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

Open-source software for exploring and analyzing large, high-dimensional image-derived data.
https://github.com/CellProfiler/CellProfiler-Analyst

cellprofiler cellprofiler-analyst image-analysis machine-learning

Last synced: 28 days ago
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Open-source software for exploring and analyzing large, high-dimensional image-derived data.

• Host: GitHub
• URL: https://github.com/CellProfiler/CellProfiler-Analyst
• Owner: CellProfiler
• License: other
• Created: 2011-11-10T18:57:45.000Z (about 13 years ago)
• Default Branch: master
• Last Pushed: 2024-08-15T22:51:06.000Z (4 months ago)
• Last Synced: 2024-09-14T02:32:48.612Z (3 months ago)
• Topics: cellprofiler, cellprofiler-analyst, image-analysis, machine-learning
• Language: Python
• Homepage: http://cellprofileranalyst.org
• Size: 70.7 MB
• Stars: 144
• Watchers: 21
• Forks: 73
• Open Issues: 75
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• awesome-biological-image-analysis - CellProfiler Analyst - Open-source software for exploring and analyzing large, high-dimensional image-derived data. (General image analysis software)

README

        


  





-----------------


|  **`Version`**  |  **`Documentation`** | **`Forum`** |

|---------------|----------------|-----------------|

| [![Build Status](https://img.shields.io/badge/version-3.0.4-green.svg)](https://cellprofileranalyst.org/releases) | [![Build Status](https://img.shields.io/badge/documentation-3.0-brightgreen.svg)](https://cellprofiler-manual.s3.amazonaws.com/CellProfiler-Analyst-3.0.0/index.html) | [![Build Status](https://img.shields.io/badge/forum-CPA-blue.svg)](https://forum.image.sc/tag/cellprofiler-analyst) |

**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.



  





## Learn more about CellProfiler Analyst

This is the developer site for CellProfiler Analyst. 

The regular home page for CellProfiler Analyst is here: https://cellprofileranalyst.org/

## Installation

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

When running from source, 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

* Python-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*


__[CellProfiler Analyst: data exploration and analysis software for complex image-based screens][bmc]__


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, David Stirling, Pearl Ryder, Beth Cimini, 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 2021, The Broad Institute of MIT and Harvard.

Distributed under the BSD license.*