681-zlib.ome.tiff | 116.1 |
| C20 | CRC20 | P37_S52_Full_A24_C59mX_E15_20220129_015324_574779-zlib.ome.tiff | 126.7 |
| C21 | CRC21 | P37_S58_Full_A24_C59nX_E15_20220224_011058_014787-zlib.ome.tiff | 106.5 |
| C22 | CRC22 | P37_S59_Full_A24_C59nX_E15_20220224_011113_455637-zlib.ome.tiff | 114.9 |
| C23 | CRC23 | P37_S60_Full_A24_C59nX_E15_20220224_011127_971497-zlib.ome.tiff | 137.2 |
| C24 | CRC24 | P37_S61_Full_A24_C59nX_E15_20220224_011149_079291-zlib.ome.tiff | 124.7 |
| C25 | CRC25 | P37_S62_Full_A24_C59nX_E15_20220224_011204_784145-zlib.ome.tiff | 111.6 |
| C26 | CRC26 | P37_S63_Full_A24_C59nX_E15_20220224_011246_458738-zlib.ome.tiff | 99.1 |
| C27 | CRC27 | P37_S64_Full_A24_C59nX_E15_20220224_011259_841605-zlib.ome.tiff | 103.9 |
| C28 | CRC28 | P37_S65_Full_A24_C59nX_E15_20220224_011333_386280-zlib.ome.tiff | 96.0 |
| C29 | CRC29 | P37_S66_Full_A24_C59nX_E15_20220224_011348_519133-zlib.ome.tiff | 76.1 |
| C30 | CRC30 | P37_S67_Full_A24_C59nX_E15_20220224_011408_506939-zlib.ome.tiff | 106.5 |
| C31 | CRC31 | P37_S74_Full_A24_C59qX_E15_20220302_234837_137590-zlib.ome.tiff | 116.1 |
| C32 | CRC32 | P37_S75_Full_A24_C59qX_E15_20220302_235001_586560-zlib.ome.tiff | 111.6 |
| C33 | CRC33_01 | P37_S76_01_A24_C59qX_E15_20220302_235136_561323-zlib.ome.tiff | 43.9 |
| C33 | CRC33_02 | P37_S76_02_A24_C59qX_E15_20220302_235158_533766-zlib.ome.tiff | 49.9 |
| C34 | CRC34 | P37_S77_Full_A24_C59qX_E15_20220302_235222_359806-zlib.ome.tiff | 128.5 |
| C35 | CRC35 | P37_S78_Full_A24_C59qX_E15_20220302_235239_498836-zlib.ome.tiff | 108.0 |
| C36 | CRC36 | P37_S79_Full_A24_C59qX_E15_20220302_235254_496641-zlib.ome.tiff | 98.2 |
| C37 | CRC37 | P37_S80_Full_A24_C59qX_E15_20220307_235159_333000-zlib.ome.tiff | 133.6 |
| C38 | CRC38 | P37_S81_Full_A24_C59qX_E15_20220302_235331_704703-zlib.ome.tiff | 117.0 |
| C39 | CRC39 | P37_S82_Full_A24_C59qX_E15_20220304_200614_832683-zlib.ome.tiff | 98.1 |
| C40 | CRC40 | P37_S83_Full_A24_C59qX_E15_20220304_200429_490805-zlib.ome.tiff | 87.7 |
| Patient | Folder name | File name | File size |
|---|---|---|---|
| C1 | CRC01 | 18459_LSP10353_US_SCAN_OR_001__093059-registered.ome.tif | 981.4 MiB |
| C2 | CRC02 | 18459_LSP10364_US_SCAN_OR_001__092347-registered.ome.tif | 719.8 MiB |
| C3 | CRC03 | 18459_LSP10375_US_SCAN_OR_001__092147-registered.ome.tif | 798.4 MiB |
| C4 | CRC04 | 18459_LSP10388_US_SCAN_OR_001__091155-registered.ome.tif | 873.1 MiB |
