Flamingo: a package for extracting and exporting annotations from H&E images
Project description
flamingo
Extract annotations from .ndpa files and map on to the .ndpi image for use in other applications
Install
conda create --name ndpi python=3.10
conda activate ndpi
conda install -c conda-forge openslide
conda install -c conda-forge openslide-python # probably better than the command above
conda install numpy matplotlib jupyterlab
pip install flamingo-histology
Example image
Example annotations (not corresponding to real regions) are provided in the example
folder for files that can be downloaded from the following locations:
Usage
import sys
from flamingo.Flamingo import HE
Openslide documentation can be found here: https://openslide.org
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