gabriel-schirmbeck

fmri-analysis-course

Materials from fMRI data analysis course for cognitive science students.

obsidian-git

Integrate Git version control with automatic backup and other advanced features in Obsidian.md

cellpose

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

DLCAnalyzer

R Scripts to analyze deep lab cut point data and related data

deeplabcut

A Bonsai interface for real-time markerless pose estimation using DeepLabCut

DLC_ROI_tool

A tool for drawing ROIs on videos and analysing deeplabcut videos.

DLC2Kinematics

a module for kinematic analysis of deeplabcut outputs

CellSeg3D

A napari plugin for direct 3D cell segmentation -- taking you through training, inference, and review of masks

AmadeusGPT

[NeurIPS 2023] We turn natural language descriptions of behaviors into machine-executable code

DLCutils

Various scripts to support deeplabcut and what to do afterwards!

Deeplabcut-OpenFieldArena

A Deeplabcut network trained to label mice in open field arena with topdown view

qRAT

tidyqpcr

quantitative PCR analysis with the tidyverse

first-steps-with-R-training

repository of the 2-day course "First steps with R in Life Sciences" from SIB-training

flexplot

flexplot: graphical data analysis

fUS_pyTools

Tools for analysis of functional ultrasound imaging data

discovr

discovr package for R to accompany Discovering Statistics Using R and RStudio

whole-brain-fUS

Whole-brain functional ultrasound imaging in awake head-fixed mice

cytoscape-tutorials

Collection of modular Cytoscape tutorials for online presentation using reveal.js

trn

code related to viviano & schneider 2015, journal of neuroscience

DeepSlice

A python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.

pyrat

PyRat is a user friendly library in python to analyze data from the DeepLabCut. Developed to help researchers unfamiliar with programming can perform animal behavior analysis more simpler.

DeepLabCut

Official implementation of DeepLabCut: Markerless pose estimation of user-defined features with deep learning for all animals incl. humans

MARS

End-user version of the Mouse Action Recognition System (MARS)