biahub

Bio-image analysis hub supporting high-throughput data reconstruction on HPC clusters with Slurm workload management.

biahub was originally developed to reconstruct data acquired on the mantis microscope using the shrimPy acquisition engine, and has since been extended to process diverse multimodal datasets. biahub reconstruction workflows rely on OME-ZARR datasets (for example, as created with iohub) which enable efficient parallelization across compute nodes. Available reconstruction routines are listed below; more information can be obtained with biahub --help.

Install

conda create -n biahub python==3.10
conda activate biahub

git clone https://github.com/czbiohub-sf/biahub.git
pip install -e ./biahub

Data reconstruction

Data reconstruction uses a command line interface. All reconstruction calls take an input -i and an output -o, and most reconstruction calls use configuration files passed via a -c option. Reconstruction workflows launch multiple Slurm jobs and can also be run locally using the -l flag.

A typical set of CLI calls to go from raw data to registered volumes looks like:

# CONVERT TO ZARR
iohub convert \
    -i ./acq_name/acq_name_labelfree_1 \
    -o ./acq_name_labelfree.zarr \
iohub convert \
    -i ./acq_name/acq_name_lightsheet_1 \
    -o ./acq_name_lightsheet.zarr

# DECONVOLVE FLUORESCENCE
# (optional) characterize the PSF
biahub characterize-psf
    -i ./beads.zarr \
    -c ./characterize_params.yml \
    -o ./report/
# estimate PSF parameters
biahub estimate-psf \
    -i ./beads.zarr \
    -c ./psf_params.yml \
    -o ./psf.zarr
# deconvolve data
biahub deconvolve \
    -i ./acq_name_lightsheet.zarr \
    -c ./deconvolve_params.yml \
    --psf-dirpath ./psf.zarr
    -o ./acq_name_lightsheet_deconvolved.zarr

# DESKEW FLUORESCENCE
# estimate deskew parameters
biahub estimate-deskew \
    -i ./acq_name_lightsheet.zarr/0/0/0 \
    -o ./deskew.yml
# apply deskew parameters
biahub deskew \
    -i ./acq_name_lightsheet.zarr/*/*/* \
    -c ./deskew_params.yml \
    -o ./acq_name_lightsheet_deskewed.zarr

# RECONSTRUCT PHASE/BIREFRINGENCE
recorder reconstruct \
    -i ./acq_name_labelfree.zarr/*/*/* \
    -c ./recon.yml \
    -o ./acq_name_labelfree_reconstructed.zarr

# STABILIZE
# estimate stabilization parameters
biahub estimate-stabilization \
    -i ./acq_name_labelfree.zarr/*/*/* \
    -o ./stabilization.yml \
    --stabilize-xy \
    --stabilize-z
# stabilize data
biahub stabilize \
    -i ./acq_name_labelfree.zarr/*/*/* \
    -c ./stabilization.yml \
    -o ./acq_name_labelfree_stabilized.zarr/*/*/*

# REGISTER
# estimate registration parameters
biahub estimate-registration \
    -s ./acq_name_labelfree_reconstructed.zarr/0/0/0 \
    -t ./acq_name_lightsheet_deskewed.zarr/0/0/0 \
    -o ./register.yml
# optimize registration parameters
biahub optimize-registration \
    -s ./acq_name_labelfree_reconstructed.zarr/0/0/0 \
    -t ./acq_name_lightsheet_deskewed.zarr/0/0/0 \
    -c ./register.yml \
    -o ./register_optimized.yml
# register data
biahub register \
    -s ./acq_name_labelfree_reconstructed.zarr/*/*/* \
    -t ./acq_name_lightsheet_deskewed.zarr/*/*/* \
    -c ./register_optimized.yml \
    -o ./acq_name_registered.zarr

# CONCATENATE CHANNELS
biahub concatenate \
    -c ./concatenate.yml \
    -o ./acq_name_concatenated.zarr

# STITCH
# estimate stitching parameters
biahub estimate-stitching \
    -i ./acq_name.zarr/*/*/* \
    -o ./stitching.yml \
    --channel DAPI
    --percent-overlap 0.05
# stitch fields of view
biahub stitch \
    -i ./acq_name.zarr/*/*/* \
    -c ./stitching.yml \
    -o ./acq_name_stitched.zarr/*/*/*

Contributing

We would appreciate the bug reports and code contributions if you use this package. If you would like to contribute to this package, please read the contributing guide.