NucleusJ

Description

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Starting from image stacks, the nuclear boundary as well as nuclear bodies are segmented. As output, NucleusJ automatically measures 15 parameters quantifying shape and size of nuclei as well as intra-nuclear objects and the positioning of the objects within the nuclear volume.

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Amira / Avizo Xtra library

Description

Collection of add-ons (recipes, scripts, demos,…) that will help you improve your day-to-day use of Amira-Avizo and PerGeos Software and make you gain both time and efficiency.
Use the Search field to look for specific keywords related to your domain of interest. The different filters also help you target specific resources.

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QuickFit 3

Description

QuickFit 3 is a data evaluation software for FCS Fluorescence Correlation Spectroscopy and imagingFCS (imFCS) measurements, developed in the group B040 (Prof. Jörg Langowski) at the German Cancer Research Center (DKFZ). Actually QuickFit 3 itself is a project manager and all functionality is added as plugins. A set of tested plugins for FCS, imagingFCS and some microscopy-related image processing tasks is supplied together with the software.

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OligoMacro Toolset

Description

OligoMacro Toolset, is an ImageJ macro-toolset aimed at isolating oligodendrocytes from wide-field images, tracking isolated cells, characterizing processes morphology along time, outputting numerical data and plotting them. It takes benefit of ImageJ built-in functions to process images and extract data, and relies on the R software in order to generate graphs.

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automated structures analysis program (ASAP)

Description

ASAP allows to automatically detect, classify and quantify structures acquired by super resolution microscopy. 

Image registration in Matlab with Image Processing Toolbox

Description

Align two images using intensity correlation, feature matching, or control point mapping

Together, Image Processing Toolbox™ and Computer Vision Toolbox™ offer four image registration solutions: interactive registration with a Registration Estimator app, intensity-based automatic image registration, control point registration, and automated feature matching. 

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Mathematica

Description

Wolfram Mathematica (usually termed Mathematica) is a modern technical computing system spanning most areas of technical computing — including neural networksmachine learningimage processinggeometrydata sciencevisualizations, and others. The system is used in many technical, scientific, engineering, mathematical, and computing fields.

DropSnake

Description

DropSnake is based on B-spline snakes (active contours) to shape and measure a drop.

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DeepCell

Description

 

DeepCell is neural network library for single cell analysis, written in Python and built using TensorFlow and Keras.

DeepCell aids in biological analysis by automatically segmenting and classifying cells in optical microscopy images. This framework consumes raw images and provides uniquely annotated files as an output.

The jupyter session in the read docs are broken, but the one from the GitHub are functional (see usage example )

deepcell

Protein Array Analyzer for ImageJ

Description

Protein array is used to analyze protein expressions by screening simultaneously several protein-molecule interactions such as protein-protein and protein-DNA interactions. In most cases, the detection of interactions leads to an image containing numerous lines of spots that will be analyzed by comparing tables of intensity values. To describe the observed different patterns of expression, users generally show histograms with the original associated images [1]. The “Protein Array Analyzer” gives a friendly way to exploit this type of analysis, thus allowing quantification, image modeling and comparative analysis of patterns.

The Protein Array Analyzer, which was programmed in ImageJ’s macro language, is an extention of the Dot Blot Analyzer, [2], [3] a graphically interfaced tool that greatly simplifying analysis of dot arrays.