adding cosmx mgc files

CONTRIBUTING.md

@@ -0,0 +1,13 @@
+# Contributing
+
+For now, only users with permissions for this repository can add/delete datasets. If you don't have the permissions but want to add a dataset, open an issue to discuss with us.
+
+## Adding a dataset
+
+1. Add one/multiple `.h5ad` file(s) under the right directory, according to the right `species` and `tissue`. E.g., `human/breast/filename.h5ad`. Each file corresponds to one slide.
+2. Fill the corresponding metadata under `metadata.csv`
+3. Commit the file as below:
+
+```sh
+
+```

human/head_and_neck/10H064210813H0208914_down.h5ad

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8465590fc130023603221dce91a7b9a4b9cc8afe03d59997e694c53d6a231e72
+size 230444828

human/head_and_neck/10H064210813H0208914_up.h5ad

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0ea1c59bd08825dd34e8d1dd4ac0b9927f81aedecf3ac03a18efd3d968885b90
+size 184409996

human/head_and_neck/13H079750314H0227010_down.h5ad

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c1cbb23719fbed6195854a14105212adfe4414d462a3c6a031532ce922fb2954
+size 230842320

human/head_and_neck/13H079750314H0227010_up.h5ad

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d9961ff4191165143ac485f8ee173d3f278ced098dbb6e78d47af5baafb826d1
+size 314299284

human/head_and_neck/14H007030716H0216858_down.h5ad

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:af25b74800ed3ce96cf00621d64ef530ee70f22bdb6521fde757f155848ffbd6
+size 161477472

human/head_and_neck/14H007030716H0216858_up.h5ad

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a1719bbf87edd46502247a7fa6289ec3705e41d33352664e85ee2dc08842fccb
+size 207763476

human/head_and_neck/14H042050615H0377937_down.h5ad

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e1d8db3941538a3a055a0d130c602d8a8b7d2a6d55410d2b1fa31ed5119e9966
+size 82446816

human/head_and_neck/14H042050615H0377937_up.h5ad

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f31cdc2eef576a725658c51d9ec857da22165feaa6698f62b2dad2bb01f3b609
+size 105643692

metadata.csv

@@ -1,16 +1,24 @@
-name,n_cells,n_genes,technology,tissue,species
-Xenium_V1_Human_Colon_Cancer_P1_CRC_Add_on_FFPE_outs,307762,422,xenium,colon,human
-Xenium_V1_Human_Colon_Cancer_P2_CRC_Add_on_FFPE_outs,340837,422,xenium,colon,human
-HumanBreastCancerPatient1_region_0,713121,500,merscope,breast,human
-Xenium_V1_FFPE_Human_Breast_IDC_With_Addon_outs,576963,380,xenium,breast,human
-Xenium_V1_FFPE_TgCRND8_2_5_months_outs,53913,346,xenium,brain,mouse
-Xenium_V1_FFPE_TgCRND8_5_7_months_outs,58682,347,xenium,brain,mouse
-Xenium_V1_FFPE_TgCRND8_17_9_months_outs,62268,347,xenium,brain,mouse
-Xenium_V1_FFPE_wildtype_5_7_months_outs,58685,347,xenium,brain,mouse
-Xenium_V1_FFPE_wildtype_2_5_months_outs,58231,347,xenium,brain,mouse
-Xenium_V1_FFPE_wildtype_13_4_months_outs,59935,347,xenium,brain,mouse
-slide_0_0,282694,200,,v2,toy
-slide_0_1,282693,200,,v2,toy
-slide_0_2,282692,200,,v2,toy
-slide_0_3,282691,200,,v2,toy
-slide_0_4,282690,200,,v2,toy
+name,n_cells,n_genes,n_proteins,technology,tissue,species
+Xenium_V1_Human_Colon_Cancer_P1_CRC_Add_on_FFPE_outs,307762,422,0,xenium,colon,human
+Xenium_V1_Human_Colon_Cancer_P2_CRC_Add_on_FFPE_outs,340837,422,0,xenium,colon,human
+HumanBreastCancerPatient1_region_0,713121,500,0,merscope,breast,human
+Xenium_V1_FFPE_Human_Breast_IDC_With_Addon_outs,576963,380,0,xenium,breast,human
+Xenium_V1_FFPE_TgCRND8_2_5_months_outs,53913,346,0,xenium,brain,mouse
+Xenium_V1_FFPE_TgCRND8_5_7_months_outs,58682,347,0,xenium,brain,mouse
+Xenium_V1_FFPE_TgCRND8_17_9_months_outs,62268,347,0,xenium,brain,mouse
+Xenium_V1_FFPE_wildtype_5_7_months_outs,58685,347,0,xenium,brain,mouse
+Xenium_V1_FFPE_wildtype_2_5_months_outs,58231,347,0,xenium,brain,mouse
+Xenium_V1_FFPE_wildtype_13_4_months_outs,59935,347,0,xenium,brain,mouse
+slide_0_0,282694,200,0,,v2,toy
+slide_0_1,282693,200,0,,v2,toy
+slide_0_2,282692,200,0,,v2,toy
+slide_0_3,282691,200,0,,v2,toy
+slide_0_4,282690,200,0,,v2,toy
+10H064210813H0208914_down,140139,0,63,cosmx,head_and_neck,human
+10H064210813H0208914_up,112155,0,63,cosmx,head_and_neck,human
+14H007030716H0216858_down,98220,0,63,cosmx,head_and_neck,human
+14H007030716H0216858_up,126341,0,63,cosmx,head_and_neck,human
+13H079750314H0227010_down,140368,0,63,cosmx,head_and_neck,human
+14H042050615H0377937_down,50300,0,63,cosmx,head_and_neck,human
+13H079750314H0227010_up,191141,0,63,cosmx,head_and_neck,human
+14H042050615H0377937_up,64347,0,63,cosmx,head_and_neck,human