flamingo-histology 0.1.2

Flamingo: a package for extracting and exporting annotations from H&E images

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:

• test3-FITC 2 (485).ndpi

Usage

import sys
from flamingo.Flamingo import HE

Openslide documentation can be found here: https://openslide.org