FinderSpiker

Calcium Imaging Signal Processing Toolbox

Experiment Profile:

• For synthetic dyes or genetically encoded indicators of calcium (neuronal) activity
• Calcium Transients Offline Detector
  • Automatic mode and Visual Inspection Mode.
• Multiple conditions (e.g. CTRL, +DRUG A, +DRUG B, etc).
• It can merge 2 different dyes (eg GCaMP/Syn + TdTomtato/cre) in the same field

See Quick User Guide

Brief Description

Optimized for Acquired Data in ImPatch and CSV exported data from Igor WaveMetrics

• Input

  • List of videos (e.g. CTRL01,.., CTRLN,DRUGA01,...,DRUGA0N,...)
  • List of ROIs Coordianates (CSV file from ImPatch)

• Output

  • Activity Matrix: R: Cells x Frames Activity as 1's
  • It identifies neural ensembles as coactive neurons
  • It creates functional network for Gephi Visualization by wiring neurons that fired together

• Algorithms

  • Calcium Transients Detection:
    • Detrending (RLAOSS)
    • Denoising (Wavelet Analysis)
    • Sparse Deconvolution (LASSO regularization)
  • Neural Ensembles Detection:
    • Hierarchichal Clustering
    • Cross Validation by Naive Bayes Classificator

• Results Visualization

  • Boxplots and Datasets for Diverse Experiments
  • Cummulative Distribution Functions of Descriptive Features:
    • Activity Features
    • Neural Ensembles Features
    • Functional Network Features (from Gephi)
  • Rebuild denoised video and Ca Transients Detection

• Third Party Software:

  • SpaRSA
  • Rain Cloud Plots
  • ReadImageJROI