Contents

Image Title Category Type Description Updated
EBImage EBImage Software Collection

EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.

05/02/2023 - 18:48
need a thumbnail Data-analysis strategies for image-based cell profiling Software Workflow

Workflow of data-analysis strategies for image-based cell profiling.

05/03/2023 - 15:53
need a thumbnail NET - Network Extraction Tool Software Collection

The ultimate goal of the NET framework is to make images of networks processable by computers. Therefore we want to have a pixel based image as input, as output we want a representation of the network visible in the image that retains as much information about the original network as possible. NET achives this by first segmenting the image and then vectorizing the network and then extracting information. The information we extract is

05/03/2023 - 11:37
ORION_example_result ORION Software Collection

ORION: Online Reconstruction and functional Imaging Of Neurons: segmentation and tracing of neurons for reconstruction.

05/03/2023 - 15:20
AveMAP AVEMAP Software Component

Measures wound-healing assay videos, 

 For each video, the velocity and the order parameter are analyzed in time and space to extract quantitative parameters characterizing the cell motility phenotype. The different conditions (videos) can then be classified according to these parameters.

03/10/2023 - 23:13
need a thumbnail NeuronMetrics Software Collection

The invention comprises a software tool, NeuronMetrics, which functions as a set of modules that run in the open-source program ImageJ. NeuronMetrics features a novel method for estimating neural “branch number” (a measure of the axonal complexity) from two-dimensional images. In addition, the tool features a novel method for modeling neural structure in large “gaps” that result from image artifacts.

 

01/29/2018 - 09:49
need a thumbnail Hessian by Philippe Thévenaz Software Component

Computes image Hessian
Based on the algorithm described in the paper below. 

Splines: A Perfect Fit for Signal and Image Processing
M. Unser
IEEE Signal Processing Magazine, vol. 16, no. 6, pp. 22-38, November 1999.
 DOI: 10.1109/79.799930
 http://ieeexplore.ieee.org/document/799930/

09/12/2017 - 17:53
need a thumbnail Laplacian by Philippe Thévenaz Software Component

Computes image Laplacian

 

Based on the algorithm described in the paper below. 

Splines: A Perfect Fit for Signal and Image Processing
M. Unser
IEEE Signal Processing Magazine, vol. 16, no. 6, pp. 22-38, November 1999.
 DOI: 10.1109/79.799930
 http://ieeexplore.ieee.org/document/799930/

09/12/2017 - 17:48
need a thumbnail Matlab compiler runtime Software 09/12/2017 - 17:00
need a thumbnail gradient by Philippe Thévenaz Software Component

Computes image gradient

 

Based on the algorithm below. 

Splines: A Perfect Fit for Signal and Image Processing
M. Unser
IEEE Signal Processing Magazine, vol. 16, no. 6, pp. 22-38, November 1999.
 DOI: 10.1109/79.799930
 http://ieeexplore.ieee.org/document/799930/

09/12/2017 - 17:14
Example of output from Neural Circuit Tracer Neural Circuit Tracer Software Collection

Neural Circuit Tracer (NCTracer) is open source software for automated and manual tracing of neurites from light microscopy stacks of images. NCTracer has more than one workflow available for neuron tracing. 

04/11/2018 - 12:01
MIB Microscopy Image Browser (MIB) Software Collection

Microscopy Image Browser (MIB) is a high-performance Matlab-based software package for advanced image processing, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets.

05/12/2023 - 17:52
AnaMorph AnaMorf Software Component

AnaMorf is a plug-in developed for the ImageJ platform (rsb.info.nih.gov/ij) to analyse the microscopic morphology of filamentous microbes. The program returns average data on a population of mycelial elements, using the descriptors projected area, circularity, total hyphal length, number of hyphal tips, hyphal growth unit, lacunarity and fractal dimension. The plug-in accepts as input a user-specified directory of images, analysing each and outputing tabulated results.

09/12/2017 - 17:43
Kappa user interface Kappa Software Component

Kappa is a Fiji plugin for Curvature Analysis.

It allows a user to measure curvature in images in a convenient way. You can trace an initial shape with a B-Spline curve in just a few clicks and then fit that curve to image data with a minimization algorithm. It’s fast and robust.

09/21/2017 - 16:50
Kota Miura (ed) "Bioimage Data Analysis", Textbook, Wiley Training Material

Bioimage Data Analysis provides detailed explanations and example workflows of combining various image processing algorithms to construct practical workflows using scripting.

http://www.imaging-git.com/olympus-website-bioimage-data-analysis

https://www.researchgate.net/publication/297738620_Bioimage_Data_Analysis

08/03/2020 - 14:50
iTrack4U iTrack4U Software Component

iTrack4U is a Java-based software using ImageJ and jMathPlot libraries, which aims at automatically tracking cells recorded in phase-contrast microscopy. It includes all tools from image files preprocessing, tracking to data extraction and visualization. 

 

Please cite Cordeliéres et. al. (2013) when using this software package!

05/21/2018 - 01:22
ImageJ Analyze Skeleton Software Component

This plugin tags all pixel/voxels in a skeleton image and then counts all its junctions, triple and quadruple points and branches, and measures their average and maximum length.

Tags are shown in a new window displaying every tag in a different color. You can find it under [Plugins>Skeleton>Analyze Skeleton (2D/3D)]. See Skeletonize3D for an example of how to produce skeleton images.

04/27/2023 - 14:09
MorphoGraphX user interface MorphoGraphX Software Collection

MorphoGraphX is a free Linux application for the visualization and analysis of 3D biological datasets. Developed by researchers, it is primarily used for the analysis and quantification of 3D live-imaged confocal data sets.

The main research interests adressed by MorphoGraphX are:

  • Shape extraction
  • Growth analysis
  • Signal quantification
  • Protein localization
03/03/2020 - 20:54
Rafael C. Gonzalez, Richard E. Woods."Digital Image Processing", Pearson, 2008 Training Material

From the publisher: "Completely self-contained–and heavily illustrated–this introduction to basic concepts and methodologies for digital image processing is written at a level that truly is suitable for seniors and first-year graduate students in almost any technical discipline.

09/12/2017 - 11:58
FigureJ FigureJ Software Component

This plugin achieves easy creation of image figures for publications, reports, projects.

  • Easy-to-design interactive figure layout.

  • Visually assign image content to panels.

  • High-quality image scaling and rotation.

  • Easy and consistent panel labels and scale bars.

  • Each panel has it's original datasource's properties and tracks achieved image processing.

  • Save and re-open editable figures.

04/29/2023 - 11:34