Repositories list

• K-mirror

  Public
  Scan field rotation with a K-mirror for fast two-photon imaging along curved planes

  neuroscienceopticscalcium-imaging+ 3

  neuroscienceopticscalcium-imagingmicroscopyneuroscience-methodstwo-photon

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks in HelmchenLabSoftware/K-mirror•33 stars in HelmchenLabSoftware/K-mirror•00 issues in HelmchenLabSoftware/K-mirror•00 pull requests in HelmchenLabSoftware/K-mirror•Updated Oct 13, 2026Oct 13, 2026

• Cascade

  Public
  Calibrated inference of spiking from calcium ΔF/F data using deep networks

  deep-learningcalcium-imagingdeconvolution+ 2

  deep-learningcalcium-imagingdeconvolutionspike-detectiontwo-photon

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •5151 forks in HelmchenLabSoftware/Cascade•171171 stars in HelmchenLabSoftware/Cascade•44 issues in HelmchenLabSoftware/Cascade•00 pull requests in HelmchenLabSoftware/Cascade•Updated Oct 4, 2026Oct 4, 2026

• delta_td

  Public
  Python

  •

  MIT License

  •00 forks in HelmchenLabSoftware/delta_td•11 star in HelmchenLabSoftware/delta_td•00 issues in HelmchenLabSoftware/delta_td•00 pull requests in HelmchenLabSoftware/delta_td•Updated Oct 1, 2026Oct 1, 2026

• multiarea_behavior_state_manuscript

  Public
  MATLAB

  •00 forks in HelmchenLabSoftware/multiarea_behavior_state_manuscript•00 stars in HelmchenLabSoftware/multiarea_behavior_state_manuscript•00 issues in HelmchenLabSoftware/multiarea_behavior_state_manuscript•00 pull requests in HelmchenLabSoftware/multiarea_behavior_state_manuscript•Updated Sep 21, 2026Sep 21, 2026

• td_dendrites

  Public
  Computational model for the manuscript 'Error representations in apical dendrites of neocortical layer 5 neurons during learning'

  saliencetemporal-differencing-learningpyramidal-neuron+ 3

  saliencetemporal-differencing-learningpyramidal-neurondendritic-computationsensory-processingtop-down-modulation

  Python

  •

  GNU General Public License v3.0

  •11 fork in HelmchenLabSoftware/td_dendrites•22 stars in HelmchenLabSoftware/td_dendrites•00 issues in HelmchenLabSoftware/td_dendrites•00 pull requests in HelmchenLabSoftware/td_dendrites•Updated Sep 19, 2025Sep 19, 2025

• multiarea_learning_manuscript

  Public
  Multiarea learning manuscript analysis code

  MATLAB

  •00 forks in HelmchenLabSoftware/multiarea_learning_manuscript•00 stars in HelmchenLabSoftware/multiarea_learning_manuscript•00 issues in HelmchenLabSoftware/multiarea_learning_manuscript•00 pull requests in HelmchenLabSoftware/multiarea_learning_manuscript•Updated Feb 25, 2025Feb 25, 2025

• Centripetal_propagation_astrocytes

  Public
  Custom code (Python or Matlab) to compute centripetal propagation from astrocytic calcium recordings using pixel-wise correlation functions

  calcium-imagingcorrelation-functionsastrocytes+ 1

  calcium-imagingcorrelation-functionsastrocyteshippocampus

  MATLAB

  •

  GNU General Public License v3.0

  •11 fork in HelmchenLabSoftware/Centripetal_propagation_astrocytes•99 stars in HelmchenLabSoftware/Centripetal_propagation_astrocytes•00 issues in HelmchenLabSoftware/Centripetal_propagation_astrocytes•00 pull requests in HelmchenLabSoftware/Centripetal_propagation_astrocytes•Updated Jan 2, 2025Jan 2, 2025

• wilhelm-sych-tmaze-analysis

  Public
  MATLAB

  •11 fork in HelmchenLabSoftware/wilhelm-sych-tmaze-analysis•00 stars in HelmchenLabSoftware/wilhelm-sych-tmaze-analysis•00 issues in HelmchenLabSoftware/wilhelm-sych-tmaze-analysis•00 pull requests in HelmchenLabSoftware/wilhelm-sych-tmaze-analysis•Updated Oct 19, 2023Oct 19, 2023

• mesostat-dev

  Public
  A library for exploratory analysis of multivariate mesoscopic neuronal signals

