prepipe-containers

Container images for the E11 preprocessing pipeline.

Images

bigstitcher-spark

BigStitcher-Spark with concurrent tile optimization enabled. Based on JaneliaSciComp/BigStitcher-Spark with patches from:

• e11bio/mpicbg — Fix TileUtil.optimizeConcurrently() crash on disconnected tiles
• e11bio/multiview-reconstruction — Re-enable concurrent solver in GlobalOptIterative

# Pull the image
docker pull ghcr.io/e11bio/bigstitcher-spark:latest

# Use in Nextflow (apptainer)
apptainer.runOptions = ''  # no bind mount needed
process {
    withName:BIGSTITCHER_MODULE {
        container = 'ghcr.io/e11bio/bigstitcher-spark:latest'
    }
}

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