CZI flow

Immunofluorescence (IF) microscopy overview:

  • The CZI file format has been developed by ZEISS to store multidimensional IF images such as:

    • z-stacks, time lapse, and multiposition experiments.

  • We rely on applications like OME Bio-Formats / OMERO, Fiji, python-bioformats to view and process czi files

  • The IF images are visualized with neuroglancer

  • The file also consists of metadata along with label and macro (RGB) images

Pipeline overview:

  • Convert czi file to OME-NGFF zarr format with OME XML

  • Generate neuroglancer meta-data from zarr sub-image for each IF image

  • Create thumbnail image from zarr label sub-image

em_workflows.czi.flow.gen_thumb(image: HedwigZarrImage, file_path: FilePath, image_name: str) → dict

Uses SimpleITK to extract and write jpeg thumbnail image for the zarr subimage

em_workflows.czi.flow.rechunk_zarr(file_path: FilePath) → None

Re-chunk the ZARR structure so that multi-channel/RGB channels are not split between chunks with the zarr_rechunk command provided by tomojs-pytools.

em_workflows.czi.flow.copy_zarr_to_assets_dir(file_path: FilePath) → None

Copy the zarr files generated from czi files using bioformats2raw to assets folder

em_workflows.czi.flow.generate_imageset(file_path: FilePath) → List[Dict]
ImageSet consists of all the assets for a particular zarr sub-image and label images
Macro image is ignored
Label image is added as an thumbnail asset
Zarr sub-images are added as neurglancerZarr asset along with their metadata
Metadata includes: - shader - dimensions - shaderParameters
em_workflows.czi.flow.generate_zarr(file_path: FilePath)

Uses bioformats2raw command to convert czi file to OME-NGFF zarr file

em_workflows.czi.flow.find_thumb_idx(callback: List[Dict]) → List[Dict]

Locate the index of label image in the image set

em_workflows.czi.flow.update_file_metadata(file_path: FilePath, callback_with_zarr: Dict) → Dict

OME-xml metadata can be informative for developers to understand why the neuroglancer view is not appropriately rendering. This function attaches xml file location as the file metadata to the zarr group

em_workflows.czi.flow.generate_czi_imageset(file_path: FilePath) → List[Dict]

Subflow for heavy lifting operation

Overview:

  • Generate zarr from czi

  • Rechunk zarr files

  • Copy zarr files to assets folder

  • Generate imageset for the assets

em_workflows.czi.flow.gen_thumb(image: HedwigZarrImage, file_path: FilePath, image_name: str) → dict

Uses SimpleITK to extract and write jpeg thumbnail image for the zarr subimage