Having difficulty to do segmentation with external images

[xwxdazhong]

Hi,

I am trying to figure out whether or not Steinbock is good for analyzing immunofluresence images.

The tif file (6000x5000pixels) comprises 3 channels, DAPI, AF647, and AF488. I ran two commands below and it works. I got panel. csv and image.csv
steinbock preprocess external panel
steinbock preprocess external images

However, when I tried to do the next step for segmentation, I got an error message.

steinbock segment deepcell --app mesmer --minmax -o masks_deepcell

Error message:
"app/entrypoint.sh: line 3: 12 Killed python -m steinbock "$@"

Could anyone kindly help me figure out which step I did wrongly with Steinbock? Thank you very much!

[victorjonathanibanez]

This is not a problem with Steinbock, but you seem to be running out of memory on your system, likely due to your large image dims. I suggest that you try to tile your image or run the segmentation on a system that has enough computational power (eg. GPU support).