Image Title Category Type Description Updated
need a thumbnail SciView Software Component

SciView is an ImageJ/FIJI plugin for 3D visualization of images and meshes. It uses the Scenery and ClearVolume infrastructure.

12/09/2018 - 19:20 Training Material 12/09/2018 - 19:03
SQUIRREL SQUIRREL Software Collection

NanoJ-SQUIRREL (Super-resolution Quantitative Image Rating and Reporting of Error Locations) is a software package designed for assessing and mapping errors and artefacts within super-resolution images. This is achieved through quantitative comparison with a reference image of the same structure (typically a widefield, TIRF or confocal image). SQUIRREL produces quantitative maps of image quality and resolution as well as global image quality metrics.

12/11/2018 - 01:54
need a thumbnail InspectJ Software Component

InspectJ is a free ImageJ/FIJI tool to inspect digital image integrity.

InspectJ_v2 is a newer version for advanced users. It applies additional features like histogram equalization and gamma correction for improved image inspections.

12/09/2018 - 18:36
need a thumbnail JavaFX Software 12/09/2018 - 18:09
need a thumbnail Maven Software 12/09/2018 - 18:09
Paintera screenshot Paintera Software Component

Paintera is a general visualization tool for 3D volumetric data and proof-reading in segmentation/reconstruction with a primary focus on neuron reconstruction from electron micrographs in connectomics. It features/supports:

12/09/2018 - 18:28
shinyHTM shinyHTM Software Component

shinyHTM is an open source, web-based tool for data exploration, image visualization and normalization of High Throughput Microscopy data. Within shinyHTM the user is guided through a linear workflow which follows the following best practices:

12/08/2018 - 17:34
ttk TTK the Topology Toolkit Software Collection

The Topology ToolKit (TTK) is an open-source library and software collection for topological data analysis in scientific visualization.

11/23/2018 - 09:15
paraviewbloodcells Paraview Software Collection

ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView’s batch processing capabilities.

11/23/2018 - 09:04
need a thumbnail Icy-OpenCV Software Component 11/07/2018 - 15:07
need a thumbnail IJ-OpenCV Software Component 11/07/2018 - 15:05
need a thumbnail Blender Software Collection 11/07/2018 - 14:24
need a thumbnail NeuroMorph Software Component 11/07/2018 - 14:23 Training Material 10/19/2018 - 11:20
Images not displayed Forum topic


The images associated to the entries are not displayed, I only see a cross icon instead.

I observed this on both chrome and microsoft edge.

10/19/2018 - 11:00
FishInspector Logo FishInspector Software Collection

The software FishInspector provides automatic feature detections in images of zebrafish embryos (body size, eye size, pigmentation). It is Matlab-based and provided as a Windows executable (no matlab installation needed).

10/19/2018 - 10:56
spot detection SpotDetectionIJ Software Workflow

This is a classical workflow for spot detection or blob like structures (vesicules, melanosomes,...)

Step 1 Laplacian of Gaussian to enhance spots . Paraeters= radius, about the average spot radius

Step 2 Detect minima (using Find Maxima with light background option to get minima). Parameter : Tolerance to Noise: to be tested, hard to predict. About the height of the enhanced feautures peaks

10/18/2018 - 18:58
Creating an ImageJ plugin / command Software Workflow

The best way to start writing an ImageJ2 plugin (ImageJ2 developers call it command and not plugin) is to download the example command from github and modify it. There is a video tutorial on the whole workflow on how to do this on youtube.

10/18/2018 - 15:34
need a thumbnail Jython for ImageJ Software 10/18/2018 - 15:20