Troubleshooting

Load Data CSV Errors¶

Symptom: CellProfiler fails with “Unable to load image”

Solution: Validate CSV paths are accessible:

# Check CSV format
head load_data.csv

# Verify image paths exist
cat load_data.csv | cut -d',' -f5 | xargs -I {} test -f {} && echo "OK"

Plugin Not Found¶

Symptom: “Plugin ‘callbarcodes’ not found”

Solution: Ensure plugin URL is accessible and pipeline has access to the internet if plugin is loaded from an online source.

Memory Errors¶

Symptom: CellProfiler crashes with out-of-memory

Solution: Increase process memory or reduce image size:

process {
    withName: 'CELLPROFILER_.*' {
        memory = { task.attempt == 1 ? 32.GB : 64.GB }
        errorStrategy = 'retry'
    }
}

Missing Images¶

Symptom: CSV has fewer rows than expected

Solution: Check filename patterns match exactly:

ls test_images/ | grep -E "P[0-9]+_[A-Z][0-9]+_[0-9]+_[0-9]+_.*\.tif"

Metadata Mismatches¶

Symptom: CellProfiler can’t group images properly

Solution: Ensure metadata columns are populated correctly:

df[['Metadata_Plate', 'Metadata_Well', 'Metadata_Site']].drop_duplicates()