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Microflow: a prototype Nextflow workflow for microscopy image preprocessing

About

This is a prototyping attempt of a common image processing workflow using Nextflow. The steps include:

  • Organizing and exporting image metadata into a YAML file.
  • Estimating shading profiles and correcting the shading effect.
  • Stitching (by M2Stitch) into a Zarr array.

All the steps are written as a Jupyter notebook and run by Papermill in the workflow.

How to use

  1. Create a list of files to process (currently AICSImageIO compatible files work).

  2. Execute the workflow. The parameters are as follows:

    • -w : The working directory for Nextflow.
    • --input_path_csv : The CSV file for the file list.
    • --common_input_path : The "root" directory of the image files. The output images are stored preserving the subdirectory structure with respect to this directory.
    • --output_path : The directory in which output images are stored.
    nextflow run path/to/microflow \
    -resume \
    -w /path/to/workdir/ \
    --input_path_csv "./file_list.txt" \
    --common_input_path "/mnt/showers/Cell-picker/240119/" \
    --output_path "/path/to/output/"

    One can also specify the following parameters:

    • --shading_estimation_strategy = "timewise" // or "all" : If "timewise", estimate the shading profile for each frame. If "all", use the all frames.
    • --shading_estimation_median_robust = "False" // or "True" : If True, use the intensities within the 2*(Median absolute deviation from median) around the median.
    • --shading_estimation_median_filter_size = 3 : Median filter size for shading correction.
    • --shading_estimation_gaussian_filter_size = 40 : Gaussian filter size for shading correction.
    • --shading_correction_mode = "additive" // or "multiplicative" : The shading correction mode.
    • --shading_correction_local_subtraction_channels = "DIA" : The channel pattern for shading correction by local intensity subtraction.
    • --shading_correction_local_subtraction_scaling = 0.1
    • --shading_correction_local_subtraction_median_disk_size = 4
    • --stitching_stitch_every_t = 0 : The frame skip for stitching. If zero, only use the first frame for stitching.
    • --stitching_target_channel = '10x_Fukai_DIA_IS' : The reference channel for stitching.

Todo

[] Adding other shading correction / stitching methods [] Reorganizing input / output image formats [] Organizing documentation [] Splitting each step to command line tools [] Deploying to nf-core