mcd-stitcher 0.1.7

MCD to Zarr conversion and stitching

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

Ensure you have the following dependencies installed:

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

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: Storage location of converted MCD files in Zarr format.

Notes:

• The zarr output folder are named after mcd file name.

2. ZARR_STITCH

Command:

zarr_stitch <zarr_folder>

Description: Stitches Zarr files into a single dataset.

Arguments:

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

Notes:

• The <zarr_folder> should only have one or multiple folder with zarr data. An empty or unexpected folder structure can throw an error.
• The output files will have _stitched.ome.tiff appended to the original filename.

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: Storage location of converted MCD files in Zarr format and the starting point for stitching Zarr files.
• --lzw: Optional flag to enable LZW compression.

4. TIFF_SUBSET

Command:

tiff_subset <tiff_path> [-c CHANNELS] [--list-channels] [--pyramid] [--tile-size] [--levels]

Description: A function that allows to removes background channels, to view all channels in a 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, --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.
• --pyramid: Create pyramidal OME-TIFF with tiling.
  • --tile-size: Tile size for pyramidal OME-TIFF. (Default: 256x256)
  • --levels: Number of pyramid levels. (Default: 4)

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"
   

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

3. Process all TIFF files in a directory:

   tiff_subset "path/to/directory"
   

   • In this example, since no channel argument is provided, the function will automatically subset channels between metals 141 to 193.

   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.

4. Pyramid and Tile generation usage

   tiff_subset "path/to/file.ome.tiff" --pyramid --tile-size 256 256 --levels 4
   

   • This will create a pyramidal OME-TIFF with 4 pyramid levels and a tile size of 256x256 pixels.

   Notes:

   • The output files will have _pyramid.ome.tiff appended to the original filename

5. Process all TIFF files in a directory default subset and pyramid/tiling

   tiff_subset "path/to/directory" --pyramid 
   

   • This will process all TIFF files in the specified directory, subset from channels 141-193 and create pyramidal OME-TIFFs with tile-size 256x256 and 4 levels.

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.