Image Title Category Type Description Updated
Icy SODA logo SODA suite Software Component

Ensemble of blocks that implement SODA method for confocal and super-resolution microscopy, in 2 and 3 dimensions

01/15/2019 - 18:12
PartSeg PartSeg Software Collection

There are many methods in bio-imaging that can be parametrized. This gives more flexibility
to the user as long as tools provide easy support for tuning parameters. On the other hand, the
datasets of interest constantly grow which creates the need to process them in bulk. Again,
this requires proper tool support, if biologist is going to be able to organize such bulk
processing in an ad-hoc manner without the help of a programmer. Finally, new image
analysis algorithms are being constantly created and updated. Yet, lots of work is necessary to

01/11/2019 - 15:39
need a thumbnail AssayScope Software Collection

AssayScope is an intuitive application dedicated to large scale image processing and data analysis. It is meant for histology, cell culture (2D, 3D, 2D+t) and phenotypic analysis. 

01/09/2019 - 12:36
need a thumbnail Python 3.6 Software 01/02/2019 - 18:15
The Allen Cell Structure Segmenter Overview ​The Allen Cell Structure Segmenter Software Collection

The Allen Cell Structure Segmenter is a Python-based open source toolkit developed at the Allen Institute for Cell Science for 3D segmentation of intracellular structures in fluorescence microscope images.

It consists of two complementary elements:

01/02/2019 - 18:15
DeconvolutionLab2 Software Component

The successor of DeconvolutionLab

DeconvolutionLab2 is freely accessible and open-source for 3D deconvolution microscopy; it can be linked to well-known imaging software platforms, ImageJ, Fiji, ICY, Matlab, and it runs as a stand-alone application.

The backbone of our software architecture is a library that contains the number-crunching elements of the deconvolution task. It includes the tool for a complete validation pipeline. Inquisitive minds inclined to peruse the code will find it fosters the understanding of deconvolution.

12/20/2018 - 19:13
need a thumbnail EBImage Software 12/19/2018 - 00:16
GaussFit OnSpot Software Component


GaussFit_OnSpot is an ImageJ plugin for fitting Gaussian profiles onto selected positions in diffraction-limited images (e.g. single molecules, protein clusters, vesicles, or stars).

The plugin performs a function fit in regions of interest (ROI) around spots marked by point selections in grayscale images. Single or multiple spots can be either selected manually with the Multi-point tool or automatically with the Find Maxima function.

12/19/2018 - 00:11
Spots colocalization (ComDet) Software Collection

Quote " finding and/or analyzing colocalization of bright intensity spots (cells, particles, vesicles, comets, dots, etc) in images with heterogeneous background (microscopy, astronomy, engineering, etc). "

Uses Gaussian-Mexican hat convolution for preprocessing.

12/17/2018 - 01:49 Training Material 12/17/2018 - 01:21
PTA2 Software Component

"PTA2 is an ImageJ1.x plugins that enable automatic particle tracking"

This plugin is developed specifically for single-molecule imaging, so it's good at tracking spots with noisy background. 

12/13/2018 - 00:46
MiToBo Software Collection

"The Microscope Image Analysis Toolbox MiToBo is an extension for the widely used image processing application ImageJ and its new release ImageJ 2.0.
MiToBo ships with a set of operators ready to be used as plugins in ImageJ. They focus on the analysis of biomedical images acquired by various types of microscopes."

12/11/2018 - 02:09
HDomeTransform3D Software Component

h-Dome transformation, useful for spot detection.

Jython code example:

from de.unihalle.informatik.MiToBo.core.datatypes.images import MTBImage
from de.unihalle.informatik.MiToBo.morphology import HDomeTransform3D
from ij import IJ

imp = IJ.getImage()
mtb = MTBImage.createMTBImage( imp.duplicate() )
hdome = HDomeTransform3D(mtb, 10.0)
mtbdone = hdome.getResultImage()
imp2 = mtbdone.getImagePlus()

12/11/2018 - 02:00
Nessys Software Collection

Nessys: Nuclear Envelope Segmentation System


Nessys is a software written in Java for the automated identification of cell nuclei in biological images (3D + time). It is designed to perform well in complex samples, i.e when cells are particularly crowded and heterogeneous such as in embryos or in 3D cell cultures. Nessys is also fast and will work on large images which do not fit in memory.

12/11/2018 - 01:58 Training Material 12/09/2018 - 19:55
FluoRenderer FluoRender Software Component

FluoRender is an interactive rendering tool for confocal microscopy data visualization. It combines the rendering of multi-channel volume data and polygon mesh data, where the properties of each dataset can be adjusted independently and quickly. The tool is designed especially for neurobiologists, allowing them to better visualize confocal data from fluorescently-stained brains, but it is also useful for other biological samples.

12/09/2018 - 19:55
3Dscript Software Collection

3Dscript is a plugin for Fiji/ImageJ for creating 3D and 4D animations of microscope data. In contrast to existing 3D visualization packages, animations are not keyframe-based, but are described by a natural language-based syntax.

12/11/2018 - 02:10
need a thumbnail Labkit Software Component

Labkit is an open-source tool to segment truly large image data using sparse training data. It has an intuitive and responsive user interface based on Big Data Viewer, allowing users to conveniently browse and annotate even terabyte sized image volumes.

Update site: Labkit

12/09/2018 - 19:35
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