Explore @uw-loci Open Source projects

UW-Madison LOCI (@uw-loci)

uw-loci

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127
Global Org. Rank 51,421 (Top 17 %)
Registered almost 13 years ago
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Java
42.9 %

Jupyter Notebook
18.4 %

MATLAB
16.3 %

Python
8.2 %

C++
4.1 %

Perl
2.0 %

M 2.0 %

Shell
2.0 %

Groovy
2.0 %

Objective-C
2.0 %
Location 🇺🇸 United States
Country Total Rank 37,909
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M 42

MATLAB
672

Groovy
1,246

Jupyter Notebook
4,122

Java
4,149

Perl
4,496

Objective-C
9,070

demo_wsi_superres

WSISR: Single image super-resolution for Whole slide Imaging using convolutional neural networks and self-supervised color normalization.

curvelets

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

he_shg_synth_workflow

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

automatic-histology-registration-pyimagej

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

Jupyter Notebook

collagen-fiber-metrics

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

Jupyter Notebook

visbio

A multi-purpose biological analysis tool

jar2lib

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

github-backup-java

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

Notebooks

Jupyter Notebook

smart-wsi-scanner

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

Jupyter Notebook

adaptive-optics

Adaptive Optics

gnn-pccp

Graph neural networks for PDAC vs CP in histology

Jupyter Notebook

knime-curvelets

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

deep-zoom-plugin

A Deep Zoom plugin for ImageJ

cppwrap-maven-plugin

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

fiber-extraction

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

opencl-demo

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

optogensim

shg_he_registration

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

misc-plugins

Miscellaneous ImageJ plugins

SETI

Sequential Erosion Tissue Imaging (SETI) Microscope Project

Jupyter Notebook

syntheticfibergenerator

generate synthetic fiber networks for algorithm validation and machine learning

SpectralAnalysis

Code for spectral separation for Fiber based spectral FLIM project

multiscale

Modules for multiscale imaging at LOCI

wiscscan-java

Java code for use as a library from WiscScan

flim-tool

MATLAB code for analyzing FLIM data

multi-lut

Simple VisAD-based tool for visualizing multispectral images

qupath-scripts

A group of QuPath scripts for various projects at LOCI.

flow-cytometry

Server application for flow cytometry with WiscScan

loci-checkstyle

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

forward-cron-job

[RETIRED] WiscScan/UW-Forward integration

visbio-imagej

ImageJ plugins for 3D visualization using the VisAD toolkit

US-Microscopy-fiducial-phantom

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

Jupyter Notebook

JCollider

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

ome-server-search

Improved search capabilities for OME Perl server [DISCONTINUED]

collagen-alignment-analysis

Tools for automated alignment and analysis of collagen fibers

Flamingo_Control

Controlling a Flamingo microscope from Python

loci-utils

Miscellaneous utilities

slide-scanner-importer

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

opencl-decon

Deconvolution in ImageJ via OpenCL [UNMAINTAINED]

adaptive-coloc

Adaptive colocalization algorithms

op-props-mc

Monte Carlo computation of optical tissue properties

4d-software-suite

LOCI 4D Software Suite [DISCONTINUED]

fusion-events

Code to identify and classify fusion events

coding-club

Lecture notes and materials from LOCI Coding Club programmer meetings.

Jupyter Notebook

slim-plotter

A tool for visualization of spectral lifetime data

polarimetry

Scripts for mueller polarimetry collaboration with U Toronto

Jupyter Notebook

pom-loci

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

jvmlink

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

ejb-hessian-fht

wavefrontRSA

Performs feedback control on a spatial light modulator based on images captured by two cameras. The feedback control implements a random search algorithm.

MR_dilution_phantom

Preclinical phantom for quantitative solution comparison in a small animal magnetic resonance imaging (MRI) machine