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

Related tags

Deep LearninggACSON
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 Repository
IDM: An Intermediate Domain Module for Domain Adaptive Person Re-ID,

Intermediate Domain Module (IDM) This repository is the official implementation for IDM: An Intermediate Domain Module for Domain Adaptive Person Re-I

Yongxing Dai 87 Nov 22, 2022
Sequence Modeling with Structured State Spaces

Structured State Spaces for Sequence Modeling This repository provides implementations and experiments for the following papers. S4 Efficiently Modeli

HazyResearch 896 Jan 01, 2023
Code for "Multi-Time Attention Networks for Irregularly Sampled Time Series", ICLR 2021.

Multi-Time Attention Networks (mTANs) This repository contains the PyTorch implementation for the paper Multi-Time Attention Networks for Irregularly

The Laboratory for Robust and Efficient Machine Learning 68 Dec 17, 2022
System-oriented IR evaluations are limited to rather abstract understandings of real user behavior

Validating Simulations of User Query Variants This repository contains the scripts of the experiments and evaluations, simulated queries, as well as t

IR Group at Technische Hochschule Köln 2 Nov 23, 2022
The final project of "Applying AI to 3D Medical Imaging Data" from "AI for Healthcare" nanodegree - Udacity.

Quantifying Hippocampus Volume for Alzheimer's Progression Background Alzheimer's disease (AD) is a progressive neurodegenerative disorder that result

Omar Laham 1 Jan 14, 2022
Fastquant - Backtest and optimize your trading strategies with only 3 lines of code!

fastquant 🤓 Bringing backtesting to the mainstream fastquant allows you to easily backtest investment strategies with as few as 3 lines of python cod

Lorenzo Ampil 1k Dec 29, 2022
catch-22: CAnonical Time-series CHaracteristics

catch22 - CAnonical Time-series CHaracteristics About catch22 is a collection of 22 time-series features coded in C that can be run from Python, R, Ma

Carl H Lubba 229 Oct 21, 2022
McGill Physics Hackathon 2021: Reaction-Diffusion Models for the Generation of Biological Patterns

DiffuseAnimals: Reaction-Diffusion Models for the Generation of Biological Patterns Introduction Reaction-diffusion equations can be utilized in order

Austin Szuminsky 2 Mar 07, 2022
LAMDA: Label Matching Deep Domain Adaptation

LAMDA: Label Matching Deep Domain Adaptation This is the implementation of the paper LAMDA: Label Matching Deep Domain Adaptation which has been accep

Tuan Nguyen 9 Sep 06, 2022
Paaster is a secure by default end-to-end encrypted pastebin built with the objective of simplicity.

Follow the development of our desktop client here Paaster Paaster is a secure by default end-to-end encrypted pastebin built with the objective of sim

Ward 211 Dec 25, 2022
A lightweight library to compare different PyTorch implementations of the same network architecture.

TorchBug is a lightweight library designed to compare two PyTorch implementations of the same network architecture. It allows you to count, and compar

Arjun Krishnakumar 5 Jan 02, 2023
Multi agent DDPG algorithm written in Python + Pytorch

Multi agent DDPG algorithm written in Python + Pytorch. It also includes a Jupyter notebook, Tennis.ipynb, as a showcase.

Rogier Wachters 2 Feb 26, 2022
Self-Supervised Monocular DepthEstimation with Internal Feature Fusion(arXiv), BMVC2021

DIFFNet This repo is for Self-Supervised Monocular DepthEstimation with Internal Feature Fusion(arXiv), BMVC2021 A new backbone for self-supervised de

Hang 94 Dec 25, 2022
Fortuitous Forgetting in Connectionist Networks

Fortuitous Forgetting in Connectionist Networks Introduction This repository includes reference code for the paper Fortuitous Forgetting in Connection

Hattie Zhou 14 Nov 26, 2022
[AAAI22] Reliable Propagation-Correction Modulation for Video Object Segmentation

Reliable Propagation-Correction Modulation for Video Object Segmentation (AAAI22) Preview version paper of this work is available at: https://arxiv.or

Xiaohao Xu 70 Dec 04, 2022
A modular application for performing anomaly detection in networks

Deep-Learning-Models-for-Network-Annomaly-Detection The modular app consists for mainly three annomaly detection algorithms. The system supports model

Shivam Patel 1 Dec 09, 2021
Pytorch Implementation of PointNet and PointNet++++

Pytorch Implementation of PointNet and PointNet++ This repo is implementation for PointNet and PointNet++ in pytorch. Update 2021/03/27: (1) Release p

Luigi Ariano 1 Nov 11, 2021
PyTorch implementation of "Supervised Contrastive Learning" (and SimCLR incidentally)

PyTorch implementation of "Supervised Contrastive Learning" (and SimCLR incidentally)

Yonglong Tian 2.2k Jan 08, 2023
Keras + Hyperopt: A very simple wrapper for convenient hyperparameter optimization

This project is now archived. It's been fun working on it, but it's time for me to move on. Thank you for all the support and feedback over the last c

Max Pumperla 2.1k Jan 03, 2023
Non-Official Pytorch implementation of "Face Identity Disentanglement via Latent Space Mapping" https://arxiv.org/abs/2005.07728 Using StyleGAN2 instead of StyleGAN

Face Identity Disentanglement via Latent Space Mapping - Implement in pytorch with StyleGAN 2 Description Pytorch implementation of the paper Face Ide

Daniel Roich 58 Dec 24, 2022