CellProfiler is free,

open-source Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use the source code, design documents, or content of the product. The open-source model is a decentralized sof ...

software designed to enable biologists without training in computer vision or programming to quantitatively measure

phenotype In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology or physical form and structure, its developmental processes, its biochemical and physiological prop ...

s from thousands of images automatically. Advanced algorithms for image analysis are available as individual modules that can be placed in sequential order together to form a pipeline; the pipeline is then used to identify and measure biological objects and features in images, particularly those obtained through

fluorescence microscopy A fluorescence microscope is an optical microscope that uses fluorescence instead of, or in addition to, scattering, reflection, and attenuation or absorption, to study the properties of organic or inorganic substances. "Fluorescence micr ...

. Distributions are available for Microsoft Windows,

macOS macOS (; previously OS X and originally Mac OS X) is a Unix operating system developed and marketed by Apple Inc. since 2001. It is the primary operating system for Apple's Mac (computer), Mac computers. Within the market of ...

, and

Linux Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which i ...

. The

source code In computing, source code, or simply code, is any collection of code, with or without comment (computer programming), comments, written using a human-readable programming language, usually as plain text. The source code of a Computer program, p ...

for CellProfiler is freely available. CellProfiler is developed by the Broad Institute's Imaging Platform.

Features

CellProfiler can read and analyze most common microscopy image formats. Biologists typically use CellProfiler to identify objects of interest (e.g. cells, colonies, ''C. elegans'' worms) and then measure their properties of interest. Specialized modules for illumination correction may be applied as pre-processing step to remove distortions due to uneven lighting. Object identification ( segmentation) is performed through machine learning or image thresholding, recognition and division of clumped objects, and removal or merging of objects on the basis of size or shape. Each of these steps are customizable by the user for their unique image assay. A wide variety of measurements can be generated for each identified cell or subcellular compartment, including

morphology Morphology, from the Greek and meaning "study of shape", may refer to: Disciplines *Morphology (archaeology), study of the shapes or forms of artifacts *Morphology (astronomy), study of the shape of astronomical objects such as nebulae, galaxies, ...

, intensity, and

texture Texture may refer to: Science and technology * Surface texture, the texture means smoothness, roughness, or bumpiness of the surface of an object * Texture (roads), road surface characteristics with waves shorter than road roughness * Texture ...

among others. These measurements are accessible by using built-in viewing and plotting data tools, exporting in a comma-delimited

spreadsheet A spreadsheet is a computer application for computation, organization, analysis and storage of data in tabular form. Spreadsheets were developed as computerized analogs of paper accounting worksheets. The program operates on data entered in ce ...

format, or importing into a

MySQL MySQL () is an open-source relational database management system (RDBMS). Its name is a combination of "My", the name of co-founder Michael Widenius's daughter My, and "SQL", the acronym for Structured Query Language. A relational database ...

SQLite SQLite (, ) is a database engine written in the C programming language. It is not a standalone app; rather, it is a library that software developers embed in their apps. As such, it belongs to the family of embedded databases. It is the mo ...

database. CellProfiler interfaces with the high-performance scientific libraries NumPy and SciPy for many mathematical operations, the Open Microscopy Environment Consortium’s Bio-Formats library for reading more than 100 image file formats,

ImageJ ImageJ is a Java-based image processing program developed at the National Institutes of Health and the Laboratory for Optical and Computational Instrumentation (LOCI, University of Wisconsin). Its first version, ImageJ 1.x, is developed in the publ ...

for use of plugins and macros, and ilastik for pixel-based classification. While designed and optimized for large numbers of two-dimensional images (the most common high-content screening image format), CellProfiler supports analysis of small-scale experiments and

time-lapse Time-lapse photography is a technique in which the frequency at which film frames are captured (the frame rate) is much lower than the frequency used to view the sequence. When played at normal speed, time appears to be moving faster and thu ...

movies.

History

CellProfiler was released in December 2005 by scientists from the

Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical Research is a non-profit research institute located in Cambridge, Massachusetts, United States that is dedicated to improving human health through basic biomedical research. It was founded as a fiscally indepen ...

and

Massachusetts Institute of Technology The Massachusetts Institute of Technology (MIT) is a Private university, private Land-grant university, land-grant research university in Cambridge, Massachusetts. Established in 1861, MIT has played a key role in the development of modern t ...

. It is currently developed and maintained by the Cimini Lab at the Imaging Platform of the

Broad Institute The Eli and Edythe L. Broad Institute of MIT and Harvard (IPA: , pronunciation respelling: ), often referred to as the Broad Institute, is a biomedical and genomic research center located in Cambridge, Massachusetts, United States. The institu ...

. Originally developed in

MATLAB MATLAB (an abbreviation of "MATrix LABoratory") is a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks. MATLAB allows matrix manipulations, plotting of functions and data, implementa ...

, it was re-written in Python and released as CellProfiler 2.0 in 2010. Version 3.0, supporting volumetric analysis of 3D image stacks and optional deep learning modules, was released in October 2017. CellProfiler 4.0 was released in September 2020 and focused on speed, usability, and utility improvements with most notable example of migration to Python 3.

Community

Because CellProfiler is a free,

project, anyone can develop their own image processing

algorithm In mathematics and computer science, an algorithm () is a finite sequence of rigorous instructions, typically used to solve a class of specific problems or to perform a computation. Algorithms are used as specifications for performing ...

s as a new module for CellProfiler and contribute it to the project. The CellProfiler website contains a forum for discussion where new users can have their questions answered, usually by the creators of the project.

References

External links

* {{DEFAULTSORT:Cellprofiler Microscopy Cell biology Free software programmed in Python