Software

 

Cellular Phenotype database

CellCognition

cellHTS2

CellH5

Cell Profiler

EBImage

imageHTS

Micropilot

Micycle

R/Bioconductor

rhdf5

WIS-PhagoTracker

WiSoft


Cell Phenotype database

The Cellular Phenotype database stores data derived from high-throughput phenotypic studies and aims at providing easy access to phenotypic data and facilitate the integration of independent phenotypic studies. Through its interface, users can search for a gene of interest, or a collection of genes, and retrieve the loss-of-function phenotypes observed, in human cells, by suppressing the expression of the selected gene(s), through RNA interference (RNAi), across independent phenotypic studies.
Similarly, users can search for a phenotype of interest and retrieve the RNAi reagents that have caused such phenotype and the associated target genes.

Information about specific RNAi reagents can also be obtained when searching for a reagent ID.

Alternatively, users can explore all datasets loaded in the database by browsing the phenotypes as well as searching studies by keyword.

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CellCognition

CellCognition is a cross-platform image analysis framework for fluorescence time-lapse microscopy. CellCognition combines object detection and machine learning for classification of morphologies with time-resolved analysis by single-cell tracking. This enables measurements of progression through morphology stages and kinetic readouts at the single-cell level.

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cellHTS2

This R/Bioconductor package provides tools for the analysis of high-throughput assays that were performed in 384-well microtitre plate (or analogous) formats. The functionality includes data import and management, normalisation, quality assessment, replicate summarisation and statistical scoring. A web report that provides detailed graphical overview over the data and analysis results is produced. In our work, we have applied the package to RNAi screens on fly and human cells, and for screens of yeast libraries.

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CellH5

CellH5 is an HDF5 data format for cell-based assays in high-content microscopy. It stores high-dimensional image data along with object measurements and inter-object relations using a graph representation. CellH5 is open source and published under the LGPL license.

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Cell Profiler

The LCC modules for Cellprofiler enable you to create an online feedback loop between a Leica microscope running HCS-A software (we will call this Matrix Screener and/or CAM server in the remainder of this document) and the batch image analysis package CellProfiler.

Creating such a feedback loop between microscope and image analysis can be useful if one wants to trigger complex and/or time-consuming confocal image acquisition protocols in response to detecting certain events (e.g. presence of certain phenotypes or cells of interest) in images captured with less complex acquisition patterns.

You can find an overview of this feedback loop concept with selected examples in the book chapter C.Tischer, V.Hilsenstein, K.Hanson, R.Pepperkok, Adaptive Fluorescence Microscopy by Online Feedback Image Analysis, in Quantitative Imaging in Cell Biology, Methods Cell Biol. 2014;123:489-503. doi: 10.1016/B978-0-12-420138-5.00026-4.

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EBImage

This R/Bioconductor package provides general purpose functionality for the reading, writing, processing and analysis of images. Furthermore, in the context of microscopy based cellular assays, EBImage offers tools to transform the images, segment cells and extract quantitative cellular descriptors.

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imageHTS

imageHTS is an R/Bioconductor package dedicated to the analysis of high-throughput microscopy-based screens. The package provides a modular and extensible framework to segment cells, extract quantitative cell features, predict cell types and browse screen data through web interfaces. Designed to operate in distributed environments, imageHTS provides a standardized access to remote data and facilitates the dissemination of high-throughput microscopy-based datasets.

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Micropilot

Quantitative microscopy relies on imaging of large cell numbers but is often hampered by time-consuming manual selection of specific cells. The 'Micropilot' software automatically detects cells of interest and launches complex imaging experiments including three-dimensional multicolor time-lapse or fluorescence recovery after photobleaching in live cells. In three independent experimental setups this allowed us to statistically analyze biological processes in detail and is thus a powerful tool for systems biology. [source PubMed]

Micropilot updates

EMBL press release | back

Micycle

Micycle is a web-based tool to enable to query two ontologically structured Knowledge Bases about Cell Cycle and Cellular Migration, both of them classified by the dominant ontology Gene Ontology, with Cell Cycle Ontology, Cell Phenotype Ontology and Cell Migration Consortium as additional ontological information.

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R/Bioconductor

R is a language and environment for statistical computing and graphics, and is widely used in functional genomics and systems biology.

R provides statistical modeling (linear and nonlinear regression, statistical tests, time-series analysis, classification, clustering). It is a highly extensible functional language. One of R's strengths is the ease with which well-designed publication-quality plots can be produced.

Bioconductor builds on top of R and provides tools for the analysis and comprehension of biological data, in particular from genomics and systems biology.

Updates:

http://www.bioconductor.org/packages/devel/bioc/html/mitoODE.html

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rhdf5

This R/Bioconductor package provides an interface between HDF5 and R.

HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting applications work on datasets that are larger than the available RAM.

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WIS-PhagoTracker

WIS-PhagoTracker is a software application for quantitative analysis of high throughput cell migration assay. The cell migration assay is based on a modified Phagokinetic tracks procedure, in which motile cells "leave their tracks" on a specialized surface. These tracks are visualized using a screening microscope.

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WiSoft

WiSoft® is a unique high-speed image analysis pipeline. WiSoft® software solutions, Athena and Minerva, are used for a wide variety of biological, biomedical and pharmaceutical applications and have been developed through a continuous dialogue with users. WiSoft® offers dedicated solutions for high-content image analysis, with specialty in high-resolution image analysis algorithms, which enables the analysis of complex biological systems.

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Seventh Framework Programme

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