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Handle Leica Matrix Screener experiment images

Project description

leicaimage

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Handle Leica Matrix Screener experiment images

The leicaimage library is a modified version of the leicaexperiment library, and was built as a drop in replacement for that library but without any xml or image processing. This also makes leicaimage work without heavy dependencies.

Overview

This is a python module for interfacing with Leica LAS AF/X Matrix Screener experiments.

The module can be used to:

  • Programmatically select slides/wells/fields/images given by attributes like:
    • slide (S)
    • well position (U, V)
    • field position (X, Y)
    • z-stack position (Z)
    • channel (C)

Features

  • Access experiment as a python object

Installation

Python 3.6+ is required. Install using pip:

pip install leicaimage

Examples

Access all images

from leicaimage import Experiment

experiment = Experiment('path/to/experiment--')

for image in experiment.images:
    ...

Access specific wells/fields

from leicaimage import Experiment

experiment = Experiment('path/to/experiment--')

# on images in well --U00--V00
for well in experiment.well_images(0, 0):
    ...

Extract attributes from file names

from leicaimage import attribute

# get all channels
channels = [attribute(image, 'C') for image in experiment.images]
min_ch, max_ch = min(channels), max(channels)

Development

Install dependencies and link development version of leicaimage to pip:

git clone https://github.com/MartinHjelmare/leicaimage.git
cd leicaimage
pip install -r requirements_dev.txt

Run tests

tox

Project details


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