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NeuroWRAP

Core Modules

The following modules are available as part of the NeuroWRAP core modules. Follow the [“Install Module” instruction] (/docs/modules/installation.html) to install them within the NeuroWRAP.

Image registration

(Corrects for motion artifacts)

  • Particle-tracking-based: Based on the work of “Motion Correction based on trackable landmarks in the image sequence” (Aghayee 2017; Holobrain U19: UMD Losert Lab)
  • DFT registration: Based on “Efficient subpixel image registration by cross-correlation” (Guizar 2008)​

Cell segmentation

(Identifies regions of interests)

  • Manual cell clicking (Holobrain U19: UMD Kanold Lab)​
  • CaImAn Automatic cell segmentation (Flatiron Institute​)
  • CITE-On Automatic cell segmentation (Holobrain U19: IIT Fellin Lab​)

Fluorescence extraction and processing

  • Fluorescent time series extraction from ROIs (Holobrain U19: UMD Kanold Lab)​
  • Sliding window dF/F calculation (Holobrain U19: UMD Kanold Lab)

Fluorescent signal analysis​

  • Suite2p spike deconvolution (Pachitariu 2017​)
  • Granger Causality analysis (Holobrain U19: UMD Babadi Lab)