gACSON software for visualization, processing and analysis of three-dimensional electron microscopy images

Related tags

Deep Learning gACSON
Overview

gACSON

gACSON software is to visualize, segment, and analyze the morphology of neurons in three-dimensional electron microscopy images.

If you use any part of gACSON in your research, please cite the software as

DOI

The segmentation algorithm used in gACSON is based on ACSON pipeline described in Abdollahzadeh, A., Belevich, I., Jokitalo, E., Tohka, J. & Sierra, A. Automated 3D Axonal Morphometry of WhiteMatter.Sci. Reports9, 6084 (2019).

Graphical user interface (GUI) for the segmentation and quantification of EM images in grey matter in MATLAB, enabling user interactive segmentation, proofreading, and correcting errors of an automated segmentation.

This software uses BM4D Matlab software, which can be found in http://www.cs.tut.fi/~foi/GCF-BM3D/

This software uses Bio-Formats 5.9.2 package, which can be found in https://www.openmicroscopy.org/bio-formats/downloads/

In order to be able to use this software, please download these two packages. They are not included to gACSON.

The path to the Bioformats has to be adjusted in file gACSON.m on the line 156.

This version of the software has been implemented and tested in Matlab R2018b.

You might also like...
Learning hidden low dimensional dyanmics using a Generalized Onsager Principle and neural networks

OnsagerNet Learning hidden low dimensional dyanmics using a Generalized Onsager Principle and neural networks This is the original pyTorch implemenati

Haijun.Yu 3 Aug 24, 2022
Scikit-event-correlation - Event Correlation and Forecasting over High Dimensional Streaming Sensor Data algorithms

scikit-event-correlation Event Correlation and Changing Detection Algorithm Theo

Intellia ICT 5 Oct 30, 2022
This is an easy python software which allows to sort images with faces by gender and after by age.

Gender-age Classifier This is an easy python software which allows to sort images with faces by gender and after by age. Usage First install Deepface

Claudio Ciccarone 6 Sep 17, 2022
Code to run experiments in SLOE: A Faster Method for Statistical Inference in High-Dimensional Logistic Regression.

Code to run experiments in SLOE: A Faster Method for Statistical Inference in High-Dimensional Logistic Regression. Not an official Google product. Me

Google Research 27 Dec 12, 2022
This is the code for "HyperNeRF: A Higher-Dimensional Representation for Topologically Varying Neural Radiance Fields".

HyperNeRF: A Higher-Dimensional Representation for Topologically Varying Neural Radiance Fields This is the code for "HyperNeRF: A Higher-Dimensional

Google 702 Jan 2, 2023
An implementation of the [Hierarchical (Sig-Wasserstein) GAN] algorithm for large dimensional Time Series Generation
An implementation of the [Hierarchical (Sig-Wasserstein) GAN] algorithm for large dimensional Time Series Generation

Hierarchical GAN for large dimensional financial market data Implementation This repository is an implementation of the [Hierarchical (Sig-Wasserstein

null 11 Nov 29, 2022
Torch-based tool for quantizing high-dimensional vectors using additive codebooks

Trainable multi-codebook quantization This repository implements a utility for use with PyTorch, and ideally GPUs, for training an efficient quantizer

Daniel Povey 41 Jan 7, 2023
An implementation of chunked, compressed, N-dimensional arrays for Python.
An implementation of chunked, compressed, N-dimensional arrays for Python.

Zarr Latest Release Package Status License Build Status Coverage Downloads Gitter Citation What is it? Zarr is a Python package providing an implement

Zarr Developers 1.1k Dec 30, 2022
The implementation for paper Joint t-SNE for Comparable Projections of Multiple High-Dimensional Datasets.

Joint t-sne This is the implementation for paper Joint t-SNE for Comparable Projections of Multiple High-Dimensional Datasets. abstract: We present Jo

IDEAS Lab 7 Dec 18, 2022
Comments
  • TODO list:

    TODO list:

    • stretch the Z-dimension in XY/XZ/YZ views
    • read the voxel sizes from Amira mesh files
    • machine-learning part - change the size of the labels or delete/modify the ones that were already placed
    • zooming kept when changing slides
    • When there are several datasets open, the slider may disappear, while the 3view plane view stays: image
    opened by AndreaBehan 0
Releases(v1.0.0)
Owner
Andrea Behanova
Andrea Behanova
GitHub
An image base contains 490 images for learning (400 cars and 90 boats), and another 21 images for testingAn image base contains 490 images for learning (400 cars and 90 boats), and another 21 images for testing

SVM Données Une base d’images contient 490 images pour l’apprentissage (400 voitures et 90 bateaux), et encore 21 images pour fait des tests. Prétrait

Achraf Rahouti 3 Nov 30, 2021
Web mining module for Python, with tools for scraping, natural language processing, machine learning, network analysis and visualization.

Pattern Pattern is a web mining module for Python. It has tools for: Data Mining: web services (Google, Twitter, Wikipedia), web crawler, HTML DOM par

Computational Linguistics Research Group 8.4k Jan 3, 2023
Finite-temperature variational Monte Carlo calculation of uniform electron gas using neural canonical transformation.

CoulombGas This code implements the neural canonical transformation approach to the thermodynamic properties of uniform electron gas. Building on JAX,

FermiFlow 9 Mar 3, 2022
PyElecCL - Electron Monte Carlo Second Checks

PyElecCL Python program to perform second checks for electron Monte Carlo radiat

Reese Haywood 3 Feb 22, 2022
Vehicle direction identification consists of three module detection , tracking and direction recognization.

Vehicle-direction-identification Vehicle direction identification consists of three module detection , tracking and direction recognization. Algorithm

null 5 Nov 15, 2022
Data Preparation, Processing, and Visualization for MoVi Data

MoVi-Toolbox Data Preparation, Processing, and Visualization for MoVi Data, https://www.biomotionlab.ca/movi/ MoVi is a large multipurpose dataset of

Saeed Ghorbani 51 Nov 27, 2022
Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. It can use GPUs and perform efficient symbolic differentiation.

============================================================================================================ `MILA will stop developing Theano <https:

null 9.6k Dec 31, 2022
Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. It can use GPUs and perform efficient symbolic differentiation.

============================================================================================================ `MILA will stop developing Theano <https:

null 9.6k Jan 6, 2023
Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. It can use GPUs and perform efficient symbolic differentiation.

============================================================================================================ `MILA will stop developing Theano <https:

null 9.3k Feb 12, 2021
Clustergram - Visualization and diagnostics for cluster analysis in Python

Clustergram Visualization and diagnostics for cluster analysis Clustergram is a diagram proposed by Matthias Schonlau in his paper The clustergram: A

Martin Fleischmann 96 Dec 26, 2022