Heath Patterson's repositories
napari-wsireg
Whole slide image registration through wsireg in napari.
regToolboxMSRC
Registration toolbox for microscopy images integrated in imaging mass spectrometry experiments
napari-imsmicrolink
napari plugin for IMS - Microscopy registration through laser ablation marks.
RegCombIMS
Code accompanying "Co-registration and analysis of multiple imaging mass spectrometry datasets targeting different analytes"
simple-imzml-to-ometiff
Simple imzML to OME-TIFF for HuBMAP data ingestion
flexformatter
create and modify naming within bruker flexImaging .mis files with a simple GUI
imsmicrolink-wsireg-notes
Notes to get started with imsmicrolink & wsireg
aicsimageio
Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python
biomic-hubmap-codex-processing
Scripts to prepare data submission to HuBMAP for VU BIOMIC's CODEX data
Cardinal_functions
Functions I wrote for CardinalMSI (http://www.cardinalmsi.org) for imaging mass spectrometry analysis.
detectron2
Detectron2 is a platform for object detection, segmentation and other visual recognition tasks.
image-transform-converters
Conversion between spatial transformations of various formats / parametrizations
ingest-validation-tools
HuBMAP data submission guidelines, and tools which check that submissions adhere to those guidelines.
ITKElastix
An ITK Python interface to elastix, a toolbox for rigid and nonrigid registration of images
napari-elx-reg-example
attempting to visualization linear 2D elastix transformations using napari's canvas model
ome-zarr-py
Experimental implementation of images in Zarr files.
random_data
some random data
regextract
Code for data analysis with Cardinal using regToolboxMSRC
registration-challenge
Code to support the registration Hackathon
vitessce
Vitessce is a visual integration tool for exploration of spatial single-cell experiments.