mcd-stitcher 0.1.6

MCD to Zarr conversion and stitching

MCD STITCHER

Stitch ROIs from MCD files into OME-TIFFs.

Installation

To install the package, use the following command:

pip install mcd_stitcher

Requirements

Ensure you have the following dependencies installed:

• click
• numpy
• pandas
• python_dateutil
• xarray
• zarr
• scikit-image

Command Line Usage

MCD to Zarr Converter

Command:

imc2zarr <mcd_folder> <zarr_folder>

Description: Converts MCD files to Zarr format.

Arguments:

• mcd_folder: The root folder of the IMC scan containing single or multiple MCD files.
• zarr_folder: Storage location of converted MCD files in Zarr format.

Zarr Dataset Stitcher

Command:

zarr_stitch <zarr_folder>

Description: Stitches Zarr files into a single dataset.

Arguments:

• zarr_folder: The folder containing Zarr files to be stitched.

Composite MCD to Zarr to Stitch Function

Command:

mcd_stitch <mcd_folder> <zarr_folder> [--lzw]

Description: Combines the MCD to Zarr conversion and Zarr stitching into a single command.

Arguments:

• mcd_folder: The root folder of the IMC scan containing single or multiple MCD files.
• zarr_folder: Storage location of converted MCD files in Zarr format and the starting point for stitching Zarr files.
• --lzw: Optional flag to enable LZW compression.

OME-TIFF Subsetter

Command:

tiff_subset <tiff_path> [-c CHANNELS] [--list-channels]

Description: Subsets OME-TIFF files based on specified channels.

Arguments:

• tiff_path: Path to the OME-TIFF file or directory containing OME-TIFF files.
• -c, --channels CHANNELS: Channels to subset, e.g., 0-5,7,10. If not provided, the script will keep all channels between metals 141 to 193.
• --list-channels: List the channels in the specified OME-TIFF file.

Examples:

1. List channels in a TIFF file:

   tiff_subset "path/to/file.ome.tiff" --list-channels
   

2. Subset channels 12 to 46:

   tiff_subset "path/to/file.ome.tiff" -c "12-46"
   

3. Process all TIFF files in a directory:

   tiff_subset "path/to/directory"
   

Notes:

• When a directory is provided, all TIFF files within the directory will be processed.
• The output files will have _filtered.ome.tiff appended to the original filename.

License

This project is licensed under the MIT License. See the LICENSE file for details.

Issues

If you encounter any issues, please open a ticket on the issue tracker.