# CellProfiler-Analyst

**Repository Path**: philloidin/CellProfiler-Analyst

## Basic Information

- **Project Name**: CellProfiler-Analyst
- **Description**: Open-source software for exploring and analyzing large, high-dimensional image-derived data. 
- **Primary Language**: Unknown
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2021-08-26
- **Last Updated**: 2025-01-03

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

<div align="center">
  <img src="http://i.imgur.com/TmujaUa.png"><br><br>
</div>
-----------------

|  **`Version`**  |  **`Documentation`** | **`Forum`** |
|---------------|----------------|-----------------|
| [![Build Status](https://img.shields.io/badge/version-2.2.1-green.svg)](http://cellprofiler.org/releases) | [![Build Status](https://img.shields.io/badge/documentation-2.2.1-brightgreen.svg)](http://cellprofiler.org/CPA/) | [![Build Status](https://img.shields.io/badge/forum-CPA-blue.svg)](http://forum.cellprofiler.org/) |

**CellProfiler Analyst** allows interactive exploration and analysis of data,
particularly from high-throughput, image-based experiments. Included is a
supervised machine learning system which can be trained to recognize complex
and subtle phenotypes, for automatic scoring of millions of cells.

<div align="center">
  <img src="http://i.imgur.com/j12EQH5.png"><br><br>
</div>

## Installation

Download [CellProfiler Analyst](https://cellprofileranalyst.org/releases)

CellProfiler Analyst requires [JDK 1.8](http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html) to be installed (not just JRE).
Check the Java path.

Please note that this is the development branch of CPA and it will be updated on regular basis. 

Find all releases [here](https://cellprofileranalyst.org/previously-released-versions-cellprofiler-analyst).

For a head start, download example dataset here: [Example Dataset for CPA (zipped)](http://d1zymp9ayga15t.cloudfront.net/content/Examplezips/cpa_2.0_example.zip)

## Developer build

Building CPA on your machine requires CellProfiler dependencies. Check the wiki
for more detailed installation instructions.

* Pandas
* Seaborn
* Scikit-learn
* Javabridge
* Verlib
* Python-bioformats

## Documentation

> https://cellprofileranalyst.org/manuals

## Wiki

> https://github.com/CellProfiler/CellProfiler-Analyst/wiki

## Forum

CellProfiler Analyst development is discussed on the CellProfiler Forum
list.  

> https://forum.image.sc/tag/cellprofiler-analyst/

## How to file new issues

Please attach sufficient information to reproduce the bug. For many
bugs, it is appropriate to attach a properties file, a training set,
or a screenshot.

## How to cite

*David Dao, Adam N Fraser, Jane Hung, Vebjorn Ljosa, Shantanu Singh and Anne E Carpenter*  
__[CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets][bioinformatics]__  
Bioinformatics (2016) doi:10.1093/bioinformatics/btw390

*Thouis R Jones, In Han Kang, Douglas B Wheeler, Robert A Lindquist, Adam Papallo, David M Sabatini, Polina Golland and Anne E Carpenter*<br>
__[CellProfiler Analyst: data exploration and analysis software for complex image-based screens][bmc]__<br>
BMC Bioinformatics (2008) doi:10.1186/1471-2105-9-482


[bioinformatics]: http://bioinformatics.oxfordjournals.org/content/early/2016/07/24/bioinformatics.btw390
[bmc]: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-482


## Contributors

David Dao, Adam Fraser, Vebjorn Ljosa, Thouis R. Jones, Jane Hung, Shantanu Singh, Mark Bray, Lee Kamentsky, Anne Carpenter

## Kudos

David Logan, Allen Goodman, Alison Kozol, Mohammad Hossein Rohban

*Copyright 2016, The Broad Institute of MIT and Harvard.
Distributed under the BSD license.*