| C5 | CRC05 | 18459_LSP10397_US_SCAN_OR_001__091631-registered.ome.tif | 1.1 GiB |
| C6 | CRC06 | 18459_LSP10408_US_SCAN_OR_001__092559-registered.ome.tif | 722.5 MiB |
| C7 | CRC07 | 18459_LSP10419_US_SCAN_OR_001__090907-registered.ome.tif | 783.5 MiB |
| C8 | CRC08 | 19510_C8_US_SCAN_OR_001__150825-registered.ome.tif | 683.8 MiB |
| C9 | CRC09 | 18459_LSP10441_US_SCAN_OR_001__091844-registered.ome.tif | 845.8 MiB |
| C10 | CRC10 | 18459_LSP10452_US_SCAN_OR_001__091355-registered.ome.tif | 583.6 MiB |
| C11 | CRC11 | 19510_C11_US_SCAN_OR_001__151039-registered.ome.tif | 558.0 MiB |
| C12 | CRC12 | 19510_C12_US_SCAN_OR_001__151249-registered.ome.tif | 849.4 MiB |
| C13 | CRC13 | 19510_C13_US_SCAN_OR_001__151503-registered.ome.tif | 917.2 MiB |
| C14 | CRC14 | 19510_C14_US_SCAN_OR_001__151737-registered.ome.tif | 852.6 MiB |
| C15 | CRC15 | 19510_C15_US_SCAN_OR_001__152234-registered.ome.tif | 1018.7 MiB |
| C16 | CRC16 | 19510_C16_US_SCAN_OR_001__152020-registered.ome.tif | 1.6 GiB |
| C17 | CRC17 | 19510_C17_US_SCAN_OR_001__152525-registered.ome.tif | 1.5 GiB |
| C18 | CRC18 | 19510_C18_US_SCAN_OR_001__152757-registered.ome.tif | 1.1 GiB |
| C19 | CRC19 | 19510_C19_US_SCAN_OR_001__153041-registered.ome.tif | 1.0 GiB |
| C20 | CRC20 | 19510_C20_US_SCAN_OR_001__153341-registered.ome.tif | 1.2 GiB |
| C21 | CRC21 | 19510_C21_US_SCAN_OR_001__153607-registered.ome.tif | 797.8 MiB |
| C22 | CRC22 | 19510_C22_US_SCAN_OR_001__092420-registered.ome.tif | 764.5 MiB |
| C23 | CRC23 | 19510_C23_US_SCAN_OR_001__154147-registered.ome.tif | 1.4 GiB |
| C24 | CRC24 | 19510_C24_US_SCAN_OR_001__091904-registered.ome.tif | 1.1 GiB |
| C25 | CRC25 | 19510_C25_US_SCAN_OR_001__154712-registered.ome.tif | 871.0 MiB |
| C26 | CRC26 | 19510_C26_US_SCAN_OR_001__092131-registered.ome.tif | 805.8 MiB |
| C27 | CRC27 | 19510_C27_US_SCAN_OR_001__155205-registered.ome.tif | 722.5 MiB |
| C28 | CRC28 | 19510_C28_US_SCAN_OR_001__155413-registered.ome.tif | 1.1 GiB |
| C29 | CRC29 | 19510_C29_US_SCAN_OR_001__155859-registered.ome.tif | 777.8 MiB |
| C30 | CRC30 | 19510_C30_US_SCAN_OR_001__155702-registered.ome.tif | 776.4 MiB |
| C31 | CRC31 | 19510_C31_US_SCAN_OR_001__160203-registered.ome.tif | 951.8 MiB |
| C32 | CRC32 | 19510_C32_US_SCAN_OR_001__160434-registered.ome.tif | 1.1 GiB |
| C33 | CRC33_01 | 19510_C33_US_SCAN_OR_001__160715-2-registered.ome.tif | 372.3 MiB |
