Contents

Image Title Category Type Description Updated
screen capture from exosomeAnalyzer TEM ExosomeAnalyzer Software Workflow

TEM ExosomeAnalyzer is a program for automatic and semi-automatic detection of extracellular vesicles (EVs), such as exosomes, or similar objects in 2D images from transmission electron microscopy (TEM). The program detects the EVs, finds their boundaries, and reports information about their size and shape.

The software has been developed in terms of project MUNI/M/1050/2013 and supported by Grant Agency of Masaryk University.

01/21/2019 - 16:43
need a thumbnail Registrationshop Software Collection, Component

It is an interactive front-end visualization for registration software based on Elasix (VTK/ITK)

01/21/2019 - 16:08
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

04/29/2023 - 15:51
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

01/16/2019 - 19:12
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 Collection, Component

DeconvolutionLab2 includes a friendly user interface to run the following deconvolution algortihms: Regularized Inverse Filter, Tikhonov Inverse Filter, Naive Inverse Filter, Richardson-Lucy, Richardson-Lucy Total Variation, Landweber (Linear Least Squares), Non-negative Least Squares, Bounded-Variable Least Squares, Van Cittert, Tikhonov-Miller, Iterative Constraint Tikhonov-Miller, FISTA, ISTA.

05/17/2023 - 09:59
GaussFit OnSpot Software Component

quote: 

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
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. 

05/03/2023 - 13:47
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."

04/30/2023 - 17:33
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)
hdome.runOp()
mtbdone = hdome.getResultImage()
imp2 = mtbdone.getImagePlus()
imp2.show()

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
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.

02/06/2019 - 23:33
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

04/28/2023 - 15:14
null SciView Software Component

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

10/15/2019 - 10:40
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.

05/02/2023 - 13:03
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