neuron

ZeroCostDL4Mic

Collection
Description

ZeroCostDL4Mic: exploiting Google Colab to develop a free and open-source toolbox for Deep-Learning in microscopy

ZeroCostDL4Mic is a collection of self-explanatory Jupyter Notebooks for Google Colab that features an easy-to-use graphical user interface. They are meant to quickly get you started on learning to use deep-learning for microscopy. 

has topic
Electron microscopy
Super-resolution microscopy
Bright field microscopy
Machine learning
has function
Image segmentation
Object detection
Image denoising
Image correction
need a thumbnail

SNEMI3D: 3D Segmentation of neurites in EM images

Submitted by Perrine on Mon, 03/06/2023 - 16:45

In this challenge, a full stack of electron microscopy (EM) slices will be used to train machine-learning algorithms for the purpose of automatic segmentation of neurites in 3D. This imaging technique visualizes the resulting volumes in a highly anisotropic way, i.e., the x- and y-directions have a high resolution, whereas the z-direction has a low resolution, primarily dependent on the precision of serial cutting.

BioImage Model Zoo

Collection
Description

BioImage.IO -- a collaborative effort to bring AI models to the bioimaging community. 

  • Integrated with Fiji, ilastik, ImJoy and more
  • Try model instantly with BioEngine
  • Contribute your models via Github

This is a database of pretrained deep Learning models. 

has topic
Digital histology
Electron microscopy
Light microscopy
Fluorescence microscopy
Machine learning
has function
Image classification
Cell segmentation
Image denoising
need a thumbnail

Neuron Tracing Vaa3D (BJUT FM Spanning Tree)

Workflow
Description

Vaa3d BJUT Fast Marching Spanning Tree algorithm dockerised workflow for BIAFLOWS

has topic
Bioimage informatics
has function
Filament tracing
Neuron image analysis
need a thumbnail

Neuron Tracing Vaa3D (MST)

Workflow
Description

3D Neuron Tracing using Dockerized version of Vaa3D Minimum Spanning Tree (MST).

has topic
Bioimage informatics
has function
Filament tracing
Neuron image analysis
need a thumbnail
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