/smfish_pipeline

Pipeline for Analysis of smFISH Images

Primary LanguageMATLABMIT LicenseMIT

smfish_pipeline

Pipeline for Analysis of smFISH Images

RNA

Module for segmentation of RNA and Transcription spots. Run "driver.m" function to initialize the process of segmentation, using a 16-bit z-stack of smFISH images.

Nuclei

Module for segmentation of nuclei and assignment of RNA and transcription objects to nearest nuclei.
"segmentation_driver.m" runs 3D connection of 2D nuclei images. "voronoi_driver.m" creates a voronoi diagram and uses it to assign RNA and transcription objects to their nearest nuclei.

Analysis

Functions for creating spatial bins and calculating statistics for analysis across space in discs.