# leicaimage
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---
**Source Code**: <a href="https://github.com/MartinHjelmare/leicaimage" target="_blank">https://github.com/MartinHjelmare/leicaimage </a>
---
Handle Leica Matrix Screener experiment images.
The leicaimage library is a modified version of the
[leicaexperiment](https://github.com/arve0/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
```python
from leicaimage import Experiment
experiment = Experiment('path/to/experiment--')
for image in experiment.images:
...
```
### Access specific wells/fields
```python
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
```python
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](https://copier.readthedocs.io/) and the
[browniebroke/pypackage-template](https://github.com/browniebroke/pypackage-template)
project template.
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"description": "# leicaimage\n\n<p align=\"center\">\n <a href=\"https://github.com/MartinHjelmare/leicaimage/actions/workflows/ci.yml?query=branch%3Amain\">\n <img src=\"https://img.shields.io/github/actions/workflow/status/MartinHjelmare/leicaimage/ci.yml?branch=main&label=CI&logo=github&style=flat-square\" alt=\"CI Status\" >\n </a>\n <a href=\"https://codecov.io/gh/MartinHjelmare/leicaimage\">\n <img src=\"https://img.shields.io/codecov/c/github/MartinHjelmare/leicaimage.svg?logo=codecov&logoColor=fff&style=flat-square\" alt=\"Test coverage percentage\">\n </a>\n</p>\n<p align=\"center\">\n <a href=\"https://python-poetry.org/\">\n <img src=\"https://img.shields.io/endpoint?url=https://python-poetry.org/badge/v0.json\" alt=\"Poetry\">\n </a>\n <a href=\"https://github.com/astral-sh/ruff\">\n <img src=\"https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json\" alt=\"Ruff\">\n </a>\n <a href=\"https://github.com/pre-commit/pre-commit\">\n <img src=\"https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white&style=flat-square\" alt=\"pre-commit\">\n </a>\n</p>\n<p align=\"center\">\n <a href=\"https://pypi.org/project/leicaimage/\">\n <img src=\"https://img.shields.io/pypi/v/leicaimage.svg?logo=python&logoColor=fff&style=flat-square\" alt=\"PyPI Version\">\n </a>\n <img src=\"https://img.shields.io/pypi/pyversions/leicaimage.svg?style=flat-square&logo=python&logoColor=fff\" alt=\"Supported Python versions\">\n <img src=\"https://img.shields.io/pypi/l/leicaimage.svg?style=flat-square\" alt=\"License\">\n</p>\n\n---\n\n**Source Code**: <a href=\"https://github.com/MartinHjelmare/leicaimage\" target=\"_blank\">https://github.com/MartinHjelmare/leicaimage </a>\n\n---\n\nHandle Leica Matrix Screener experiment images.\n\nThe leicaimage library is a modified version of the\n[leicaexperiment](https://github.com/arve0/leicaexperiment) library,\nand was built as a drop in replacement for that library but without any xml\nor image processing. This also makes leicaimage work without heavy dependencies.\n\n## Overview\n\nThis is a python module for interfacing with _Leica LAS AF/X Matrix Screener_\nexperiments.\n\nThe module can be used to:\n\n- Programmatically select slides/wells/fields/images given by attributes like:\n - slide (S)\n - well position (U, V)\n - field position (X, Y)\n - z-stack position (Z)\n - channel (C)\n\n## Installation\n\nInstall this via pip (or your favourite package manager):\n\n`pip install leicaimage`\n\n## Usage\n\n### Access all images\n\n```python\nfrom leicaimage import Experiment\n\nexperiment = Experiment('path/to/experiment--')\n\nfor image in experiment.images:\n ...\n```\n\n### Access specific wells/fields\n\n```python\nfrom leicaimage import Experiment\n\nexperiment = Experiment('path/to/experiment--')\n\n# on images in well --U00--V00\nfor well in experiment.well_images(0, 0):\n ...\n```\n\n### Extract attributes from file names\n\n```python\nfrom leicaimage import attribute\n\n# get all channels\nchannels = [attribute(image, 'C') for image in experiment.images]\nmin_ch, max_ch = min(channels), max(channels)\n```\n\n## Credits\n\nThis package was created with\n[Copier](https://copier.readthedocs.io/) and the\n[browniebroke/pypackage-template](https://github.com/browniebroke/pypackage-template)\nproject template.\n\n",
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