Image Title Category Type Description Updated
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
need a thumbnail Eclipse Software 10/18/2018 - 15:17
need a thumbnail IntelliJ Software 10/18/2018 - 15:17
scikit-learn logo. scikit-learn (sklearn) Software Collection

Scikit-learn (sklearn) is a python library used for machine learning. sklearn contains simple and efficient tools for data mining and data analysis. Modules and functions include those for classification, regression, clustering, dimensionality reduction, model selection and data preprocessing. Many people have contributed to sklearn (list of authors)

10/19/2018 - 11:34
3-D Density Kernel Estimation Software Workflow

3-D density kernel estimation (DKE-3-D) method, utilises an ensemble of random decision trees for counting objects in 3D images. DKE-3-D avoids the problem of discrete object identification and segmentation, common to many existing 3-D counting techniques, and outperforms other methods when quantification of densely packed and heterogeneous objects is desired. 

10/18/2018 - 12:29
Microscope autopilot Software Collection, Component

AutoPilot is the open source project that hosts the general algorithm for fast and robust assessment of local image quality, an automated computational method for image-based mapping of the three-dimensional light-sheet geometry inside a fluorescently labeled biological specimen, and a general algorithm for data-driven optimization of the system state of light-sheet microscopes capable of multi-color imaging with multiple illumination and detection arms.

10/18/2018 - 15:16
ImageJ1 - ImageJ2 transition cheat sheet Training Material

This cheat sheet contains pairs of code snippets explaining how to transform existing code from running in ImageJ1 to ImageJ2.

10/18/2018 - 15:17
Simultaneous ImageJ script and plugin development Training Material

A short tutorial on how to develop, deploy and run ImageJ/Fiji scripts and Java plugins within your IDE simultaneously

10/18/2018 - 15:20
Minimum cost Z surface projection Software Component

This plugin detects a minimum cost z-surface in a 3D volume. A z surface is a topographic map indicating the altitude z as a function of the position (x,y) in the image. The cost of the surface depends on pixel intensity the surface is going through. This plugin find the z-surface with the lowest intensity in an image.

10/18/2018 - 15:16
Interactive watershed Software Component

The interactive Watershed Fiji plugin provides an interactive way to explore local maxima and threshold values while a resulting label map is updated on the fly.

After the user has found a reliable parameter configuration, it is possible to apply the same parameters to other images in a headless mode, for example via ImageJ macro scripting.

10/18/2018 - 11:07
need a thumbnail Jupyter notebook Software 10/18/2018 - 10:44