Metadata-Version: 2.1
Name: leicaimage
Version: 0.2.0
Summary: Handle Leica Matrix Screener experiment images
Home-page: https://github.com/MartinHjelmare/leicaimage
Author: Martin Hjelmare
Author-email: marhje52@gmail.com
License: MIT
Download-URL: https://github.com/MartinHjelmare/leicaimage/archive/master.zip
Description: # leicaimage
        
        [![build-status-image]][travis]
        
        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)
        
        ## Features
        
        - Access experiment as a python object
        
        ## Installation
        
        Python 3.6+ is required. Install using `pip`:
        
        ```bash
        pip install leicaimage
        ```
        
        ## Examples
        
        ### 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)
        ```
        
        ## Development
        
        Install dependencies and link development version of leicaimage to pip:
        
        ```bash
        git clone https://github.com/MartinHjelmare/leicaimage.git
        cd leicaimage
        pip install -r requirements_dev.txt
        ```
        
        ### Run tests
        
        ```bash
        tox
        ```
        
        [build-status-image]: https://travis-ci.com/MartinHjelmare/leicaimage.svg?branch=master
        [travis]: https://travis-ci.com/MartinHjelmare/leicaimage
        
Keywords: leicaimage
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.6
Description-Content-Type: text/markdown
