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) , former_name = eidgenössische polytechnische Schule , image = ETHZ.JPG , image_size = , 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

* * {{Image_Processing_Software Computer vision software Data mining and machine learning software Microscopy Cell biology Biochemistry Free software programmed in Python