Repositories list

• 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 (CCM) - techniques which can account for non-linear dynamics to reconstruct attractors from time series data.

  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, logistic and linear regression.

  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

  •243•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

  •408•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

  •26•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