CellProfiler
Encyclopedia
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. 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
.
Distributions are available for for Microsoft Windows
, Mac OS
, Mac OS X
, and Linux
. The source code for CellProfiler is freely available. CellProfiler is developed by the Broad Institute's
Imaging Platform.
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
, intensity, and texture
among others. These measurements are accessible by using built-in viewing and plotting data tools, exporting in a comma-delimited
spreadsheet
format or imported into a MySQL
or SQLite
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
for use of plugins and macros, and ilastik for pixel-based classification. While designed and optimized for two-dimensional images (the most common high-content screening image format), CellProfiler supports analysis of small-scale experiments and time-lapse
movies.
. It is currently developed and maintained by the Carpenter Lab http://www.broadinstitute.org/~anne/ at the Imaging Platform of the Broad Institute
.
Originally developed in MATLAB
, it was re-written in Python
and released as CellProfiler 2.0 in 2010.
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.
Phenotype
A phenotype is an organism's observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior...
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
Pipeline
-Science and industry:* Pipeline transport, a conduit made from pipes connected end-to-end for long-distance fluid transport* Plastic Pressure Pipe Systems, for fluid handling* Milking pipeline, used on a dairy farm to transport fluid milk...
; the pipeline is then used to identify and measure
biological objects and features in images, particularly those obtained through fluorescence microscopy
Fluorescence microscope
A fluorescence microscope is an optical microscope used to study properties of organic or inorganic substances using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption...
.
Distributions are available for for Microsoft Windows
Microsoft Windows
Microsoft Windows is a series of operating systems produced by Microsoft.Microsoft introduced an operating environment named Windows on November 20, 1985 as an add-on to MS-DOS in response to the growing interest in graphical user interfaces . Microsoft Windows came to dominate the world's personal...
, Mac OS
Mac OS
Mac OS is a series of graphical user interface-based operating systems developed by Apple Inc. for their Macintosh line of computer systems. The Macintosh user experience is credited with popularizing the graphical user interface...
, Mac OS X
Mac OS X
Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...
, and Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...
. The source code for CellProfiler is freely available. CellProfiler is developed by the Broad Institute's
Broad Institute
The Broad Institute is a genomic medicine research center located in Cambridge, Massachusetts, United States. Although it is independently governed and supported as a 501 nonprofit research organization, the institute is formally affiliated with the Massachusetts Institute of Technology, Harvard...
Imaging Platform.
Features
CellProfiler can read and analyze most common microscopy image formats. Biologgists typically use CellProfiler to identify objects of interest (e.g. cells, colonies, C. elegansCaenorhabditis elegans
Caenorhabditis elegans is a free-living, transparent nematode , about 1 mm in length, which lives in temperate soil environments. Research into the molecular and developmental biology of C. elegans was begun in 1974 by Sydney Brenner and it has since been used extensively as a model...
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
Segmentation (image processing)
In computer vision, segmentation refers to the process of partitioning a digital image into multiple segments . The goal of segmentation is to simplify and/or change the representation of an image into something that is more meaningful and easier to analyze...
) is performed through machine learning or image thresholding
Thresholding (image processing)
Thresholding is the simplest method of image segmentation. From a grayscale image, thresholding can be used to create binary images Thresholding is the simplest method of image segmentation. From a grayscale image, thresholding can be used to create binary images Thresholding is the simplest method...
, 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 (biology)
In biology, morphology is a branch of bioscience dealing with the study of the form and structure of organisms and their specific structural features....
, intensity, and texture
Texture (visual arts)
In the visual arts, texture is the perceived surface quality of a work of art. It is an element of two-dimensional and three-dimensional design and is distinguished by its perceived visual and physical properties...
among others. These measurements are accessible by using built-in viewing and plotting data tools, exporting in a comma-delimited
Comma-separated values
A comma-separated values file stores tabular data in plain-text form. As a result, such a file is easily human-readable ....
spreadsheet
Spreadsheet
A spreadsheet is a computer application that simulates a paper accounting worksheet. It displays multiple cells usually in a two-dimensional matrix or grid consisting of rows and columns. Each cell contains alphanumeric text, numeric values or formulas...
format or imported into a MySQL
MySQL
MySQL officially, but also commonly "My Sequel") is a relational database management system that runs as a server providing multi-user access to a number of databases. It is named after developer Michael Widenius' daughter, My...
or SQLite
SQLite
SQLite is an ACID-compliant embedded relational database management system contained in a relatively small C programming library. The source code for SQLite is in the public domain and implements most of the SQL standard...
database.
CellProfiler interfaces with the high-performance scientific libraries NumPy and SciPy
SciPy
SciPy is an open source library of algorithms and mathematical tools for the Python programming language.SciPy contains modules for optimization, linear algebra, integration, interpolation, special functions, FFT, signal and image processing, ODE solvers and other tasks common in science and...
for many mathematical operations, the Open Microscopy Environment Consortium’s Bio-Formats library for reading more than 100 image file formats, ImageJ
ImageJ
ImageJ is a public domain, Java-based image processing program developed at the National Institutes of Health. ImageJ was designed with an open architecture that provides extensibility via Java plugins and recordable macros. Custom acquisition, analysis and processing plugins can be developed using...
for use of plugins and macros, and ilastik for pixel-based classification. While designed and optimized for two-dimensional images (the most common high-content screening image format), CellProfiler supports analysis of small-scale experiments and time-lapse
Time-lapse microscopy
Time-lapse microscopy is microscopy in which the same object is photographed at regular time intervals over several hours....
movies.
History
CellProfiler was released in December 2005 by scientists from the Whitehead Institute for Biomedical Research and Massachusetts Institute of TechnologyMassachusetts Institute of Technology
The Massachusetts Institute of Technology is a private research university located in Cambridge, Massachusetts. MIT has five schools and one college, containing a total of 32 academic departments, with a strong emphasis on scientific and technological education and research.Founded in 1861 in...
. It is currently developed and maintained by the Carpenter Lab http://www.broadinstitute.org/~anne/ at the Imaging Platform of the Broad Institute
Broad Institute
The Broad Institute is a genomic medicine research center located in Cambridge, Massachusetts, United States. Although it is independently governed and supported as a 501 nonprofit research organization, the institute is formally affiliated with the Massachusetts Institute of Technology, Harvard...
.
Originally developed in MATLAB
MATLAB
MATLAB is a numerical computing environment and fourth-generation programming language. Developed by MathWorks, MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages,...
, it was re-written in Python
Python (programming language)
Python is a general-purpose, high-level programming language whose design philosophy emphasizes code readability. Python claims to "[combine] remarkable power with very clear syntax", and its standard library is large and comprehensive...
and released as CellProfiler 2.0 in 2010.
Community
Because CellProfiler is a free, open-source project, anyone can develop their own image processing algorithmAlgorithm
In mathematics and computer science, an algorithm is an effective method expressed as a finite list of well-defined instructions for calculating a function. Algorithms are used for calculation, data processing, and automated reasoning...
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.