Metadata-Version: 2.1
Name: wsic
Version: 0.8.0
Summary: Whole Slide Image (WSI) conversion for brightfield histology images
Home-page: https://github.com/john-p/wsic
Author: John Pocock
Author-email: j.c.pocock@warwick.ac.uk
Keywords: wsic
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Provides-Extra: all
Provides-Extra: test
Provides-Extra: docs
Provides-Extra: cli
Provides-Extra: ux
Provides-Extra: performance
Provides-Extra: formats
Provides-Extra: codecs
Provides-Extra: jpeg2000
License-File: LICENSE
License-File: AUTHORS.md

# wsic

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Whole Slide Image (WSI) conversion for brightfield histology images.

**Note: This is in early development and there will likely be frequent
and breaking changes.**

Provides a command line interface (CLI) for easy convertion between
formats:

```bash
Usage: wsic convert [OPTIONS]

  Convert a WSI.

Options:
  -i, --in-path PATH              Path to WSI to read from.
  -o, --out-path PATH             The path to output to.
  -t, --tile-size <INTEGER INTEGER>...
                                  The size of the tiles to write.
  -rt, --read-tile-size <INTEGER INTEGER>...
                                  The size of the tiles to read.
  -w, --workers INTEGER           The number of workers to use.
  -c, --compression [blosc|deflate|jpeg xl|jpeg-ls|jpeg|jpeg2000|lzw|png|webp|zstd]
                                  The compression to use.
  -cl, --compression-level INTEGER
                                  The compression level to use.
  -d, --downsample INTEGER        The downsample factor to use.
  -mpp, --microns-per-pixel <FLOAT FLOAT>...
                                  The microns per pixel to use.
  -ome, --ome / --no-ome          Save with OME-TIFF metadata (OME-XML).
  --overwrite / --no-overwrite    Whether to overwrite the output file.
  -to, --timeout FLOAT            Timeout in seconds for reading a tile.
  -W, --writer [auto|jp2|svs|tiff|zarr]
                                  The writer to use. Overrides writer detected
                                  by output file extension.
  -h, --help                      Show this message and exit.
```

![A demonstration of converting a JP2 file to a pyramid
TIFF.](https://github.com/John-P/wsic/raw/main/docs/_static/wsic_convert_demo.gif)

## Features

- Read image data from:
  - [OpenSlide](https://openslide.org/) Formats:
    - Aperio SVS (.svs)
    - Hamamatsu (.vms, .vmu, .ndpi)
    - Leica (.scn)
    - Mirax MRXS (.mrxs)
    - Sakura (.svslide)
    - Trestle (.tif)
    - Ventana (.bif, .tif)
    - Generic tiled TIFF (.tif; DEFLATE, JPEG, and Webp
      compressed)
  - Other Tiled TIFFs
    ([tifffile](https://github.com/cgohlke/tifffile) supported
    formats)
    - E.g. JPEG XL compressed
  - [OME-TIFF](https://docs.openmicroscopy.org/ome-model/5.6.3/ome-tiff/)
    (via ([tifffile](https://github.com/cgohlke/tifffile))
  - [JP2](https://jpeg.org/jpeg2000/) (via
    [glymur](https://glymur.readthedocs.io/en/latest/) and
    [OpenJPEG](https://www.openjpeg.org/))
  - [Zarr](https://zarr.readthedocs.io/en/stable/) / NGFF (single
    array or pyramid group of arrays)
  - [DICOM WSI](https://dicom.nema.org/dicom/dicomwsi/) (via
    [wsidicom](https://github.com/imi-bigpicture/wsidicom))
- Write image data to:
  - Tiled / Pyramid Generic TIFF
  - OME-TIFF
  - JP2
  - Pyramid Zarr (NGFF)
- Custom tile size
- Compression codecs
- Lossless repackaging / transcoding (to zarr/NGFF) from:
  - SVS (JPEG compressed)
  - OME-TIFF (single image, JPEG and JPEG2000 (J2K) compressed)
  - Generic Tiled TIFF (JPEG, JPEG2000, and WebP compressed)
  - DICOM WSI (JPEG and JPEG2000 (J2K) compressed)

## Dependencies

- numpy
- zarr
- click (CLI)

### Optional Dependencies

- [OpenSlide](https://openslide.org/) and
  [openslide-python](https://pypi.org/project/openslide-python/)
  (reading OpenSlide Formats)
- [tifffile](https://github.com/cgohlke/tifffile) (reading tiled
  TIFFs)
- [wsidicom](https://github.com/imi-bigpicture/wsidicom) (reading
  DICOM WSI)
- [glymur](https://glymur.readthedocs.io/en/latest/) and
  [OpenJPEG](https://www.openjpeg.org/) (reading JP2)
- [tqdm](https://github.com/tqdm/tqdm) (progress bars)
- [scipy](https://www.scipy.org/) (faster pyramid downsampling)
- [opencv-python](https://pypi.org/project/opencv-python/) (even
  faster pyramid downsampling)
- [imagecodecs](https://github.com/cgohlke/imagecodecs) (additional
  codecs and transcoding)

## To-Dos

For a list of To-Dos see [the project
board](https://github.com/users/John-P/projects/1/views/1).

