Metadata-Version: 2.1
Name: hnccorr
Version: 2019.6.1
Summary: HNCcorr algorithm for cell detection in calcium-imaging.
Home-page: https://github.com/hochbaumGroup/HNCcorr
Author: Quico Spaen
Author-email: qspaen@berkeley.edu
License: Non-commercial license. Not an open-source license.
Description: # HNCcorr
        
        **2019/06/25 the HNCcorr software is currently being updated. The missing parts will be completey in the next few days.**
        
        The HNCcorr algorithm identifies cell bodies in two-photon calcium imaging movies. We provide a Python 3 (recommended) implementation as well as a Matlab implementation. The software is freely available for non-commercial use (see license for details).
        
        The HNCcorr algorithm is described in detail in our [eNeuro paper](http://www.eneuro.org/content/6/2/ENEURO.0304-18.2019):
        
        Spaen, Q., Asín-Achá, R., Chettih, S. N., Minderer, M., Harvey, C., and Hochbaum, D. S. (2019). HNCcorr: A novel combinatorial approach for cell identification in calcium-imaging movies. eNeuro, 6(2).
        
        ### Example (Python)
        ```python
        from hnccorr import HNCcorr, Movie
        from hnccorr.example import load_example_data
        
        movie = Movie(
            "Example movie", load_example_data()  # downloads sample Neurofinder dataset
        )
        H = HNCcorr.from_config()  # Initialize HNCcorr with default configuration
        H.segment(movie)
        
        H.segmentations  # List of identified cells
        H.segmentations_to_list()  # Export list of cells (for Neurofinder)
        ```
        
        ## Installation Instructions (Python 3)
        You can install HNCcorr directly from the Python Package Index with pip:
        ```bash
        pip install hnccorr
        ```
        Or you can install your local copy by executing the following command from the main directory:
        ```bash
        pip install .
        ```
        
        On Windows you may need to install a [C-compiler for Python](https://wiki.python.org/moin/WindowsCompilers).
        
        ## Installation Instructions (Matlab)
        The Matlab implementation was used to generate the results in the eNeuro manuscript and is now superseded by the Python implementation. The Matlab implementation is available in the `matlab` folder. See the README file in this folder for instructions.
        
        ## Documentation
        The documentation is hosted at [ReadTheDocs](TBD).
        
        ## Hyperparameters
        TO DO
        
        ## Tests
        The tests for HNCcorr use the `pytest` package. You can execute them with the `pytest` command in the main directory.
        
Keywords: Cell detection,Neuroscience,Calcium imaging
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python :: 3
Description-Content-Type: text/markdown
