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@dafishcode Meyer Lab

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    23 repositories

    • zebrafishtrack_analysis

      Public
      The R script bundle used for importing data from tracker and for behavioural analysis
      R
      •1•0•0•0•Updated Jan 9, 2023Jan 9, 2023

    • empirical_dynamic_modelling

      Public
      Repo for running empirical dynamic modelling techniques on data - using lagged coordinate embedding to perform simplex projection and convergent cross mapping (…
      Jupyter Notebook
      •1•2•0•0•Updated Jan 8, 2023Jan 8, 2023

    • criticality

      Public
      Repo contains code for algorithms which calculate the spatiotemporal cascade of activity and measures critical statistics.
      Jupyter Notebook
      •1•1•0•0•Updated Jan 8, 2023Jan 8, 2023

    • development_network_model

      Public
      Repo for simulating spiking network models over development to understand mechanisms shaping self organising criticality in the brain.
      Python
      •0•2•0•0•Updated Jan 8, 2023Jan 8, 2023

    • seizure_detection

      Public
      This repo is used for detecting the timecourse of seizure events in generalised and focal seizures in larval zebrafish PTZ data.
      Jupyter Notebook
      •1•0•0•0•Updated Jan 8, 2023Jan 8, 2023

    • img_process

      Public
      Scripts for pre-processing image data in python
      Jupyter Notebook
      •1•1•0•0•Updated Jan 8, 2023Jan 8, 2023

    • seizure_dynamics

      Public
      Repo for calculating eigenspectra, population smoothness and velocity in spontaneous dynamics.
      Jupyter Notebook
      •1•1•0•1•Updated Jan 8, 2023Jan 8, 2023

    • zebrafish_mutant_analysis

      Public
      Repo for analysing zebrafish mutant neural dynamics.
      Jupyter Notebook
      •1•0•0•0•Updated Jan 8, 2023Jan 8, 2023

    • avalanche_model

      Public
      Repo for building spiking networks for modelling avalanche dynamics.
      Jupyter Notebook
      •1•0•0•0•Updated Jan 8, 2023Jan 8, 2023

    • vcortex_encoding

      Public
      Repo for analysing dimensionality of spontaneous and evoked activity, and encoding of stimuli in the layers of the visual cortex, using dimensionality reduction…
      Jupyter Notebook
      •1•0•0•0•Updated Jan 7, 2023Jan 7, 2023

    • zebrafishtrack_cam

      Public
      Controls the camera on the behavioural rig, alllows triggering when larvae appear in ROI, and recording for fixed duration (timeout def10min)
      C++
      •1•0•0•0•Updated Jul 13, 2022Jul 13, 2022

    • PatchWarp

      Public
      Image processing pipeline to correct motion artifacts and complex image distortions in neuronal calcium imaging data.
      MATLAB
      •
      GNU General Public License v2.0
      •7•0•0•0•Updated Apr 27, 2022Apr 27, 2022

    • rec2track_qt

      Public
      Tool for behavioural recording and stimuli presentation during 2photon imaging
      behaviorimaging
      C++
      •1•0•0•0•Updated Apr 14, 2022Apr 14, 2022

    • TailTracker

      Public
      Want to track the tail motion from the Zfish mounted on the 2p scope? Here is an application got offline tracking for the 2p scope setup
      tracking
      Makefile
      •0•0•0•0•Updated Apr 11, 2022Apr 11, 2022

    • suite2p

      Public
      cell detection in calcium imaging recordings
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •269•0•0•0•Updated Mar 31, 2022Mar 31, 2022

    • cellpose

      Public
      a generalist algorithm for cellular segmentation
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •584•0•0•0•Updated Mar 23, 2022Mar 23, 2022

    • suite2p_analysis_py

      Public
      Working with suite2p segmented functional images
      Jupyter Notebook
      •2•1•0•0•Updated Mar 3, 2022Mar 3, 2022

    • ontogenyofhunting_pub

      Public
      Code associated with the article "Learning steers the ontogeny of an efficient hunting sequence in zebrafish larva."
      R
      •
      Creative Commons Zero v1.0 Universal
      •2•0•0•0•Updated Sep 9, 2020Sep 9, 2020

    • SfN19

      Public
      Dynamic Poster for SfN 2019
      HTML
      •
      MIT License
      •2•1•1•0•Updated Jun 12, 2020Jun 12, 2020

    • Lightsheet_Zebrafish

      Public
      Preprocessing steps for light sheet imaging in zebrafish
      Jupyter Notebook
      •0•0•0•0•Updated Feb 3, 2020Feb 3, 2020

    • stytra

      Public
      A modular package to control stimulation and track behaviour
      Python
      •
      GNU General Public License v3.0
      •30•0•0•0•Updated Jan 30, 2020Jan 30, 2020

    • Lightsheet-Cell-Segment

      Public
      Trialling cell segmentation algorithms for light sheet imaging in zebrafish
      Python
      •0•0•0•0•Updated Nov 26, 2018Nov 26, 2018

    • Education-Optics

      Public
      A repository of CAD files for 3D printable optical components.
      10•0•0•0•Updated Dec 12, 2017Dec 12, 2017