Preprocessing module for large histological images.
Reason this release was yanked:
typo
Project description
HistoPrep
Preprocessing large histological slides for machine learning made easy!
Description
This module allows you to cut and preprocess large histological slides. Some of the features include:
- Cut large whole slide image (WSI) into tiles of desired size.
- Dearray individual tissue microarray (TMA) spots from a large slide image.
- Easily detect and discard blurry images or images with artifacts after cutting.
- Save a lot of tears while preprocessing images.
Installation
# install as a module
pip install histoprep
# install as an executable
git clone https://github.com/jopo666/HistoPrep
Requirements
python >= 3.8
and openslide
sudo apt-get install openslide-tools
Usage
HistoPrep can be used either as a module...
import histoprep as hp
cutter = hp.Cutter('/path/to/slide', width=512, overlap=0.25)
cutter.save('/path/to/output_folder')
or as an excecutable!
python3 HistoPrep cut ./input_dir ./output_dir --width 512 --overlap 0.25 --img_type jpeg
Examples
Detailed examples with best practices:
Documentation
Work in progress! Each function does have a detailed __doc__
explaining the use of each argument.
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