Contents

Image Title Category Type Description Updated
need a thumbnail softWoRx 5.0 Software Collection softWoRx® 5.0 is the latest in DeltaVision image acquisition software. Find samples, acquire images and process data quickly and efficiently with the intuitive user interface. softWoRx 5.0 includes visualization and measurement tools and exports data in a wide variety of formats making it a versatile tool for more than just image acquisition. 09/12/2017 - 20:05
need a thumbnail SimuCell Software Collection An open-source framework to synthetically generate fluorescent microscopic images of cellular population. 09/13/2017 - 12:13
need a thumbnail ImagePro Software Collection Image-Pro software includes the latest tools for scientific and industrial image analysis and image processing. Capture, process, measure, share, visualize and compare. ImagePro Insight ImagePro Priemier 09/12/2017 - 20:05
ITK-SNAP Software Collection

ITK-SNAP is a software application used to segment structures in 3D medical images. It can also be used as a 3D annotation tool for deep learning. It is based on ITK, VTK libraries.

 03/15/2023 - 15:48
need a thumbnail Micro-Manager Software Collection - 09/13/2017 - 12:13
Matamorph user interface Metamorph Software Collection

Metamorph provides all tools needed to perform analysis of acquired images with user-friendly application modules for biology-specific analysis such as cell signaling, cell counting, and protein expression.

 09/12/2017 - 20:05
Huygens Software Collection

The Huygens Software Suite consists of different image processing packages with functionalities that include deconvolution, interactive analysis, and volume visualization of 2D-3D multi-channel and time series images from fluorescence microscopes such as widefield, confocal, multi-photon, spinning disk, Array Detector, STED, and Light Sheet

 10/15/2019 - 12:25
need a thumbnail GNU Octave Software Collection "GNU Octave is a high-level language, primarily intended for numerical computations."* It can also be used for image processing, statistics and plotting as well as Matlab. "GNU Octave is also freely redistributable software. You may redistribute it and/or mod- ify it under the terms of the GNU General Public License as published by the Free Software Foundation."* * 09/13/2017 - 12:13
CATMAID CATMAID Software Collection

**Collaborative Annotation Toolkit for Massive Amounts of Image Data** CATMAID is a Collaborative Annotation Toolkit for Massive Amounts of Image Data. It is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by GoogleMaps, with which it shares basic navigation concepts, enhanced to allow the exploration of 3D biological image data acquired by optical or physical sectioning microscopy techniques.

 04/29/2023 - 15:23
need a thumbnail Avizo Software Collection Wherever three-dimensional data sets need to be processed, in materials science, geosciences, environmental or engineering applications, Avizo offers abundant state-of-the-art features within an intuitive workflow and easy-to-use graphical user interface. Avizo is packaged in different Editions, with optional eXtension modules. 09/12/2017 - 20:05
Image restoration with AutoQuant AutoQuant Software Collection

Deconvolution software

 09/12/2017 - 20:05
Amira's interface Amira Software Collection

Amira is 3D visualization and analysis software for life sciences.
 

" Amira software is a powerful, multifaceted 3D platform for visualizing, manipulating, and understanding life sciences data from computed tomography, microscopy, MRI, and many other imaging modalities. 
With incredible speed and flexibility, Amira software enables advanced 3D imaging workflows for specialists in research areas ranging from molecular and cellular biology to neuroscience and bioengineering. "

 05/19/2021 - 21:27
need a thumbnail OpenCV Software Collection OpenCV is released under a BSD license and hence it’s free for both academic and commercial use. It has C++, C, Python and Java interfaces and supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for computational efficiency and with a strong focus on real-time applications. Written in optimized C/C++, the library can take advantage of multi-core processing. Adopted all around the world, OpenCV has more than 47 thousand people of user community and estimated number of downloads exceeding 6 million. 09/13/2017 - 12:13
need a thumbnail OpenMOLE Software Collection OpenMOLE (Open MOdeL Experiment) is a workflow engine designed to leverage the computing power of distributed execution environments for naturally parallel processes. A process is told naturally parallel if the same computation runs many times for a set of different inputs, such as model experiment or data processing… It is free software distributed under the AGPLv3 free software license. 09/12/2017 - 20:05
need a thumbnail Volocity Software Collection - 09/13/2017 - 12:13
need a thumbnail Find Focused Slices Software Component

An ImageJ plugin for selecting a plane in focus among multiple slices image stack. The algorithm uses normalized variance. A short tutorial is available in the plugin web page (above).

 03/03/2020 - 10:17
NeuronStudio_standaloneapp_window_overview NeuronStudio Software Collection

Neuron studio is a software package to reconstruct neurons from 3D confocal images. Reconstruction can be done manually, semi-manually or fully automatic. The images as well as the detected objects are rendered in 3D. A spine detection and classification function is also included. Results can be exported as a text file with coords of the spines. It seems that active development has stopped in 2009.

 04/27/2023 - 13:03
3D microtubules Microtubules Tool (3D) Software Workflow

The tool measures the total length of the microtubules in a 3D image.

See: http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Microtubules_Tool_(3…

You can find a test image here.

 05/03/2023 - 10:48
ImageJ toolbar of the arabidopsis seedlings tool Arabidopsis Seedlings Tool Software Workflow

The Arabidopsis Seedlings Tool allows to analyze the germination and seedling growth of Arabidopsis (Arabidopsis thaliana) in liquid culture. It measures the surface of green pixels per well in images containing multiple wells. It can be run in batch mode on a series of images. It writes a spreadsheet file with the measured area per well and saves a control image showing the green surface that has been detected per well. 

 05/03/2023 - 15:07
need a thumbnail Cell segmentation by EBImage, R Software Workflow 09/13/2017 - 12:13