Dataset processing progress

[ngreenwald]

This issue can be used to track the progress of each of the datasets we're planning on incorporating

Name	Description	Create conversion matrix	QC sample images	Download full dataset	Preprocess dataset	Train individual model	Finalize conversion matrix	# proofread fovs	# proofread cells
TONIC	Samples from TONIC study	✅	✅	✅	✅	✅	✅	3	8,068
MSK Colon	Vectra dataset of colon images	✅	✅	✅	✅	✅	✅	3	40,004
MSK Pancreas	Vectra dataset of pancrease images	✅	✅	✅	✅	✅	✅	3	0
Hickey CRC	CODEX CRC	✅	✅	✅	✅	✅	✅	3	0
Decidua	MIBI Decidua study	✅	✅	✅	✅	✅	✅	3	0
COVID placentitis	IF study of covid	✅	❌	❌	❌	❌	❌	0	0
Enable dataset 1	CODEX dataset	✅	❌	❌	❌	❌	❌	0	0
Enable dataset 2	CODEX dataset	❌	❌	❌	❌	❌	❌	0	0
Enable dataset 3	CODEX dataset	❌	❌	❌	❌	❌	❌	0	0
CyCIF dataset 1	Candace downloaded for pixel clustering	❌	❌	❌	❌	❌	❌	0	0
CyCIF dataset 2	Sorger CRC https://www.cell.com/cell/pdf/S0092-8674(22)01571-9.pdf	❌	❌	❌	❌	❌	❌	0	0
IMC dataset 1	TBD, waiting to hear back	❌	❌	❌	❌	❌	❌	0	0
IMC dataset 2	TBD, waiting to hear back	❌	❌	❌	❌	❌	❌	0	0
TB panel 1	MIBI TB study	❌	❌	❌	❌	❌	❌	0	0
TB panel 2	MIBI TB study	❌	❌	❌	❌	❌	❌	0	0
additional datasets	PICI, HTAN, HuBMAP, CIMAC	❌	❌	✅	❌	❌	❌	0	0
Multiplex IF MSK	https://www.nature.com/articles/s41597-023-02108-z#Abs1	❌	❌	❌	❌	❌	❌	0	0
CHL IMC	https://pubmed.ncbi.nlm.nih.gov/38113419/	❌	❌	❌	❌	❌	❌	0	0
Bodenmiller IMC 5 tissues 40-plex	https://zenodo.org/records/12912567	❌	❌	✅	❌	❌	❌	0	0
MIBI GBM	Ben & Hadeeshas dataset	❌	❌	✅	❌	❌	❌	0	0
template dataset	Copy this row to add another dataset	❌	❌	❌	❌	❌	❌	0	0
Sorger CycIF 34 tissues 64-plex	https://www.biorxiv.org/content/10.1101/2023.11.15.567196v1.full.pdf	❌	❌	❌	❌	❌	❌	0	0
SegPath dataset	8-plex IF, 18 tissues	❌	❌	❌	❌	❌	❌	0	0