Samui

[shkwon17]

1. Upload "raw" IF image data for n=10 tissue samples to Samui browser

• [x] IF data for each capture area contains a total of 6 fluorescence channels.

A. DAPI (DAPI; equivalent to DAPI in the DLPFC Visium-SPG data) B. Abeta (Opal520; equivalent to NeuN in the DLPFC Visium-SPG data) C. pTau (Opal570; equivalent to TMEM119 in the DLPFC Visium-SPG data) D. GFAP (Opal620; equivalent to GFAP in the DLPFC Visium-SPG data) E. MAP2 (Opal690; equivalent to OLIG2 in the DLPFC Visium-SPG data) F. Lipofuscin (Autofluorescence; equivalent to Lipofuscin in the DLPFC Visium-SPG data)

• [x] A protein name for each channel (i.e., channel name) is different than that of the DLPFC Visium-SPG data. Each channel name has to be renamed into any of the following protein names: DAPI, Abeta, pTau, GFAP, MAP2, and lipofuscin, based on their matching fluorophores.

A. DAPI -> DAPI (so, no change is needed) B. NeuN -> Abeba C. TMEM119 -> pTau D. GFAP -> GFAP (so, no change is needed) E. OLIG2 -> MAP2 F. Lipofuscin -> Lipofuscin (so, no change is needed)

• [x] Channel order

2. To be determined about what to do with segmentation data

[shkwon17]

https://jhu-genomics.slack.com/archives/C01GJ0F731Q/p1680624699684989?thread_ts=1680122865.953319&cid=C01GJ0F731Q

Revisiting the channel names.

[shkwon17]

Probably will not contain segmentation data for the time issue.

[shkwon17]

https://jhu-genomics.slack.com/archives/C01GJ0F731Q/p1680972156753509

Nick, cc me(Leo) & Keri when you email Bill for a new bucket (in case you don’t have one already), so either of us can approve it ASAP

[shkwon17]

https://jhu-genomics.slack.com/archives/C01GJ0F731Q/p1681139175130379

List of information we expect from Samui