leicaimage
Source Code: https://github.com/MartinHjelmare/leicaimage
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)
Installation
Install this via pip (or your favourite package manager):
pip install leicaimage
Usage
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)
Credits
This package was created with Copier and the browniebroke/pypackage-template project template.
1 maintainer
Metadata
1 maintainer
Release files for leicaimage 0.6.0
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