nhpatterson Goto Github PK

aicsimageio

Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python

aimsmsrc

Code and data accompanying Advanced Imaging Mass Spectrometry 2019 (AIMS.2019) R workshop

bfio

Interface to the Bioformats Java library

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.

codex-common-acquisition-metadata

detectron2

Detectron2 is a platform for object detection, segmentation and other visual recognition tasks.

flexformatter

create and modify naming within bruker flexImaging .mis files with a simple GUI

image-transform-converters

Conversion between spatial transformations of various formats / parametrizations

imsmicrolink-wsireg-notes

Notes to get started with imsmicrolink & wsireg

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

napari: a fast, interactive, multi-dimensional image viewer for python

napari-elx-reg-example

attempting to visualization linear 2D elastix transformations using napari's canvas model

napari-geojson

napari-imsmicrolink

napari plugin for IMS - Microscopy registration through laser ablation marks.

napari-wsireg

Whole slide image registration through wsireg in napari.

ome-zarr-py

Experimental implementation of images in Zarr files.

random_data

some random data

reg3dims

R Cardinal extension to perform automated registration of sequential 2D imaging mass spectrometry data to 3D

regcombims

Code accompanying "Co-registration and analysis of multiple imaging mass spectrometry datasets targeting different analytes"

regextract

Code for data analysis with Cardinal using regToolboxMSRC

registration-challenge

Code to support the registration Hackathon

regtoolboxmsrc

Registration toolbox for microscopy images integrated in imaging mass spectrometry experiments

simple-imzml-to-ometiff

Simple imzML to OME-TIFF for HuBMAP data ingestion

vitessce

Vitessce is a visual integration tool for exploration of spatial single-cell experiments.

wsimap

wsireg

multimodal whole slide image registration in a graph structure