| C33 | CRC33_02 | 19510_C33_US_SCAN_OR_001__160715-registered.ome.tif | 408.8 MiB |
| C34 | CRC34 | 19510_C34_US_SCAN_OR_001__160949-registered.ome.tif | 1.2 GiB |
| C35 | CRC35 | 19510_C35_US_SCAN_OR_001__161209-registered.ome.tif | 1.0 GiB |
| C36 | CRC36 | 19510_C36_US_SCAN_OR_001__161442-registered.ome.tif | 693.5 MiB |
| C37 | CRC37 | 19510_C37_US_SCAN_OR_001__161733-registered.ome.tif | 1.2 GiB |
| C38 | CRC38 | 19510_C38_US_SCAN_OR_001__162018-registered.ome.tif | 1.1 GiB |
| C39 | CRC39 | 19510_C39_US_SCAN_OR_001__162343-registered.ome.tif | 701.5 MiB |
| C40 | CRC40 | 19510_P37-S83_C40_US_SCAN_OR_001__163912-registered.ome.tif | 890.5 MiB |
| Patient | Folder name | File name | File size (MiB) |
|---|---|---|---|
| C1 | CRC01 | P37_S29-CRC01-mask.ome.tif | 262.8 |
| C2 | CRC02 | P37_S30-CRC02-mask.ome.tif | 212.5 |
| C3 | CRC03 | P37_S31-CRC03-mask.ome.tif | 316.5 |
| C4 | CRC04 | P37_S32-CRC04-mask.ome.tif | 286.0 |
| C5 | CRC05 | P37_S33-CRC05-mask.ome.tif | 208.7 |
| C6 | CRC06 | P37_S34-CRC06-mask.ome.tif | 196.8 |
| C7 | CRC07 | P37_S35-CRC07-mask.ome.tif | 189.7 |
| C8 | CRC08 | P37_S57-CRC08-mask.ome.tif | 199.4 |
| C9 | CRC09 | P37_S37-CRC09-mask.ome.tif | 215.5 |
| C10 | CRC10 | P37_S38-CRC10-mask.ome.tif | 226.5 |
| C11 | CRC11 | P37_S43-CRC11-mask.ome.tif | 205.7 |
| C12 | CRC12 | P37_S44-CRC12-mask.ome.tif | 142.9 |
| C13 | CRC13 | P37_S45-CRC13-mask.ome.tif | 244.2 |
| C14 | CRC14 | P37_S46-CRC14-mask.ome.tif | 250.4 |
| C15 | CRC15 | P37_S47-CRC15-mask.ome.tif | 299.9 |
| C16 | CRC16 | P37_S48-CRC16-mask.ome.tif | 443.2 |
| C17 | CRC17 | P37_S49-CRC17-mask.ome.tif | 566.2 |
| C18 | CRC18 | P37_S50-CRC18-mask.ome.tif | 341.8 |
| C19 | CRC19 | P37_S51-CRC19-mask.ome.tif | 266.9 |
| C20 | CRC20 | P37_S52-CRC20-mask.ome.tif | 391.8 |
| C21 | CRC21 | P37_S58-CRC21-mask.ome.tif | 231.2 |
| C22 | CRC22 | P37_S59-CRC22-mask.ome.tif | 240.5 |
| C23 | CRC23 | P37_S60-CRC23-mask.ome.tif | 391.5 |
| C24 | CRC24 | P37_S61-CRC24-mask.ome.tif | 329.4 |
| C25 | CRC25 | P37_S62-CRC25-mask.ome.tif | 103.7 |
| C26 | CRC26 | P37_S63-CRC26-mask.ome.tif | 253.4 |
| C27 | CRC27 | P37_S64-CRC27-mask.ome.tif | 278.2 |
| C28 | CRC28 | P37_S65-CRC28-mask.ome.tif | 263.5 |
| C29 | CRC29 | P37_S66-CRC29-mask.ome.tif | 297.5 |
| C30 | CRC30 | P37_S67-CRC30-mask.ome.tif | 159.6 |
| C31 | CRC31 | P37_S74-CRC31-mask.ome.tif | 233.2 |
