Rebecca Senft's repositories
FISH-IHC-Colocalization-in-ImageJ
An ImageJ macro for 2D colocalization of IHC signals in ImageJ and counting RNAscope puncta within cells.
profiling-recipe
Image-based Profiling Recipe
2021-Video-Games
Code for making graphs in R with stats on the video games my partner and I played in 2021
2023-Video-Games
R code to visualize video game data from 2023!
auto-basket-detector-2D
ImageJ macro scripts for analyzing fluorescent microscopy images: segmenting cells, divide into quadrants, and quantify innervation
CellProfiler
An open-source application for biological image analysis
CellProfiler-Analyst
Open-source software for exploring and analyzing large, high-dimensional image-derived data.
CellProfiler-plugins
Community-contributed and experimental CellProfiler modules.
core
Core classes and components used by CellProfiler
example-workflows
These are example workflows created via COBA's support of Driving Biomedical Projects (DBP) via our P41 grant from the NIH.
Fiji-Figure-Generator
Useful scripts for saving multichannel fluorescence images for use in figures and saving relevant metadata
fpbase-interactive-app
Toy r shiny app for querying fpbase
jump-orf-data
New ORF data repo
MicCheck-uploader
Uploader app for custom microscopy metadata examples for MicCheck
MicCheck-v2
Updated version of Microscopy Metadata Checklist app (shiny)
MicCheck_v2
Shiny app for microscopy metadata reporting
MicroscopyForBeginnersReferenceGuide
A Beginner's guide to microscopy, from sample prep to acquisition, image analysis, and data interpretation
Mouse-Wheel-Running-Analysis
Scripts for analyzing wheel running data from custom raspberry pi system in R
quarto-web
Quarto website
quarto-website-template
Fork to create a Quarto website
rsenft1.github.io
my personal academic website and blog
tutorials
CellProfiler tutorial pipelines and images