running marker_profiling_example

[AlexBouz]

Greetings and thank you for sharing this fantastic tool, i'm running the example script and got stuck at the last processing step, any comment is appreciated!

[eric-czech]

Hi @AlexBouz , the configuration for that example project assumes there are at least 2 gpus present. I changed it to avoid this in the future, but as a workaround you can update the processor.args.gpus argument (set it to "gpus: [0]") in the experiment_pha.yaml file at cytokit/pub/config/cellular-marker and run the notebook again (from the start). Alternatively, you could update the cell that creates the configurations to do this for you:

cytokit config editor --base-config-path=/lab/repos/cytokit/pub/config/cellular-marker/experiment_pha.yaml --output-dir=$1
set name 'Cellular Marker Example'
set acquisition.region_height 1
set acquisition.region_width 1
set acquisition.num_z_planes 7
set environment.index_symlinks '{z:{1:14,2:15,3:16,4:17,5:18,6:19,7:20}}'
set processor.args.gpus '[0]'
save_variant v00/config
exit

[AlexBouz]

Hi Eric, thank you for your help, i went for the workaround for ease of use by adding the set processor.args.gpus '[0]' to the cell, the full script was run,

for the run explorer UI, it opened as expected!

I'm still getting familiar with your tool and hope to test it with my own images in ome multitiff format

[AlexBouz]

Hi Eric, sorry to bother again, but i'm looking for the codex mouse spleen notebooks available to test with cytokit (cy5_montage, file_eda, and segmentation_debug), the linkhttp://welikesharingdata.blob.core.windows.net/forshare/index.html has lot of files and it's hard to tell which input was used, any guidance is appreciated!

[eric-czech]

Hey @AlexBouz , glad that example worked for you. The files I had used are all under the "Deconvolved Z-stacks" section with the subheading BALBc-1. For reference, here are the URLs for all 63:

https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X01_Y01.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X01_Y02.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X01_Y03.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X01_Y04.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X01_Y05.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X01_Y06.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X01_Y07.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X01_Y08.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X01_Y09.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X02_Y01.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X02_Y02.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X02_Y03.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X02_Y04.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X02_Y05.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X02_Y06.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X02_Y07.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X02_Y08.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X02_Y09.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X03_Y01.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X03_Y02.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X03_Y03.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X03_Y04.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X03_Y05.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X03_Y06.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X03_Y07.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X03_Y08.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X03_Y09.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X04_Y01.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X04_Y02.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X04_Y03.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X04_Y04.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X04_Y05.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X04_Y06.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X04_Y07.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X04_Y08.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X04_Y09.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X05_Y01.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X05_Y02.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X05_Y03.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X05_Y04.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X05_Y05.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X05_Y06.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X05_Y07.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X05_Y08.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X05_Y09.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X06_Y01.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X06_Y02.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X06_Y03.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X06_Y04.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X06_Y05.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X06_Y06.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X06_Y07.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X06_Y08.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X06_Y09.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X07_Y01.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X07_Y02.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X07_Y03.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X07_Y04.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X07_Y05.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X07_Y06.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X07_Y07.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X07_Y08.tif
https://welikesharingdata.blob.core.windows.net/forshare/BALBc-slide1/BALBc-1_X07_Y09.tif