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About

This Docker container is to facilitate the extraction of metadata from CZI images using bftools. The container includes all necessary dependencies and provides a streamlined environment for working with CZI image files. By utilizing this Docker image, users can efficiently manage and process CZI metadata without the hassle of manual software installations and configurations and this could be used also in automatic workflows and pipelines.

Usage

Build a container

docker build -t bftools-container .

Run the container with mounted data folder

For interactive run

docker run -v /path/to/your/images:/data -it bftools-container

and then

bfconvert -noflat -omexml-only -format json /data/your_image.czi /data/metadata.json

For non-interactive

docker run --rm -v /path/to/your/images:/data bftools-container bfconvert -noflat -omexml-only -format json /data/your_image.czi /data/metadata.json