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hubmapconsortium / ccf-asct-reporter

HRA ASCT+B Reporter
https://hubmapconsortium.github.io/ccf-asct-reporter/
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FTU support? #164

Open bherr2 opened 3 years ago

bherr2 commented 3 years ago

v1 tables have support for FTU/n/x columns, but we never used or processed them. It is still unclear exactly how they should be processed/used. This issue is to figure that out.

From @emquardokus :

FTU = functional tissue unit and although it EXISTED in v1 tables, it was not used correctly by SMEs and we did not really USE these columns in the ASCT+B reporter. I’m not certain how this would be implemented for the ASCT+B reporter visualization, but I could think of a few things.

CC: @katyb @emquardokus

katyb commented 3 years ago

Fauzan's work focuses on FTUs. Ultimately, we will have at least one, sometimes multiple FTUs per organ. In Y4, I hope we can have 2D SVGs (and some 3D ML generated 3D FTU GLB files) for 22 organs. All AS/CT that show in Fauzan's SVGs/GLBs should have data in the FTU column in MASTER tables.

emquardokus commented 3 years ago

Functional tissue unit (FTU) is a multiple AS entity and can be a part of another AS and has a several of cell types associated with them. Example: nephron is a multiple AS structure and is the true functional unit of the kidney, but the renal corpuscle is composed of the glomerulus (capillary bed), the capillary bed itself has both venous and arterial vessels, bowman's capsule (space around the capillary bed). There are many cell types that are part of the FTU, and some organs have more than one type of FTU. So ideally we could capture all the different types of FTU by name/label/ID which will also relate them to the AS that make up the FTU and all the CT that make up the FTU.