Software Interfaces

Software for analyzing CellProfiler-produced data

SoftwareDescriptionInterface

CellProfiler		 CellProfiler is free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. CellProfiler has built-in tools in the Data Tools menu in the main window to generate a few types of plots using data from a CellProfiler output file.

CellProfiler Analyst		 CellProfiler Analyst allows analysis, exploration and machine-learning of data produced by CellProfiler that has been deposited into a comma-delimited file (.csv), or a MySQL or SQLite database. CellProfiler Analyst can be used with image-based screening data that follows a simple format: One image table with rows of images and columns of data and one object table with rows of objects (e.g., cells) and columns of data. CellProfiler's ExportToDatabase module or data tool produces tables in the proper format.

Excel
Calc
 Spreadsheet programs like these are useful for plotting small amounts of data. Excel is a commercial program (Microsoft), whereas Calc (OpenOffice) is open-source and freely-available. Comma- or tab-delimited files can be generated by the CellProfiler ExportToSpreadsheet module or data tool. Note that Excel is limited to 256 columns and ~65,536 rows of data.

R
Python
Any analysis or visualization tools that can query a database (such as R or python+pylab) can be used to analyze data that has been deposited into a MySQL database. Databases containing image and/or object data can be produced using the CellProfiler ExportToDatabase module or data tool.

FCS Express Image Cytometry		 FCS Express 4 Image Cytometry (De Novo Software) applies population based analytical tools common in flow cytometry to image cytometry. The package allows the user to review and analyze the multi-parametric data sets and relate results back to the original images for confirmation of results in a Microsoft Office style user interface with a wide range of analytical and reporting capabilities. FCS Express 4 software can import comma-delimited files produced by the CellProfiler ExportToSpreadsheet module or data tool.

GenePattern		 GenePattern (Broad Institute) puts sophisticated computational methods into the hands of the biomedical research community. A simple application interface gives a broad audience access to a growing repository of analytic tools for genomic data, while an API supports computational biologists. CellProfiler can format and export image-based data as a GenePattern GCT file (.gct) through the ExportToSpreadsheet module or data tool.

KNIME		 KNIME (University of Konstanz) is a modular data exploration platform that enables the user to visually create data flows, selectively execute some or all analysis steps, and later investigate the results through interactive views on data and models. The HC/DC platform includes a CellProfiler Reader node for import of per-well values.

MATLAB		 MATLAB (Mathworks) is a high-level language and interactive environment for data analysis and visualization. MATLAB can be used to directly analyze the data in a CellProfiler output file.

Spotfire		 Spotfire (TIBCO) is a comprehensive software platform that allows researchers to analyze data, using predictive and complex statistics in the analysis. SpotFire is able to import tab-delimited files of data generated by the CellProfiler ExportToSpreadsheet (for small data sets) or ExportToDatabase modules or data tools (for large data sets).

Software Partnerships

CellProfiler has partnered with academic and commercial groups to create a variety of software interfaces. These efforts not only expand the functionality of CellProfiler and CellProfiler Analyst but also leverage the strengths of other packages.

SoftwareDescriptionInterface

BioFormats		 Bio-Formats is a standalone Java library for reading and writing microscopy file formats. The primary goal of Bio-Formats is to facilitate the exchange of microscopy data between both different software packages and different organizations, by converting proprietary microscopy data into the OME data model standard. CellProfiler 2.0 is packaged with Bio-Formats and uses it to read/write images from disk, as well as write movies

Ilastik		 Ilastik is a tool for pixel-based classification of 2,3 and 4D images. The user first trains a classifier by identifying areas of images that fall into one of several classes, such as cell body, nucleus, background or membrane. The classifier can then be applied to those and similar images to identify areas in those images that correspond to the trained classes. Ilastik can save a user's classifier to a file; CellProfiler will read a classifier file and apply its classifiers to an image using the ClassifyPixels module to produce a probability map: an image whose intensity is higher for parts of images that are likely to be the chosen class.

ImageJ		 ImageJ is a public domain image processing program providing extensibility via Java plugins and recordable macros. Custom acquisition, analysis and processing plugins can be developed using a built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems. CellProfiler can load images for processing into ImageJ, run a macro and retrieve the results for downstream analysis via the RunImageJ module.

Open Microscopy Environment (OME)		 OMERO is a Java Enterprise application for visualization, management, and analysis of biological image data. The software consists of the OMERO server which can be accessed by a number of different clients. The OMERO clients allow the scientist to remotely manage, view, annotate and measure multi-dimensional images from anywhere. OMERO can also be extended to support data analysis.

In progress: CellProfiler will provide modules for importing and exporting of images and image data directly to an OMERO server.
OME currently has a module which runs the CellProfiler 1.0 engine to retrieve images for processing and uploads measurements and generated images back to the OMERO server; a similar bridge is in development for CellProfiler 2.0.

iBrain
openBIS
OpenBIS is a data management framework to track and annotate raw data for screening, proteomics, FACS and deep sequencing data. iBRAIN is a platform for performing image analysis on large datasets automatically. The SyBIT project, part of SystemsX, delivers integrated analysis pipelines that use CellProfiler as a building block. SyBIT has developed automated workflows for data exchange and analysis based on the openBIS database, CellProfiler, and iBRAIN, using cluster infrastructures for data processing. The project continues to tailor these workflows to suit the research needs of several systems biology projects.