KNeuroViz video(demo)

(Poster) https://github.com/Virusuki/KNeuroViz/blob/master/files/KNeuroViz_poster.pdf
(youtube demo) https://youtu.be/wJ-n5PRnLTQ

KNeuroViz

The KNeuroViz is extended to a system with user-convenient and detailed analytical functions based on Neuroglancer. and Web visualization and analysis for neuroimaging datasets. Powered by Neuroglancer.

Features

In addition to the latest Neuroglancer features, KNeuroViz adds:

• Segmentation ID list window
• 3D Neuron mesh export .ctm or .obj file (KBrain-map App) function
• Input data loading button
• powerful serverless computing and multi storage(local/cloud)
• Automated pre-processing for visualization of KNeuroViz
• Processing and accessing terabytes of KNeuroViz 3D images, mesh obj, and ctm data

Installation

Pre-processing

KNeuroVIz preprocessing setup manual

1. sudo apt-get install g++ python3-dev # recommend Python3
2. pip install numpy
3. Download igneous source. You will want to use the master branch from the KNeuroViz fork of igneous.
4. cd igneous and pip install -r requirements.txt
5. python setup.py develop
6. Download KNeuroViz_preprocessing.py Tool from the python tool folder

Post-processing

A note about CORS: Failure to access a data source. As a security measure, browsers will in many prevent a webpage from accessing the true error code associated with a failed HTTP request. It is therefore often necessary to check the developer tools to see the true cause of any HTTP request error. see Cross-origin resource sharing (CORS)

1. Install nodejs and npm https://docs.npmjs.com/downloading-and-installing-node-js-and-npm

The KNeuroViz system is a built-in system running on a KBrain-map portal in private cloud. So, there are two cases in order to visualize the ouput of KNeuroViz preprocessing. Select as follows: (2.A-neuroglancer and 2.B-KNeuroViz 3D viewer)

2-1. views the results of KNeuroViz pre-processing with a neuroglancer.

• 2.A.1. Download igneous source. You will want to use the master branch from the KNeuroViz fork of neuroglancer.
• 2.A.2 nvm install stable
• 2.A.3 npm i
• 2.A.4 npm run dev-server

2-2. is a neuroglancer based extended KNeuroViz post-processing 3D viewer. However, since the post-processing viewer is linked with our private KBrain-map portal, we share it as a source file. we share it as a source file. (You can use it by modifying the input part of the loading data in the provided source file.) KNeuroViz viewer 3D features include:

• (1). Segmentation ID list window
• (2). 3D Neuron mesh export .ctm or .obj file (KBrain-map App) function
• (3). Input data loading button

Viewing a Precomputed 3D chunk Volume data on FileDisk or NAS

If you have Pre-computed 3D chunk data onto local disk and It can be used as input data for KNeuroViz :

1. npm install -g http-server
2. http-server -p port_number -a IP_addr --cors

• Then you can use KNeuroViz's input data URL format.

3. precomputed://http://IP_addr/chunk_dataset_layer

Deployment

We are operating the KBrain-map portal in a private cloud environment, and we will guide you through the source code and commands to set up a simple http-based ftp server to use KNeuroViz.

Segmentation data

TO BE UPLOADED.