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Advanced Cell Classifier

Advanced Cell Classifier is a data analyzer program to evaluate cell-based high-content screens and tissue section images. The basic aim is to provides a very accurate high-content screen analysis with minimal user interaction, offering access to a variety of advanced machine learning methods.

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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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Counting Clumped Cells

Workflow Language: 
ImageJ Macro Language
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Neuron studio is a software package to reconstruct neurons from 3D confocal images. Reconstruction can be done manually, semi-manually or fully automatic. The images as well as the detected objects are rendered in 3D.
A spine detection and classification function is also included. Results can be exported as a text file with coords of the spines.

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ilastik (the image learning, analysis, and segmentation toolkit) provides non-experts with a menu of pre-built image analysis workflows. ilastik handles data of up to five dimensions (time, 3D space, and spectral dimension). Its workflows provide an interactive experience to give the user immediate feedback on the quality of the results yielded by her chosen parameters and/or labelings.

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Imaris is a software for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy images. It performs interactive volume rendering that lets users freely navigate even very large datasets (hundreds of GB). It performs both manual and automated detection and tracking of biological “objects” such as cells, nuclei, vesicles, neurons, and many more. ImarisSpots for example is a tool to detect “spherical objects” and track them in time series. Besides the automated detection it gives the user the ability to manually delete and place new spots in 3D space.

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EBImage is an open source image processing and analysis package for the statistical programming language R. Its primary goal is to enable automated analysis of large sets of images such as those obtained in high-throughput screening. An extensive range of basic image processing and feature extraction methods are provided. EBImage is available through the Bioconductor software project (



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