| C32 | CRC32 | P37_S75-CRC32-mask.ome.tif | 202.8 |
| C33 | CRC33_01 | P37_S76_01-CRC33_01-mask.ome.tif | 80.6 |
| C33 | CRC33_02 | P37_S76_02-CRC33_02-mask.ome.tif | 101.1 |
| C34 | CRC34 | P37_S77-CRC34-mask.ome.tif | 446.7 |
| C35 | CRC35 | P37_S78-CRC35-mask.ome.tif | 292.9 |
| C36 | CRC36 | P37_S79-CRC36-mask.ome.tif | 242.7 |
| C37 | CRC37 | P37_S80-CRC37-mask.ome.tif | 341.9 |
| C38 | CRC38 | P37_S81-CRC38-mask.ome.tif | 421.7 |
| C39 | CRC39 | P37_S82-CRC39-mask.ome.tif | 244.7 |
| C40 | CRC40 | P37_S83-CRC40-mask.ome.tif | 321.7 |
| Patient | Folder name | File name | File size (MiB) |
|---|---|---|---|
| C1 | CRC01 | P37_S29-CRC01.csv | 775.5 |
| C2 | CRC02 | P37_S30-CRC02.csv | 604.9 |
| C3 | CRC03 | P37_S31-CRC03.csv | 974.5 |
| C4 | CRC04 | P37_S32-CRC04.csv | 866.7 |
| C5 | CRC05 | P37_S33-CRC05.csv | 423.0 |
| C6 | CRC06 | P37_S34-CRC06.csv | 527.5 |
| C7 | CRC07 | P37_S35-CRC07.csv | 490.9 |
| C8 | CRC08 | P37_S57-CRC08.csv | 550.8 |
| C9 | CRC09 | P37_S37-CRC09.csv | 567.4 |
| C10 | CRC10 | P37_S38-CRC10.csv | 681.6 |
| C11 | CRC11 | P37_S43-CRC11.csv | 482.7 |
| C12 | CRC12 | P37_S44-CRC12.csv | 340.6 |
| C13 | CRC13 | P37_S45-CRC13.csv | 684.5 |
| C14 | CRC14 | P37_S46-CRC14.csv | 707.8 |
| C15 | CRC15 | P37_S47-CRC15.csv | 876.2 |
| C16 | CRC16 | P37_S48-CRC16.csv | 1.3 |
| C17 | CRC17 | P37_S49-CRC17.csv | 1.7 |
| C18 | CRC18 | P37_S50-CRC18.csv | 1.0 |
| C19 | CRC19 | P37_S51-CRC19.csv | 703.2 |
| C20 | CRC20 | P37_S52-CRC20.csv | 1.1 |
| C21 | CRC21 | P37_S58-CRC21.csv | 639.9 |
| C22 | CRC22 | P37_S59-CRC22.csv | 625.6 |
| C23 | CRC23 | P37_S60-CRC23.csv | 1.0 |
| C24 | CRC24 | P37_S61-CRC24.csv | 945.2 |
| C25 | CRC25 | P37_S62-CRC25.csv | 199.8 |
| C26 | CRC26 | P37_S63-CRC26.csv | 727.4 |
| C27 | CRC27 | P37_S64-CRC27.csv | 892.5 |
| C28 | CRC28 | P37_S65-CRC28.csv | 700.8 |
| C29 | CRC29 | P37_S66-CRC29.csv | 951.4 |
| C30 | CRC30 | P37_S67-CRC30.csv | 396.2 |
| C31 | CRC31 | P37_S74-CRC31.csv | 576.7 |
| C32 | CRC32 | P37_S75-CRC32.csv | 475.5 |
| C33 | CRC33_01 | P37_S76_01-CRC33_01.csv | 212.5 |
| C33 | CRC33_02 | P37_S76_02-CRC33_02.csv | 279.8 |
| C34 | CRC34 | P37_S77-CRC34.csv | 1.4 |
| C35 | CRC35 | P37_S78-CRC35.csv | 877.6 |
| C36 | CRC36 | P37_S79-CRC36.csv | 695.7 |
| C37 | CRC37 | P37_S80-CRC37.csv | 996.7 |
| C38 | CRC38 | P37_S81-CRC38.csv | 1.3 |
| C39 | CRC39 | P37_S82-CRC39.csv | 795.9 |
| C40 | CRC40 | P37_S83-CRC40.csv | 998.6 |