  Python

  •

  MIT License

  •00 forks in HelmchenLabSoftware/mesostat-dev•00 stars in HelmchenLabSoftware/mesostat-dev•00 issues in HelmchenLabSoftware/mesostat-dev•00 pull requests in HelmchenLabSoftware/mesostat-dev•Updated Aug 16, 2023Aug 16, 2023

• manual-multisession-alignment

  Public
  A tool for manually track neurons across days

  MATLAB

  •22 forks in HelmchenLabSoftware/manual-multisession-alignment•11 star in HelmchenLabSoftware/manual-multisession-alignment•00 issues in HelmchenLabSoftware/manual-multisession-alignment•00 pull requests in HelmchenLabSoftware/manual-multisession-alignment•Updated Aug 15, 2023Aug 15, 2023

• contrast-marker-video-tracker

  Public
  MATLAB

  •00 forks in HelmchenLabSoftware/contrast-marker-video-tracker•00 stars in HelmchenLabSoftware/contrast-marker-video-tracker•1414 issues in HelmchenLabSoftware/contrast-marker-video-tracker•00 pull requests in HelmchenLabSoftware/contrast-marker-video-tracker•Updated Jul 15, 2022Jul 15, 2022

• dlc-scripts

  Public
  This library contains scripts for DeepLabCut used for joint and whisker tracking, as well as some auxiliary video processing scripts

  Jupyter Notebook

  •11 fork in HelmchenLabSoftware/dlc-scripts•00 stars in HelmchenLabSoftware/dlc-scripts•00 issues in HelmchenLabSoftware/dlc-scripts•00 pull requests in HelmchenLabSoftware/dlc-scripts•Updated Apr 22, 2022Apr 22, 2022

• CaImAn_DendriteAnalysis

  Public
  Jupyter notebooks for analysis of dendritic two-photon calcium imaging data using the CaImAn toolbox.

  pythonneurosciencecalcium-imaging

  pythonneurosciencecalcium-imaging

  Jupyter Notebook

  •33 forks in HelmchenLabSoftware/CaImAn_DendriteAnalysis•77 stars in HelmchenLabSoftware/CaImAn_DendriteAnalysis•00 issues in HelmchenLabSoftware/CaImAn_DendriteAnalysis•00 pull requests in HelmchenLabSoftware/CaImAn_DendriteAnalysis•Updated Sep 16, 2019Sep 16, 2019

• CaImAn_LocomotionAnalysis

  Public
  Jupyter notebooks for analysis of Pia's two-photon calcium imaging data using the the CaImAn toolbox.

  Jupyter Notebook

  •11 fork in HelmchenLabSoftware/CaImAn_LocomotionAnalysis•11 star in HelmchenLabSoftware/CaImAn_LocomotionAnalysis•00 issues in HelmchenLabSoftware/CaImAn_LocomotionAnalysis•00 pull requests in HelmchenLabSoftware/CaImAn_LocomotionAnalysis•Updated Nov 29, 2018Nov 29, 2018

• blink-detector-ipy3

  Public
  A pipeline designed to process mouse blink videos, extract blink events and collect blinking statistics

  Jupyter Notebook

  •00 forks in HelmchenLabSoftware/blink-detector-ipy3•00 stars in HelmchenLabSoftware/blink-detector-ipy3•00 issues in HelmchenLabSoftware/blink-detector-ipy3•00 pull requests in HelmchenLabSoftware/blink-detector-ipy3•Updated Oct 3, 2018Oct 3, 2018

• CaImAn_legacy

  Public
  Jupyter Notebook

  •

  GNU General Public License v2.0

  •00 forks in HelmchenLabSoftware/CaImAn_legacy•00 stars in HelmchenLabSoftware/CaImAn_legacy•00 issues in HelmchenLabSoftware/CaImAn_legacy•00 pull requests in HelmchenLabSoftware/CaImAn_legacy•Updated May 16, 2018May 16, 2018

• HHNE

  Public
  Happy Hifo NWB Editor

  Python

  •

  GNU General Public License v3.0

  •00 forks in HelmchenLabSoftware/HHNE•00 stars in HelmchenLabSoftware/HHNE•00 issues in HelmchenLabSoftware/HHNE•00 pull requests in HelmchenLabSoftware/HHNE•Updated Nov 29, 2017Nov 29, 2017

• OCIA

  Public
  Calcium Imaging Analysis pipeline with a flexible framework

  MATLAB

  •

  GNU General Public License v3.0

  •33 forks in HelmchenLabSoftware/OCIA•33 stars in HelmchenLabSoftware/OCIA•00 issues in HelmchenLabSoftware/OCIA•00 pull requests in HelmchenLabSoftware/OCIA•Updated Nov 9, 2017Nov 9, 2017