Image Title Category Type Description Updated
test name traning material Training Material


03/01/2019 - 18:04
kljl Forum topic


02/06/2019 - 22:18
need a thumbnail rmwfONtestsite Software Workflow 02/03/2019 - 17:48
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
need a thumbnail sklearn Software 10/18/2018 - 12:29
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
need a thumbnail Jupyter Software 10/18/2018 - 10:44
NEUBIAS TS1 Training Material 04/08/2019 - 11:41
need a thumbnail ImageJ/FIJI Software 10/17/2018 - 19:50
find maxima comparison. Find Maxima (Python) Software Workflow


Maxima finding algorithm recreated from implementation in Fiji(ImageJ)

This is a re-implementation of the java plugin written by Michael Schmid and Wayne Rasband for ImageJ. The original java code source can be found in: 

10/18/2018 - 10:50
Introduction to ImageJ macro language Training Material

In this session, we will cover the basics of ImageJ macro programming using a simple example: how to quantify signal enrichment at the nuclear rim? Trainees will (re)discover how to record actions, plan a workflow and organise their code. This session will alternate presentation of technical points, to be directly applied during practical exercises. The macro will progressively complexify as new notions are taught.

04/08/2019 - 11:43