Software
For software download and detailed instructions:
- GitHub: https://camriatunc.github.io
BrkRaw
A comprehensive tool to access raw Bruker Biospin MRI data
The ‘BrkRaw’ is a python module designed to provide a comprehensive tool to access raw data acquired from Bruker Biospin preclinical MRI scanner. This module is also compatible with the zip compressed data to enable use of the archived data directly.
The module is comprised of four components, including graphical user interface (GUI), command-line tools, high-level and low-level python APIs. - GitHub: https://github.com/BrkRaw/bruker
- Documentation: https://github.com/BrkRaw/brkraw.github.io
RodentMRISkullStripping
U-Net based automatic Rat brain-mask Segmentation tool
The ‘RodentMRISkullStripping’ is a python module designed to provide an automatic rodent skull stripping. This module is a deep-learning-based framework, U-Net, to automatically identify the rodent brain boundaries in MR images. The whole framework is implemented using Keras with TensorFlow as the backend.
- 2D U-Net GitHub: https://github.com/CAMRIatUNC/RodentMRISkullStripping
- 3D U-Net GitHub: https://github.com/CAMRIatUNC/RodentMRISkullStripping3D
- Documentation: https://github.com/CAMRIatUNC/RodentMRISkullStripping/blob/master/documentation.pdf
FindMissingPoint
Used to find the missing points of spectrum data from Ocean View spectrometers
Spectroscopic-VTI-T1
Spectroscopic VTI T1 measurement sequence. Modified from Bruker’s NSPECT sequence, on PV6.0.1.
Superoxide-Spin-Lattice-Relaxivity
This repository contains the functions, scripts and data used to analyze and plot the main findings of “Superoxide free radical spin-lattice relaxivity: A quench-assisted MR study”.
Matlab codes for photometry data analysis
Tools for process photometry spectra data acquired using Ocean Insight spectrometer system, including to read the spectra data from Ocean View .txt output, to segregate mixed multi-spectra, and to resolve interleaving recorded spectra. Additional tools for dynamic frequency power analysis and hemodynamic response function calculation are also included.