Discover uw-loci/SpectralAnalysis Open Source project

Curvelet-Transform based fibrillar collagen quantification (CurveAlign and CT-FIRE)

curvelets

Non-disruptive collagen characterization in clinical histopathology using cross-modality image synthesis

he_shg_synth_workflow

Registration of histological images using stitching and registration plugins in FIJI via PyImageJ

automatic-histology-registration-pyimagej

Deep generative models for collagen fiber centerline segmentation and extraction in cancer tissue

collagen-fiber-metrics

A multi-purpose biological analysis tool

visbio

[RETIRED] Jar2lib tool for generating C++ proxy classes for a Java library

jar2lib

C++

github-backup-java

Backs up all GitHub-stored information about a repository to a dedicated branch.

Notebooks

Trainable multi-modal whole slide image scanner built on motorized microscope

smart-wsi-scanner

adaptive-optics

Adaptive Optics

Graph neural networks for PDAC vs CP in histology

gnn-pccp

Integration of curvelet analysis into KNIME (University of Konstanz / LOCI collaboration)

knime-curvelets

A Deep Zoom plugin for ImageJ

deep-zoom-plugin

[RETIRED] Maven plugin for generating C++ proxy classes for a Java library

cppwrap-maven-plugin

FIbeR Extraction (FIRE) - A tool for extracting network architecture from 3D, confocal images of biopolymer networks

fiber-extraction

A demonstration of how to call OpenCL from ImageJ [UNMAINTAINED]

opencl-demo

optogensim

Intensity-based registration of bright-field and second-harmonic generation images of histopathology tissue sections

shg_he_registration

Miscellaneous ImageJ plugins

misc-plugins

Sequential Erosion Tissue Imaging (SETI) Microscope Project

SETI

generate synthetic fiber networks for algorithm validation and machine learning

syntheticfibergenerator

Modules for multiscale imaging at LOCI

multiscale

Java code for use as a library from WiscScan

wiscscan-java

MATLAB code for analyzing FLIM data

flim-tool

Simple VisAD-based tool for visualizing multispectral images

multi-lut

A group of QuPath scripts for various projects at LOCI.

qupath-scripts

Groovy

flow-cytometry

Server application for flow cytometry with WiscScan

Objective-C

loci-checkstyle

LOCI's Checkstyle extensions, for checking source code style.

[RETIRED] WiscScan/UW-Forward integration

forward-cron-job

Shell

visbio-imagej

ImageJ plugins for 3D visualization using the VisAD toolkit

An example of image registration between Ultrasound and multiphoton microscopy, as well as analyzing the robustness of the transform.

US-Microscopy-fiducial-phantom

A java library to build clients for the SuperCollider server architecture.

JCollider

Improved search capabilities for OME Perl server [DISCONTINUED]

ome-server-search

Perl

collagen-alignment-analysis

Tools for automated alignment and analysis of collagen fibers

Controlling a Flamingo microscope from Python

Flamingo_Control

loci-utils

Miscellaneous utilities

Aperio and Ventana slide scanner importer plugin for FIJI/ImageJ, to be used for WiscScan XYZ grid generation.

slide-scanner-importer

Deconvolution in ImageJ via OpenCL [UNMAINTAINED]

opencl-decon

Adaptive colocalization algorithms

adaptive-coloc

Monte Carlo computation of optical tissue properties

op-props-mc

4d-software-suite

LOCI 4D Software Suite [DISCONTINUED]

Code to identify and classify fusion events

fusion-events

Lecture notes and materials from LOCI Coding Club programmer meetings.

coding-club

A tool for visualization of spectral lifetime data

slim-plotter

Scripts for mueller polarimetry collaboration with U Toronto

polarimetry

OBSOLETE - Use https://github.com/scijava/pom-scijava instead!

pom-loci

jvmlink

[RETIRED] A library for communicating between a Java Virtual Machine and other programs (e.g., C++ applications) via sockets.

C++

ejb-hessian-fht