Image Title Category Type Description Updated
need a thumbnail Spot Detection Dmap (ImageJ) Software Workflow

This workflow detects spots in a 2D image by filtering the image by Laplacian of Gaussian (user defined radius), thresholding (user defined threshold) and finding local intensity maxima in mask distance map (Dmap).

01/23/2020 - 13:35
Nuclei segmentation in histopathology images Dataset

This dataset has been announced in the paper "Segmentation of Nuclei in Histopathology Images by deep regression of the distance map" in Transaction on Medical Imaging on the 13th of August.
This dataset consists of 50 annotated images, divided into 11 patients.

01/22/2020 - 10:12
MoNuSeg - Multi-organ nuclei segmentation challenge Dataset

The dataset for this challenge was obtained by carefully annotating tissue images of several patients with tumors of different organs and who were diagnosed at multiple hospitals. This dataset was created by downloading H&E stained tissue images captured at 40x magnification from TCGA archive. H&E staining is a routine protocol to enhance the contrast of a tissue section and is commonly used for tumor assessment (grading, staging, etc.).

01/08/2020 - 12:09
need a thumbnail 3D cell tracking using Gaussian Mixture Model (TGMM) Software Workflow

TGMM is a cell tracking solution for large 3D volume (typically lightsheet).

It detects cell nuclei by fitting gaussians on their fluorescent intensity.

It can run on GPU using CUDA and is called via the command line.

12/19/2019 - 15:30
need a thumbnail PSFj Software Collection

PSFj is a software tool that automatically analyses the full field-of-view (FOV) performance of a given fluorescence microscope/objective lens combination with respect to its optical resolution and chromatic aberrations. PSFj provides reporting functions to document the momentary performance of a system and it allows for the export of the obtained data, e.g. for image restoration purposes. PSFj is based on ImageJ and JAVA, and runs on Windows, Mac, and Linux PCs as a stand-alone application.

12/19/2019 - 14:35
NucleusJ Software Collection


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.

12/13/2019 - 00:51
Amira logo Amira / Avizo Xtra library Software Collection, Workflow

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.

11/22/2019 - 13:08
need a thumbnail Epina Image Lab Software Collection

Epina ImageLab is a Microsoft Windows-based multisensor imaging tool for processing and analyzing hyperspectral images. It is a modular system consisting of a basic engine, a graphical user interface, a chemometrics toolbox and optional user-supplied modules. It supports the most important spectroscopic imaging techniques, such as UV/Vis, infrared, Raman, THz, optical emission/absorption, and mass spectrometry.

11/22/2019 - 06:12
QuickFit 3 Software Collection, Component

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.

11/22/2019 - 06:07
Replace Red with Magenta Software Component

This plugin converts all occurrences of red in a red/green image with magenta, effectively replacing it with a magenta/green merge.

Note: the plugin completely ignores the blue channel, and replaces it with a copy of the red channel.

11/12/2019 - 00:13
need a thumbnail Napari image viewer Software Component

napari is a fast, interactive, multi-dimensional image viewer for Python. It’s designed for browsing, annotating, and analyzing large multi-dimensional images. It’s built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (e.g. numpyscipy). It includes critical viewer features out-of-the-box, such as support for large multi-dimensional data, and layering and annotation.

11/08/2019 - 10:22
need a thumbnail OligoMacro Toolset Software Workflow

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.

10/27/2019 - 21:44
need a thumbnail MATLAB Wavelet toolbox Software Collection 10/18/2019 - 18:39
automated structures analysis program (ASAP) Software Workflow

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

10/18/2019 - 13:10
need a thumbnail Icy Spot Tracking Software Component

Up to version 2 it was known as the ‘Probabilistic particle tracker’ plugin.

10/18/2019 - 13:17
need a thumbnail Icy Label Extractor Software Component 10/17/2019 - 16:56
need a thumbnail Image registration in Matlab with Image Processing Toolbox Software Collection, Component

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. 

10/17/2019 - 13:49
Adaptive Pixel Representation Software Collection

A content-adaptive representation of fluorescence microscopy images called Adaptive Particle Representation (APR), which replaces the regular grid of pixels with particles positioned according to image content. This overcomes storage bottlenecks, as data compression does, but additionally overcomes memory and processing bottlenecks, since the APR can directly be used in processing without going back to pixels.

10/16/2019 - 18:01
Mathematica Software Collection

Wolfram Mathematica (usually termed Mathematica) is a modern technical computing system spanning most areas of technical computing — including neural networksmachine learningimage processinggeometrydata science

10/16/2019 - 14:51
LBADSA Software Component

LBADSA is based on the fitting of the Young-Laplace equation to the image data to measure drops.

10/16/2019 - 13:24