README.md

eozinpy

Python bindings for eozin. Note: This project is only tested on Ubuntu 22.04.

How to install on Ubuntu 22.04

Install python virtualenv and build essentials on Ubuntu

$ sudo apt update && sudo apt upgrade
$ sudo apt install python3-venv build-essential

Install rust compiler See rust-lang.org/tools/install for details.

$ curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
$ source "$HOME/.cargo/env"

Create venv and install eozin

$ python3 -m venv env
$ source env/bin/activate
$ pip install -e .

Python APIs

Eozin read_region method, and properties such as level_count, level_dimensions, and dimensions are intended to mimic OpenSlide's methods and properties.

class Eozin:
    level_count: int
    level_dimensions: list[tuple[int, int]]
    dimensions: tuple[int, int]
    level_tile_sizes: list[tuple[int, int]]

    def __new__(path: str) -> Eozin:
    def read_region(location: tuple[int, int], level: int, size: tuple[int, int]) -> PIL.Image.Image:
    def read_tile(level: int, x: int, y: int) -> PIL.Image.Image:

Usages

from eozinpy import Eozin

e = Eozin("/path/to/digital_pathology/file")
print(e.level_count)
location = (100, 200)
level = 0
size = (200, 150)
img = e.read_region(location, level, size)
img.save()  # img is an instance of Pillow Image