multi channel images

[tischi]

@martinschorb does the python library support multi channel images as an input?
if so, what names does it give the individual channels?
(cc @K-Meech)

[constantinpape]

No, it currently doesn't support multi channel images. This would need to be handled by a user in preprocessing.

[martinschorb]

here's my hacks to enable the functionality to extract single channels from multi-channel stacks while importing them in MoBIE:

constantinpape/cluster_tools#42

constantinpape/elf#81

[martinschorb]

This works now (at least with OME-Zarr), correct?
Would it be relevant to adjust LUT in the corresponding views as well when adding such a source, or do we want to leave that up to the user?

[JonasHell]

Not sure if this is still under discussion but I had the same issue and tried to solve it like this:

import argparse
import os
import mobie
import xml.etree.ElementTree as ET


def get_number_of_channels_from_ome_metadata(xml_file):
    tree = ET.parse(xml_file)
    root = tree.getroot()
    # all the tags have this weird prefix
    channel_tag = "{http://www.openmicroscopy.org/Schemas/OME/2016-06}Channel"
    channels = list(root.iter(channel_tag))
    # potential alternative:
    # root[1][2].findall("{http://www.openmicroscopy.org/Schemas/OME/2016-06}Channel")
    # other alternative:
    # open data and read number of channels from shape
    return len(channels)


def add_multichannel_zarr_image(
    zarr_file,
    zarr_key,
    mobie_project_directory,
    dataset_name,
    is_default_dataset=False,
):
    file_format = "ome.zarr"
    image_name = zarr_file.split('/')[-1].split('.')[0]
    xml_file = os.path.join(zarr_file, "OME/METADATA.ome.xml")
    num_channels = get_number_of_channels_from_ome_metadata(xml_file)
    sources = [f"{image_name}_ch{channel}" for channel in range(num_channels)]
    # add image volume once (by this added as a source, but never used as one)
    mobie.add_image(
            input_path=zarr_file,
            input_key=zarr_key,
            root=mobie_project_directory,
            dataset_name=dataset_name,
            image_name=image_name,
            file_format=file_format,
            view={},  # manually add view at the end
            is_default_dataset=is_default_dataset,
            move_only=True,
            resolution=None,  # not needed since we just move data
            chunks=None,  # not needed since we just move data
            scale_factors=None,  # not needed since we just move data
        )
    # add each channel as a seperate source
    for channel, channel_name in enumerate(sources):
        dataset_folder = os.path.join(mobie_project_directory, dataset_name)
        _, image_metadata_path = mobie.utils.get_internal_paths(
            dataset_folder,
            file_format,
            image_name
        )
        mobie.metadata.add_source_to_dataset(
            dataset_folder=dataset_folder,
            source_type="image",
            source_name=channel_name,
            image_metadata_path=image_metadata_path,
            view={},
            channel=channel
        )
    display_settings = [
        {"contrastLimits": [0, 65535], "color": "white"},
        {"contrastLimits": [50, 65535], "color": "green"},
        {"contrastLimits": [10, 65535], "color": "blue"}
    ]
    # add one view to visualize all channels at once
    mobie.view_utils.create_view(
        dataset_folder=dataset_folder,
        view_name=image_name,
        sources=[[source] for source in sources],
        display_settings=display_settings,
        menu_name="volumes",
        overwrite=True
    )


def get_args():
    parser = argparse.ArgumentParser()
    parser.add_argument(
        "--input_file",
        "-f",
        type=str,
        help="Path to the input file. Must be a zarr file converted by"
        "bioformats2raw.",
    )
    parser.add_argument(
        "--input_key",
        "-k",
        default="0",
        type=str,
        help="Key of the data inside the input file.",
    )
    parser.add_argument(
        "--mobie_project_folder",
        "-p",
        default="./data",  # or os.getcwd()? or even hardcode?
        type=str,
        help="Path to the MoBIE project folder.",
    )
    parser.add_argument(
        "--dataset_name",
        "-d",
        default="all_volumes",
        type=str,
        help="Name of the dataset to add the data to."
        "If it does not exist, it will be created.",
    )
    parser.add_argument(
        "--is_default_dataset",
        "-i",
        default=False,
        type=bool,
        help="Whether this dataset should be the default one.",
    )
    return parser.parse_args()


def main():
    args = get_args()
    add_multichannel_zarr_image(
        args.input_file,
        args.input_key,
        args.mobie_project_folder,
        args.dataset_name,
        args.is_default_dataset,
    )


if __name__ == "__main__":
    main()

Sry for copy pasting, the code is not on GitHub yet...

[constantinpape]

I will follow up in mobie/mobie-viewer-fiji#1093 to see if this works it all. Once we have figured that out we can see about the color maps (best to do that in a separate issue then.)

[martinschorb]

WIP to enable adding a single channel to MoBIE
#130

We might be able to extend that to general multi-channel application.