Robert Serafin's repositories
falsecolor
FalseColor Python is a rapid digital staining module designed for translating two-channel fluorescence images (i.e. a nuclear and cytoplasmic stain) to the traditional H&E histopathology color space.
dipy
DIPY is the paragon 3D/4D+ imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.
ifmodels
Package for
MosaicPlannerLive
MosaicPlanner is a python based GUI program for acquiring array tomography data using MicroManager as an interface.
nucleid_3d
Nuclear feature extractor for 3D segmented image data
OTLS-cellpose
Nuclear segmentation and feature extraction pipelines for 3D OTLS datasets using the cellpose segmentation framework
otlsnuc
intensity enhanced watershed segmentation