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155 search results found

ExTrack MLE for diffusive noisy single-particle tracks

Tipi4icy ⭐ 10

tipi4icy is a collection of Icy plugins based on TiPi

Adaptive_interference_inference ⭐ 10

A mathematical optimization problem, inspired by an apparent paradox in the physics of optical measurement. Read the micro-publication here: https://andrewgyork.github.io/adaptive_interferenc

Python workflow tool for generating meshes from 2D and 3D image data

Software used by the AGH team during the ANHIR challenge.

Simtoolbox ⭐ 9

All released versions of SIMToolbox MATLAB codes

Microscpsf Imagej ⭐ 9

ImageJ plugin for the fast generation of microscopy PSF

Deephistreg ⭐ 9

Code used to create the DeepHistReg submission to the ANHIR challenge.

Brightfield Drift Correction 3d ⭐ 8

Acquire bright field images along with the super resolution data and use it to track drift in 3D with nanometer precision!

Adaptive Optics plugin for MicroManager

Zfvascularquantification ⭐ 8

#ZVQ - Zebrafish Vascular Quantification - https://doi.org/10.1242/dev.199720

Maskflow Fiji ⭐ 8

A Fiji plugin for object detection and tracking based on MaskRCNN.

Ps_decomp ⭐ 8

Periodic plus smooth image decomposition, as described by Moisan (http://www.math-info.univ-paris5.fr/~moisan/paper

Image reading, metadata management, and image writing for Microscopy images in Python

Trackhack ⭐ 7

Single-particle tracking program

Radio-Frequency Ultrasound Localization Microscopy

navigate - open source light-sheet microscope controls

Itkioopenslide ⭐ 7

An ITK ImageIO module for the OpenSlide library.

Pymontecarlo ⭐ 7

Python interface for Monte Carlo simulation programs

Napari Czann Segment ⭐ 7

Semantic Segmention and Image2Image using DeepLearning ONNX models packaged as *.czann files.

python library for numerical focusing (refocusing, autofocusing) of complex wave fields

Simplipytem ⭐ 7

Package to make analysis of transmission electron microscopy images simple.

Cytominer Database ⭐ 7

A package for storing morphological profiling data.

Cmeanalysis ⭐ 7

clathrin-mediated endocytosis analysis

Ara_tools ⭐ 6

Analysis of mouse brain STP data with respect to the Allen Reference Atlas

Bioimager ⭐ 6

A .NET microscopy imaging application based on Bio library. Supports various microscopes by using imported libraries & GUI automation. Supports XInput game controllers to move stage, take images, run ImageJ macros on images or Bio C# scripts.

Bakingtray ⭐ 6

Serial-section automated anatomy extension for ScanImage

A toolbox for optical simulation. The implementation of phase-retrieval algorithm is included.

A .NET library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.

ERNet: Segmentation of Endoplasmic Reticulum microscopy images using modified CNN-based image restoration models.

Dicomslide ⭐ 6

Python library for reading whole slide images in DICOM format

Maes_microscopy ⭐ 6

Official repo for Recursion's accepted spotlight paper at NeurIPS 2023 Generative AI & Biology workshop.

Cellocity ⭐ 6

Scientific software for analysis of confluent cell dynamics.

Compactionanalyzer ⭐ 6

Evaluates the fiber orientation and intensity around cells that compact collagen tissue as measure of contractile strength.

Single Layer 3d Tfm ⭐ 6

Repository for single-layer 3D TFM for measuring cellular displacements and tractions with epifluorescence microscopy

A cross platform version of Bio library & program. Bio is a library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.

Napari Psf Analysis ⭐ 6

A napari plugin to analysis point spread functions.

A Python library to numerically recover the complex wavefield information of samples from Digital Holographic Microscopy (DHM) recordings. Phase compensation, phase-shifting methods, and numerical propagators for different configurations and types of recordings in DHM are provided.

Toolkit for simulating real-time control systems for super-resolution microscopy.

[WACV 2024] Reference implementation of "AnyStar: Domain randomized universal star-convex 3D instance segmentation"

Reconstruct ⭐ 5

Source code for Reconstruct

Vectorial Light Sheet Simulation ⭐ 5

Vectorial ray tracing software for light-sheet microscopes

A .NET library for working with scientific image data in TIFF files

Inline_holo ⭐ 5

Python code for inline holography using through-focus image series.

Lucyd Deconvolution ⭐ 5

A Feature-Driven Richardson-Lucy Deconvolution Network

Correlescence ⭐ 5

spatial and temporal cross correlations in 1D and 2D for fluorescent microscopy (ImageJ plugin)

This repository provides a collection of tools to simplify reading CZI (Carl Zeiss Image) pixel and metadata in Python. In addition it also contains other useful utilities to visualize CZI images inside Napari.

Superresolution visualization of 3D protein localization data from a range of microscopes

Simplemscanner ⭐ 5

Simple MATLAB scanning software for demo purposes

Pycudasirecon ⭐ 5

CUDA-accelerated reconstruction for 3D-structured-illumination

Fast and Flexible Volume Compression Library

Napari Apr Viewer ⭐ 5

Create and view APR images in napari

RDM4mic working group - research data management for microscopy data

Flowcatchr ⭐ 5

A framework for tracking and analyzing flowing blood cells in time lapse microscopy images

Rescan_line_sted ⭐ 5

A scientific publication, describing a way to improve microscopy. This repository hosts everything you need to reproduce our results. Read the publication here: https://andrewgyork.github.io/rescan_line_sted

101-155 of 155 search results

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