TeraStitcher

Bio Image Analyst
Biologist
Developper
microscopist

TeraStitcher is a free tool that enables the stitching of Teravoxel-sized tiled microscopy images even on workstations with relatively limited resources of memory (<8 GB) and processing power. It exploits the knowledge of approximate tile positions and uses ad-hoc strategies and algorithms designed for such very large datasets. The produced images can be saved into a multiresolution representation to be efficiently visualized (e.g. Vaa3D-TeraFly) and processed.

NeuronMetrics

Bio Image Analyst
microscopist

The invention comprises a software tool, NeuronMetrics, which functions as a set of modules that run in the open-source program ImageJ. NeuronMetrics features a novel method for estimating neural “branch number” (a measure of the axonal complexity) from two-dimensional images. In addition, the tool features a novel method for modeling neural structure in large “gaps” that result from image artifacts.

 

QuantCenter

QuantCenter is the framework for 3DHISTECH image analysis applications. with the goal of helping the pathologists to diagnose in an easier way. QuantCenter, is optimized for whole slide quantification. It has a linkable algorithm concept that tries to provide an easy-to-use and logical workflow. The user has different quantification modules that he or she could link one after other to fine-tune or to speed up the analysis.

Neurolucida

Neurolucida is a powerful tool for creating and analyzing realistic, meaningful, and quantifiable neuron reconstructions from microscope images. Perform detailed morphometric analysis of neurons, such as quantifying 1) the number of dendrites, axons, nodes, synapses, and spines, 2) the length, width, and volume of dendrites and axons, 3) the area and volume of the soma, and 4) the complexity and extension of neurons. See 10.3389/fnins.2012.00049

TurtleSeg: 3D Image Segmentation Software

TurtleSeg is an interactive 3D image segmentation tool. TurtleSeg has an automated system, Spotlight, for automatically directing the user towards the next steps. Typically, a user loads a 3D image and then manually contour a sparse number of slices, the full 3D segmentation can then be built automatically.

WaveTracer

WaveTracer is a plugin for Metamorph. It represents a functional method for real-time reconstruction with automatic feedback control, without compromising the localization accuracy. It relies on a wavelet segmentation algorithm, together with a mix of CPU/GPU implementation.

Vision4D

arivis Vision4D is a modular software for working with multi-channel 2D, 3D and 4D images of almost unlimited size independent of available RAM. Many imaging systems, such as high speed confocal, Light Sheet/ SPIM and 2 Photon systems, can produce a huge amount of multi-channel data, which arivis Vision4D handles without constraints. Terabyte ready arivis Vision4D main functionality: Easy import of most image formats from microsopes as well as biological formats High performance interactive 3D / 4D rendering on standard PCs and laptops with 3D Graphics Support Intuitive tools for

Labview

A commercial software traditionally used in Industry and Engineering/Science to enable fast software development and deployment of a very broad range of devices control. Labview enables graphically oriented programming (no text-based coding) and offers many ready-made tools to perform basic tasks on complex data (including image data), maths operation, data handling and representation.

Visiopharm

The software is designed for pathologists. Image analysis protocols are built from graphical user interfaces; there is no need for programming experience or an extensive training program. Cloud and deployed solutions are available. Visiopharm can be employed to develop workflows (apps) for the user. Modular structure with multiple packages: VisiomorphDP™ TissuemorphDP™ Arrayimager™ Tissuealign™ Visiomorph™ Tissuemorph™ Microimager™ Fluoimager™