3D confocal noise simulator

Description

This Matlab code simulates the noise of the confocal laser scanning microscope depending on the depth in the image stack (serial sections). Using the stack of binary images, it applies different levels of noise in the signal and background parts of the images to simulate confocal images. This is useful for generating "virtual ground truth" images with known values of sample rotation and distortion. 

TeraStitcher

Description

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.

Globals for Images · SimFCS

Description

Software for analysis, visualization, simulation, and acquisition  of data from spectroscopy and fluorescence microscopy.

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NeuronMetrics

Description

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.

 

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QuantCenter

Description

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.

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Neurolucida

Description

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

Neurolucida example

TurtleSeg: 3D Image Segmentation Software

Description
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.
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WaveTracer

Description

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.

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Vision4D

Description
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 stitching and alignment to create large multi-dimensional image stacks Immediate 2D, 3D and 4D visualization, annotation and analysis regardless of image size Creation, import, and export of 4D Iso-surfaces Powerful Analysis Pipeline for 3D /4D image analysis (cell segmentation, tracking, annotation, quantitative measurement and statistics, etc) Semi-automatic/manual segmentation and tracking with interactive Track Editor Easy design and export of 3D / 4D High Resolution Movies Seamless integration of custom workflows via Matlab API and Python scripting Data sharing for collaboration A user friendly software, easy to learn and use for any life scientist
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Labview

Description
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. For Image processing and analysis, Labview offers the integrated "NI Vision" tool, used in image-based quality control of production lines with a broad selection of Image-based filters/operations. In microscopy, Labview can be used efficiently to perform any kind of instrument control, and in particular "Feedback Microscopy" (also called intelligent microscopy, etc...) where the live analysis of a captured image will update the target of the microscope to make it understand where to image efficiently.
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