Metadata-Version: 2.1
Name: cellfinder-napari
Version: 0.0.12rc0
Summary: Efficient cell detection in large images
Home-page: https://cellfinder.info
Author: Adam Tyson
Author-email: code@adamltyson.com
License: GPL-3.0
Project-URL: Source Code, https://github.com/brainglobe/cellfinder-napari
Project-URL: Bug Tracker, https://github.com/brainglobe/cellfinder-napari-issues
Project-URL: Documentation, https://docs.brainglobe.info/cellfinder-napari/
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Framework :: napari
Classifier: Topic :: Software Development :: Testing
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Operating System :: OS Independent
Classifier: License :: OSI Approved :: BSD License
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Provides-Extra: dev
License-File: LICENSE

# cellfinder-napari

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[![Website](https://img.shields.io/website?up_message=online&url=https%3A%2F%2Fcellfinder.info)](https://cellfinder.info)
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### Efficient cell detection in large images (e.g. whole mouse brain images)

This package implements the cell detection algorithm from 
[Tyson, Rousseau & Niedworok et al. (2021)](https://www.biorxiv.org/content/10.1101/2020.10.21.348771v2) 
for [napari](https://napari.org/index.html), based on the 
[cellfinder-core](https://github.com/brainglobe/cellfinder-core) package.

This algorithm can also be used within the original 
[cellfinder](https://github.com/brainglobe/cellfinder) software for 
whole-brain microscopy analysis.

----
![raw](https://raw.githubusercontent.com/brainglobe/cellfinder-napari/master/resources/cellfinder-napari.gif)

**Visualising detected cells in the cellfinder napari plugin**

----
## Instructions

### Installation
Once you have [installed napari](https://napari.org/index.html#installation). 
You can install napari either through the napari plugin installation tool, or 
directly from PyPI with:
```bash
pip install cellfinder-napari
```

### Usage
Full documentation can be 
found [here](https://docs.brainglobe.info/cellfinder-napari). 
 
This software is at a very early stage, and was written with our data in mind. 
Over time we hope to support other data types/formats. If you have any 
questions or issues, please get in touch by 
[email](mailto:code@adamltyson.com?subject=cellfinder-napari), 
[on the forum](https://forum.image.sc/tag/brainglobe) or by 
[raising an issue](https://github.com/brainglobe/cellfinder-napari/issues).


---
## Illustration

### Introduction
cellfinder takes a stitched, but otherwise raw dataset with at least 
two channels:
 * Background channel (i.e. autofluorescence)
 * Signal channel, the one with the cells to be detected:
 
![raw](https://raw.githubusercontent.com/brainglobe/cellfinder/master/resources/raw.png)
**Raw coronal serial two-photon mouse brain image showing labelled cells**


### Cell candidate detection
Classical image analysis (e.g. filters, thresholding) is used to find 
cell-like objects (with false positives):

![raw](https://raw.githubusercontent.com/brainglobe/cellfinder/master/resources/detect.png)
**Candidate cells (including many artefacts)**


### Cell candidate classification
A deep-learning network (ResNet) is used to classify cell candidates as true 
cells or artefacts:

![raw](https://raw.githubusercontent.com/brainglobe/cellfinder/master/resources/classify.png)
**Cassified cell candidates. Yellow - cells, Blue - artefacts**

## Citing cellfinder

If you find this plugin useful, and use it in your research, please cite the preprint outlining the cell detection algorithm:
> Tyson, A. L., Rousseau, C. V., Niedworok, C. J., Keshavarzi, S., Tsitoura, C., Cossell, L., Strom, M. and Margrie, T. W. (2021) “A deep learning algorithm for 3D cell detection in whole mouse brain image datasets’ PLOS Computational Biology, 17(5), e1009074
[https://doi.org/10.1371/journal.pcbi.1009074](https://doi.org/10.1371/journal.pcbi.1009074)


**If you use this, or any other tools in the brainglobe suite, please
 [let us know](mailto:code@adamltyson.com?subject=cellfinder-napari), and 
 we'd be happy to promote your paper/talk etc.**


