MCD to Zarr conversion and stitching
Project description
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
The following dependencies will 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: (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] [-f CHANNELS] [-p]
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.
- -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.
- -p: Enables the creation of a pyramidal OME-TIFF with tiling.
Notes:
- 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" -f -p
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 MIT License. See the LICENSE file for details.
Issues
If you encounter any issues, please open a ticket on the issue tracker.
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