mcd-stitcher

MCD STITCHER

A package made for stitching ROIs into OME-TIFFS and additional OME-TIFF editing tools

Installation

To install the package, use the following command:

pip install mcd_stitcher

Requirements

Python >3.11

The following packages will installed automatically:

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

Command Line Usage

1. IMC2ZARR

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: (Optional) Storage location of converted MCD files in Zarr format. If not provided, the output folder <mcd_folder>/Zarr_converted will be automatically created.

Notes:

• The Zarr output folders are named after the MCD file names.
• Progress and errors will be printed to the console for better monitoring.

2. ZARR_STITCH

Command:

zarr_stitch <zarr_folder>

Description: Stitches Zarr files into a multi-channeled OME-TIFF.

Arguments:

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

Notes:

• The <zarr_folder> should only contain folders with Zarr data. Empty or unexpected folder structures will be skipped.
• Errors encountered during processing will be logged to error_log.txt in the input directory.
• The output files will have _stitched.ome.tiff appended to the original filename.
• Success messages will be printed for each processed folder.

3. MCD_STITCH

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: (Optional) Storage location of converted MCD files in Zarr format and the starting point for stitching Zarr files. If not provided, the output folder <mcd_folder>/Zarr_converted will be automatically created.
• --lzw: Optional flag to enable LZW compression.

4. TIFF_SUBSET

Command:

tiff_subset <tiff_path> [-c] [-p] [-f CHANNELS]

Description: A function that allows you to remove background channels, view all channels in an OME-TIFF, and generate OME-TIFF with pyramid and tiles.

Arguments:

• tiff_path: Path to the OME-TIFF file or directory containing OME-TIFF files.
• -c: Lists all channels in the OME-TIFF file.
• -p: Enables the creation of a pyramidal OME-TIFF with tiling.
• -f CHANNELS: Filters and subsets channels. Provide channels to subset, e.g., "0-5,7,10". If no channels are provided, default filtering is applied.

Notes:

• Order of arguments: The -f flag (if used) must be the last argument in the command.
• Default filtering: Automatically subsets all channels for metals tags between 141 to 193.
• Pyramid and Tiling: The hardcoded tile size is (256x256) and pyramid levels as 4.
• Errors encountered during processing will be logged to error_log.txt in the input directory.

Examples:

• List channels in a TIFF file:

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

• Subset channels 12 to 46:

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

  • Other possible combinations: "1,6,20" or "5,6-10,55,60"

• Subset all TIFF files in a directory:

  tiff_subset "path/to/directory" -f
  

  Notes:

  • In this example, since no channel argument is provided, the function will automatically use default filtering.
  • 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.

• Subset Tiff files with Pyramid and Tile Generation:

  tiff_subset "path/to/file.ome.tiff" -p -f	
  

  Notes:

  • This will create a pyramidal OME-TIFF with default filtering.
  • The output files will have _filtered_pyramid.ome.tiff appended to the original filename.

License

This project is licensed under the GNU General Public License v3.0 License. See the LICENSE file for details.

Issues

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