## Other Tools

There are many other great tools in this space. Below are some other
tools for converting WSIs.

### bfconvert

Part of the Bio-Formats command line tools. Uses bioformats to convert
from many formats to OME-TIFF.

<https://www.openmicroscopy.org/bio-formats/downloads/>

### biofromats2raw

Convert from Bio-Formats formats to zarr.

<https://github.com/glencoesoftware/bioformats2raw>

### isyntax2raw

Convert from Philips' iSyntax format to a zarr.

<https://github.com/glencoesoftware/isyntax2raw>

### wsidicomiser

Convert OpenSlide images to WSI DICOM.

<https://github.com/sectra-medical/wsidicomizer>

## Credits

This package was created with
[Cookiecutter](https://github.com/audreyr/cookiecutter) and the
[audreyr/cookiecutter-pypackage](https://github.com/audreyr/cookiecutter-pypackage)
project template.


# History

## 0.8.0 (2023-04-01)

- Add DICOM writer.
- Avoid decoding entire TIFF before conversion starts.
- TIFFReader can now expose a dask array view (using tiffile Zarr view
  underneath).
- Add overwrite option to transcode CLI mode.
- Refactor to use persistent worker subprocesses. This avoids recreating
  the reader object for each region read. For some reader such as
  DICOMWSIReader this significantly improves performance.
- General refactoring and code cleanup.
- Bug fixes:
  - Fix writing MPP for SVSWriter.
  - Remove OpenSlide thumbnail generation method. This would cause the
    process to run out of memory for some files and the base
    implementation works just as well without this memory issue.

## 0.7.0 (2022-12-15)

- Normalise TIFF array axes (to YXC order) when reading using tiffile.
- Bug fixes:
  - Fix reading/writing JP2 resoluion metadata (vres/hres are in m not
    cm).
  - Join child processes when finishing writing / exiting.
  - Copy the reader tile size for transcode mode.
  - Return None for MPP when JP2 has no resolution box.
  - Set resolution units to cm when writing TIFFs.
  - Use the MPP from the reader when writing JP2.
  - Add a zarr intermediate for JP2 writing (allows different read and
    write tile sizes).

## 0.6.1 (2022-10-21)

- Select Writer class based on file extension from CLI.
- Bug fixes:
  - Fix writing MPP to NGFF v0.4.
  - Change coordinate transformation ordering.
  - Fix reading TIFF resolution tag. Previously only the numerator of
    the resolution fraction was being read.
  - Other minor bug fixes.

## 0.6.0 (2022-10-03)

- Add ability to write resolution metadata to JP2. Thanks to
  @quintusdias for helping get this implemented in glymur.
- Remove QOI codec code as this is not included in imagecodes. Thanks to
  Christoph Gohlke for adding this.
- Add a "How do I?" documentation page.

## 0.5.1 (2022-06-27)

- Bug fixes:
  - Fix parsing of OpenSlide MPP to float.

## 0.5.0 (2022-06-25)

- Add ability to transcode/repackage to a TIFF file (from DICOM or SVS).
- Refactor `ZarrReaderWriter` to seperate `ZarrWriter` and `ZarrReader`.
- Bug fixes:
  - Fix thumbnaiul generation for zarr.
  - Fix NGFF metadata `CoordinateTransformation` field default factor.

## 0.4.0 (2022-06-20)

- Add ability to write JPEG compressed SVS files.
- Add support for thumbnail generation and a CLI command.
- Swap from strings to enums for codecs and color spaces.

## 0.3.0 (2022-05-13)

- Remove unused CLI debug option.
- Add generation of OME-NGFF metadata (JSON .zattrs file).
- Add timeout when copying tiles to prevent indefinite hanging.
- Improve joining/termination of child processes at shutdown.
- Use the TIFF resolution tag if present.
- Add `get_tile` method to all `Reader` classes.
- Update supported Python versions to 3.8, 3.9, 3.10.
- Bug fixes:
  - Fix and issue with concatenation of pyramid downsamples.
  - Add a custom Queue class for multiprocessing on macOS.
  - Fix handling of `pyramid_downsamples` argument when `None`.

## 0.2.0 (2022-03-22)

- Add Support To Read DICOM WSI and transform to zarr.

## 0.1.0 (2022-02-22)

- First release on PyPI.
