nilseling
commented
1 year ago Hi @ssaintsoon
When you click on the ? in the app, a help page pops up. Have a look at this to see if your question gets answered. In brief, you gate per image. So if you want to gate CD8 T cells on 4 images you will need to download 4 files.
Hi, I'm currently trying steinbock pipeline to process IMC datasets, and following ImagingWorkshop2023 sessions now. I didn't participate in the workshop, so I'm not sure if it's appropriate to leave a question here. Please tell me if it's inappropriate. Also, I have to mention that I have no experiences with R or other programming tools, so please understand that questions can be silly.
With downloaded raw data (Patient1-4.zip), I successfully ran all of codes (except spillover correction) until 'Manual labeling of cells'. I noticed cytomappershiny is needed, so I ran the code.
library(cytomapper) if (interactive()) { cytomapperShiny(object = spe, mask = masks, image = images, cell_id = "ObjectNumber", img_id = "sample_id") }
The only code I change was "image = images_comp" to "image = images" because I didn't correct spillover.
With the code, cytomappershiny (v1.12.0) was appeared, so I manually gated cells. (With 2 plots, Ecad-CD3+ --> CD8 and CD4, and Patient1_001.) I checked CD8+ selection was appropriate for other images (Patient1_002, Patient2_001, ...) and saved gated-cells as 'CD8.rds'.
But I noticed that 'gated-cells' subfolder has 4 numbers of CD8.rds (like CD8_1.rds, CD8_2.rds, ...) 1) One of my question is, why there are 4 kinds of cell.rds? Is it because the number of patients is 4? If I can open the file, it might be confirmed but idk how to open it or visualize it.
2) Second, my 'CD8.rds' was only few hundred KB but CD8_1.rds was a thousand KB. So I suspected it is ROI-merged .rds (I mean, gated cells in Patient_1_001 ~ 003 were concatenated into CD8_1 and so on) If it's correct, does it mean I have to saved gated-cells for all of individual ROIs, like CD8_1_001.rds, CD8_1_002.rds, CD8_1_003.rds ?
3) Hoch et al. (2022) showed masks also could be loaded on image, but I couldn't find out any options in my window. How can it be loaded?
Any comments or suggestions will be very helpful. Thanks for careful answers in community.