Tools for computational pathology

Official MATLAB implementation of the "Sparse deconvolution" -v1.0.3

Pretraining a foundation model for generalizable fluorescence microscopy-based image restoration

Self-Supervised Vision Transformers for multiplexed imaging datasets

Official Python implementation of the 'Sparse deconvolution'-v0.3.0

Precision current source, with optional optical feedback, for driving LEDs and laser diodes

ZetaStitcher is a tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.

Point Spread Function calculations for fluorescence microscopy.

An open-source Python library for the analysis of luminescence lifetime and hyperspectral images using the phasor approach.

Neuroclear is a deep-learning-based Python module to train a deep neural network for the task of applying super-resolution to degraded axial resolution in fluorescence microscopy, using a single image stack.

A convex 3D deconvolution algorithm for low photon count fluorescence imaging

Resolution Enhancement Algorithm using Deblurring by Pixel Reassignment. This repository implements cutting-edge techniques for improving image resolution and clarity by reassigning pixels to correct for blur. Ideal for microscopy, photography, image processing, and computational optics researchers.

Single-cell fluorescence microscopy data analysis

File format agnostic low level, high performance API to read and process time-tagged-time resolved (TTTR) data for single-molecule and image spectroscopy)

GLabViz - Interactive Analysis and Visualization Application for Scientific Data written in Python using Qt and pyqtrgaph

PyFRAP: A Python based FRAP analysis tool box

Read and write PicoQuant PTU and related files (PHU, PCK, PCO, PFS, PUS, PQRES, PQDAT, PQUNI, SPQR, and BIN).

Real-time, interactive exploration of 3D image stacks

Read Olympus image files (OIF and OIB).

Read Becker & Hickl SDT files.

Plug-and-Play ADMM scheme based on an adaptive denoiser using the Schroedinger equation's solutions of quantum physics.

DDRS4PALS - A software for the acquisition and simulation of positron lifetime spectra (PALS) using the DRS4 evaluation board.

RNA smFISH oligos/probes design tool

Laboratory for Fluorescence Dynamics (LFD) file formats.

Pair correlation function analysis of fluorescence fluctuations in big image time series.

A set of ImageJ plugins to quantify dynamics, morphology, and fluorescence of microglial cells.

Read Leica image files (LIF, LOF, XLIF, XLCF, XLEF, and LIFEXT).

pipeline that converts Deepcell generated instance segmentation masks of nuclei from an ome-tiff to Cell Objects with auto-generated cytoplasms in QuPath

Step-by-step instruction to quantify fluorescence intensities from timelapse imaging experiments

An ImageJ plugin to quantify ciliary shape, length, and fluorescence.