Tensorflow

Description

"An open source machine learning framework for everyone "

TensorFlow™ is an open source software library for high performance numerical computation. Its flexible architecture allows easy deployment of computation across a variety of platforms (CPUs, GPUs, TPUs), and from desktops to clusters of servers to mobile and edge devices. Originally developed by researchers and engineers from the Google Brain team within Google’s AI organization, it comes with strong support for machine learning and deep learning and the flexible numerical computation core is used across many other scientific domains.

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TensorFlow

Isotropic Super-Resolution for EM

Description

Super-resolve anisotropic EM data along low-res axis with deep learning.

 

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MOST-Raytracer

Description

This project was designed for vectorize and analyze the  blood vessels in the mouse brain.

This plugin requires the definition of seed point detection settings by the user (Semi-automated).

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Simple Tracing DF-Tracing

Description

We have developed a novel approach, named DF-Tracing, to tackle this challenge. This method first extracts the neurite signal (foreground) from a noisy image by using anisotropic filtering and automated thresholding. Then, DF-Tracing executes a coupled distance-field (DF) algorithm on the extracted foreground neurite signal and reconstructs the neuron morphology automatically. Two distance-transform based “force” fields are used: one for “pressure”, which is the distance transform field of foreground pixels (voxels) to the background, and another for “thrust”, which is the distance transform field of the foreground pixels to an automatically determined seed point. The coupling of these two force fields can“push” a “rolling ball” quickly along the skeleton of a neuron, reconstructing the 3D cell morphology.

Simple Tracing - DT-fields

ORION

Description

ORION: Online Reconstruction and functional Imaging Of Neurons: segmentation and tracing of neurons for reconstruction.

A project to develop tools that explore single neuron function via sophisticated image analysis. ORION software bridges advanced optical imaging and compartmental modeling of neuronal function by rapidly, accurately, and robustly generating, from structural image data, a cylindrical morphology model suitable for simulating neuronal function. The goal of this project is to develop a computational and experimental framework to allow real-time mapping of functional imaging data (e.g., spatio-temporal patterns of dendritic voltages or intracellularions) to neuronal structure, during the very limited duration of an acute experiment.

ORION_example_result

Hessian by Philippe Thévenaz

Description

Computes image Hessian
Based on the algorithm described in the paper below. 

Splines: A Perfect Fit for Signal and Image Processing
M. Unser
IEEE Signal Processing Magazine, vol. 16, no. 6, pp. 22-38, November 1999.
 DOI: 10.1109/79.799930
 http://ieeexplore.ieee.org/document/799930/

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Laplacian by Philippe Thévenaz

Description

Computes image Laplacian

 

Based on the algorithm described in the paper below. 

Splines: A Perfect Fit for Signal and Image Processing
M. Unser
IEEE Signal Processing Magazine, vol. 16, no. 6, pp. 22-38, November 1999.
 DOI: 10.1109/79.799930
 http://ieeexplore.ieee.org/document/799930/

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gradient by Philippe Thévenaz

Description

Computes image gradient

 

Based on the algorithm below. 

Splines: A Perfect Fit for Signal and Image Processing
M. Unser
IEEE Signal Processing Magazine, vol. 16, no. 6, pp. 22-38, November 1999.
 DOI: 10.1109/79.799930
 http://ieeexplore.ieee.org/document/799930/

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Neural Circuit Tracer

Description

Neural Circuit Tracer (NCTracer) is open source software for automated and manual tracing of neurites from light microscopy stacks of images. NCTracer has more than one workflow available for neuron tracing. 


"The Neural Circuit Tracer is open source software built using Java (Sun Microsystems) and Matlab (MathWorks, Inc., Natick MA). It is based on the core of ImageJ (http://rsbweb.nih.gov/ij) and the graphic user interface has been developed by using Java Swings. The software combines anumber of functionalities of ImageJ with several newly developed functions for automated and manual tracing of neurites. The Neural Circuit Tracer is designed in a way
that will allow the users to add any plug-ins developed for ImageJ. More importantly, functions written in MatLab and converted into Java with Matlab JA toolbox can also be added to the Neural Circuit Tracer." 

Example of output from Neural Circuit Tracer

Microscopy Image Browser (MIB)

Description

Microscopy Image Browser (MIB) is a high-performance Matlab-based software package for advanced image processing, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets.

MIB is a freely available, user-friendly software for effective image processing of multidimensional datasets that improves and facilitates the full utilization of acquired data and enables quantitative analysis of morphological features. Its open-source environment enables fine tuning and possibility of adding new plug-ins to customize the program for specific needs of any research project.

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MIB