Issue: Unable to run Ilastik with different image sizes.

[giacuong171]

Description of the bug

Hi Molkart Team,
I encountered an issue while running Molkart with ilastik pre-trained models (pixel_classification and multicut). The pre-trained models are generated by manually picking the cells from training subset generated from molkart. And my original dataset contains different image sizes. This discrepancy in image sizes seems to have caused the error.

I have attached the log file for your reference.

bug_report.txt

Command used and terminal output

nextflow run main.nf --input ../samplesheet.csv --outdir ../training_set --create_training_subset
nextflow run main.nf --input ../samplesheet.csv --outdir ../training_set -profile mamba,apptainer --segmentation_method cellpose,ilastik,mesmer

Relevant files

No response

System information

No response

[kbestak]

Closing as discussion continued on Slack