CellCognition is a free
open-source computational framework for quantitative analysis of high-throughput
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 microscop ...
(
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 thus ...
) images in the field of
bioimage informatics Bioimage informatics is a subfield of bioinformatics and computational biology. It focuses on the use of computational techniques to analyze bioimages, especially cellular and molecular images, at large scale and high throughput. The goal is to o ...
and systems microscopy. The CellCognition framework uses
image processing,
computer vision and
machine learning
Machine learning (ML) is a field of inquiry devoted to understanding and building methods that 'learn', that is, methods that leverage data to improve performance on some set of tasks. It is seen as a part of artificial intelligence.
Machine ...
techniques for single-cell tracking and classification of cell morphologies. This enables measurements of temporal progression of cell phases, modeling of cellular dynamics and generation of
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 pr ...
map.
Features
CellCognition uses a computational pipeline which includes
image segmentation
In digital image processing and computer vision, image segmentation is the process of partitioning a digital image into multiple image segments, also known as image regions or image objects ( sets of pixels). The goal of segmentation is to simpli ...
,
object detection
Object detection is a computer technology related to computer vision and image processing that deals with detecting instances of semantic objects of a certain class (such as humans, buildings, or cars) in digital images and videos. Well-researched ...
,
feature extraction
In machine learning, pattern recognition, and image processing, feature extraction starts from an initial set of measured data and builds derived values (features) intended to be informative and non-redundant, facilitating the subsequent learning a ...
,
statistical classification
In statistics, classification is the problem of identifying which of a set of categories (sub-populations) an observation (or observations) belongs to. Examples are assigning a given email to the "spam" or "non-spam" class, and assigning a diagn ...
,
tracking
Tracking may refer to:
Science and technology Computing
* Tracking, in computer graphics, in match moving (insertion of graphics into footage)
* Tracking, composing music with music tracker software
* Eye tracking, measuring the position of t ...
of individual cells over time, detection of class-transition motifs (e.g. cells entering mitosis), and
HMM correction of classification errors on class labels.
The software is written in Python 2.7 and binaries are available for Windows and Mac OS X.
History
CellCognition (Version 1.0.1) was first released in December 2009 by scientists from the Gerlich Lab and the Buhmann group at the
Swiss Federal Institute of Technology Zürich
(colloquially)
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, image = ETHZ.JPG
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, established =
, type = Public
, budget = CHF 1.896 billion (2021)
, rector = Günther Dissertori
, president = Joël Mesot
, a ...
and the Ellenberg Lab at the
European Molecular Biology Laboratory
The European Molecular Biology Laboratory (EMBL) is an intergovernmental organization dedicated to molecular biology research and is supported by 27 member states, two prospect states, and one associate member state. EMBL was created in 1974 and ...
Heidelberg. The latest release is 1.6.1 and the software is developed and maintained by the Gerlich Lab at the
Institute of Molecular Biotechnology
The Institute of Molecular Biotechnology (IMBA) is an independent biomedical research organisation founded by the Austrian Academy of Sciences in cooperation with the pharmaceutical company Boehringer Ingelheim. The institute employs around 250 ...
.
Application
CellCognition has been used in
RNAi
RNA interference (RNAi) is a biological process in which RNA molecules are involved in sequence-specific suppression of gene expression by double-stranded RNA, through translational or transcriptional repression. Historically, RNAi was known by ...
-based screening, applied in basic
cell cycle
The cell cycle, or cell-division cycle, is the series of events that take place in a cell that cause it to divide into two daughter cells. These events include the duplication of its DNA (DNA replication) and some of its organelles, and sub ...
study, and extended to unsupervised modeling.
References
External links
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{{Image_Processing_Software
Computer vision software
Data mining and machine learning software
Microscopy
Cell biology
Biochemistry
Free software programmed in Python