Pinned Repositories
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
Micro_Morph
savagedude3's Repositories
savagedude3/Micro_Morph
savagedude3/3DMorph
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.
savagedude3/astro_brian
savagedude3/biocoding_resources
A collection of helpful resources I've found for learning to program for neurobiology.
savagedude3/ChIP-seq-analysis
ChIP-seq analysis notes from Ming Tang
savagedude3/Circle.js
A function collection for working with circles
savagedude3/comp-glia-book
savagedude3/compbio_src
Introduction to Computational Biology - source Rmarkdown files
savagedude3/cyop
savagedude3/Excel-Reverse-Complement
A simple add-in for Excel supplying functions to calculate the reverse, complement, and reverse-complement of a nucleotide sequence
savagedude3/favuzzi_synaptic-analyses
savagedude3/fiji
A "batteries-included" distribution of ImageJ :battery:
savagedude3/ilastik4ij
ImageJ plugins to run ilastik workflows
savagedude3/introImageJMacros
savagedude3/IsoPops
R package for analysis of isoform-diverse transcript datasets
savagedude3/MintChIP
pipeline for MintChIP
savagedude3/mmqt
Microglia morphology quantification tool
savagedude3/napari-training-course
Lectures for a napari training course
savagedude3/pfb2019
Programming for Biology 2019
savagedude3/prep_calendar_app
savagedude3/Publications
Scripts used in published papers
savagedude3/puncta-analyzer
Puncta Analyzer for ImageJ2
savagedude3/rocketchip
savagedude3/shiny.rstudio.com-tutorial
Slides and exercises for the video tutorial at https://shiny.rstudio.com/tutorial/
savagedude3/skimage-tutorials
skimage-tutorials: a collection of tutorials for the scikit-image package.
savagedude3/social-behavior-analysis
Work in progress Python code for analyzing deeplabcut output for social behavior.
savagedude3/Syn_Bot_Helper
ImageJ/Fiji plugin to skeletonize binary images
savagedude3/SynQuant
A Fiji plugin that automatically quantify synapses from multi-channel fluorescence microscopy images.
savagedude3/SynQuant_MATLAB_Java
Example of calling SynQuant from MATLAB
savagedude3/tf_unet
Generic U-Net Tensorflow implementation for image segmentation