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==3.11 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:

```sh

CONVERT TO ZARR

iohub convert \ -i ./acqname/acqnamelabelfree1 \ -o ./acqnamelabelfree.zarr \ iohub convert \ -i ./acqname/acqnamelightsheet1 \ -o ./acqnamelightsheet.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 ./acqnamelightsheet.zarr \ -c ./deconvolveparams.yml \ --psf-dirpath ./psf.zarr -o ./acqnamelightsheetdeconvolved.zarr

DESKEW FLUORESCENCE

estimate deskew parameters

biahub estimate-deskew \ -i ./acqnamelightsheet.zarr/0/0/0 \ -o ./deskew.yml

apply deskew parameters

biahub deskew \ -i ./acqnamelightsheet.zarr///* \ -c ./deskewparams.yml \ -o ./acqnamelightsheetdeskewed.zarr

RECONSTRUCT PHASE/BIREFRINGENCE

biahub reconstruct \ -i ./acqnamelabelfree.zarr///* \ -c ./recon.yml \ -o ./acqnamelabelfree_reconstructed.zarr

STABILIZE

estimate stabilization parameters

biahub estimate-stabilization \ -i ./acqnamelabelfree.zarr///* \ -o ./stabilization.yml \ --stabilize-xy \ --stabilize-z

stabilize data

biahub stabilize \ -i ./acqnamelabelfree.zarr///* \ -c ./stabilization.yml \ -o ./acqnamelabelfree_stabilized.zarr///*

REGISTER

estimate registration parameters

biahub estimate-registration \ -s ./acqnamelabelfreereconstructed.zarr/0/0/0 \ -t ./acqnamelightsheetdeskewed.zarr/0/0/0 \ -o ./register.yml

optimize registration parameters

biahub optimize-registration \ -s ./acqnamelabelfreereconstructed.zarr/0/0/0 \ -t ./acqnamelightsheetdeskewed.zarr/0/0/0 \ -c ./register.yml \ -o ./register_optimized.yml

register data

biahub register \ -s ./acqnamelabelfreereconstructed.zarr///* \ -t ./acqnamelightsheetdeskewed.zarr///* \ -c ./registeroptimized.yml \ -o ./acqname_registered.zarr

CONCATENATE CHANNELS

biahub concatenate \ -c ./concatenate.yml \ -o ./acqnameconcatenated.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 ./acqname.zarr///* \ -c ./stitching.yml \ -o ./acqname_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.