Analysis Packages - Aharoni-Lab/Miniscope-v4 GitHub Wiki

We currently recommend using the following combination of packages for Miniscope analysis:

  • Removing Horizontal Noise from Recordings provides information and a link to a short Python Jupyter Notebook we wrote to remove the main sources of noise in V4 Miniscope imaging data. Miniscope versions v4.40 isolate the source of this noise in hardware so the denoising Jupyter Notebook shouldn't be needed for those versions of the system.

  • Image Registration: NoRMCorre or Dario Ringach's recursive image registration algorithm. NoRMCorre can correct for both local and global rigid motion while Dario's approach works just on a global level.

  • Neuron segmentation and activity extraction: CNMF-E works extremely well for Miniscope imaging. It can denoise, demix, and deconvolve neural activity.

  • Tracking neurons across days: CellReg

Luckily, multiple groups are working on analysis packages which combine the approaches listed above into a single workflow:

  • CaImAn: "Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization." This toolbox is very well maintained by the Simons Foundation and generally has the most up-to-date versions of NoRMCorre and CNMF.

  • MiniscoPy: "A package to analyse calcium imaging data recorded with the Miniscope." This package is being developed by Adrien Peyrache's lab at McGill and is based on the CaImAn toolbox.

  • MiniscopeAnalysis: "Analysis package for miniscope data Written by Guillaume Etter (Sylvain Williams Lab, McGill University) This is an updated version of the Miniscope analysis package developed by Daniel Aharoni at UCLA in collaboration with the Golshani lab, Silva lab, and Khaki lab. It combines core functions of the original ms analysis package with NormCorre alignment and CNMFE source extraction."

  • MIN1PIPE: "MIN1PIPE is a fully automatic, Matlab-based toolbox, solving the full range problems in 1-photon calcium imaging in one package: data enhancement → movement morrection → signal extraction. It requires minimal parameter-tuning and integrates the semi-auto options. Each inidividual module can also be easily adapted for the 2-photon imaging setting."