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Preprocessing WSI

Divide Whole Slide Images (WSI) into tile-like segments and save the images after removing backgrounds and debris.
Tile images equivalent to x10, x20, and x40 magnifications are stored.

Update

Aug 18, 2023

• Solving error messages caused by using scipy.ndimage.morphology.

Jun 8, 2023

• Solving errors that occur with the latest version of Numpy.

Sep 28, 2021

• Revised to save tile images at x10 magnification by default, along with minor code modifications related to this change.

Sep 27, 2021

• Revised the code for background and noise removal (keep_tile) to run in a multiprocessing environment.
  For a sample slide (1900 tile images), the processing time improved from approximately 25 minutes to about 5 minutes.

Supported Formats

• Aperio (.svs, .tif)
• Hamamatsu (.ndpi, .vms, .vmu)
• Leica (.scn)
• MIRAX (.mrxs)
• Philips (.tiff)
• Sakura (.svslide)
• Trestle (.tif)
• Ventana (.bif, .tif)
• Generic tiled TIFF (.tif)

Rquirements

Confirmed to work in the following environment (compatible with the latest versions of all libraries).

• Python 3.7.4
• openslide-python
• numpy
• pandas
• Pillow
• scipy
• scikit-image
• rich
• tqdm

Installation

1. Install OpenSlide
   Linux
   1-1. sudo apt-get install build-essential
   1-2. sudo apt-get install openslide-tools
   1-3. sudo apt-get install python-openslide

2. pip install openslide-python

Directory Structure

.   
├─ input .. Directory for placing the Whole Slide Images (WSI) to be processed.  
├─ output .. Directory where the tile images are saved after processing.  
├─ notebooks .. Notebooks for code verification 
└─ src  
　　└─ preprocessing.py

Usage

1. cd src
2. python preprocessing.py --<arg1> --<arg2>

Example

• In cases of processing specimens like cytology samples that have many margins.
  python preprocessing.py --tissue_threshold 0.3

• In cases where only tile images equivalent to x20 and x40 magnifications are desired to be saved.
  python preprocessing.py --sample_size 256 512

Argument

python preprocessing.py --help