analysis

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FLIM / SLIM Analysis

Workflow Language: 
C
C++
Java
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Vaa3D

Vaa3D [1, 2, 3] is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions ... It is also Open Source, supports a very simple and powerful plugin interface and thus can be extended & enhanced easily...

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Volocity

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Endrov


Endrov started development in 2007 by Johan Henriksson in the group of Thomas Bürglin group / Karolinska insitutet. At that time it was merely a tool to support the analysis of C. elegans embryogenesis. It was decided to not base it on ImageJ because little of it could be reused, many of the problems came from the core design. Since then the scope of Endrov has expanded to be useful for all image processing and be able to replace ImageJ.

dscho's picture

EBImage

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 (www.bioconductor.org).

Strengths

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ImgLib2

ImgLib2 is a generic, multi-dimensional data processing library allowing for processing algorithms to be defined in a data-type, dimension, and container independent manner. Due to its interface-based design, it is easy to write adapters to virtually all existing data containers. It is the basis of KNIME, ImageJ2 and a couple of Fiji plugins.

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Fiji

Fiji is just ImageJ: a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. The main focus of Fiji is to assist research in life sciences. It is a free, open-source, community-driven project.

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PALMsiever

PALMsiever is a MATLAB-based application that allows the filtering (sieving) and analysis of localization-microscopy data. It provides the ability to render the data using different visualization algorithms and perform simple measurements on the point-localization data. It is extensible using simple MATLAB scripts and a number of plugins is already provided with the software itself, including a clustering algorithm and 3D rendering [1].

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