savagedude3

Micro_Morph

3DMorph

3DMorph is a MATLAB-based script that analyzes microglia morphology from 3D data. Outputs include cell and territorial volume, branch length, and number of branch and end points.

astro_brian

biocoding_resources

A collection of helpful resources I've found for learning to program for neurobiology.

ChIP-seq-analysis

ChIP-seq analysis notes from Ming Tang

Circle.js

A function collection for working with circles

comp-glia-book

compbio_src

Introduction to Computational Biology - source Rmarkdown files

cyop

Excel-Reverse-Complement

A simple add-in for Excel supplying functions to calculate the reverse, complement, and reverse-complement of a nucleotide sequence

favuzzi_synaptic-analyses

fiji

A "batteries-included" distribution of ImageJ :battery:

ilastik4ij

ImageJ plugins to run ilastik workflows

introImageJMacros

IsoPops

R package for analysis of isoform-diverse transcript datasets

MintChIP

pipeline for MintChIP

mmqt

Microglia morphology quantification tool

napari-training-course

Lectures for a napari training course

pfb2019

Programming for Biology 2019

prep_calendar_app

Publications

Scripts used in published papers

puncta-analyzer

Puncta Analyzer for ImageJ2

rocketchip

shiny.rstudio.com-tutorial

Slides and exercises for the video tutorial at https://shiny.rstudio.com/tutorial/

skimage-tutorials

skimage-tutorials: a collection of tutorials for the scikit-image package.

social-behavior-analysis

Work in progress Python code for analyzing deeplabcut output for social behavior.

Syn_Bot_Helper

ImageJ/Fiji plugin to skeletonize binary images

SynQuant

A Fiji plugin that automatically quantify synapses from multi-channel fluorescence microscopy images.

SynQuant_MATLAB_Java

Example of calling SynQuant from MATLAB

tf_unet

Generic U-Net Tensorflow implementation for image segmentation