Sam-Freitas/LightSaver

Fluorescent analysis of individualized C. elegans

Language: MATLAB - Size: 1.55 GB - Last synced: about 5 hours ago - Pushed: about 16 hours ago - Stars: 5 - Forks: 4

Dana-Farber-AIOS/pathml

Tools for computational pathology

Language: Python - Size: 218 MB - Last synced: 2 days ago - Pushed: 11 days ago - Stars: 368 - Forks: 80

cgohlke/ptufile

Read PicoQuant PTU and related files

Language: Python - Size: 264 KB - Last synced: 4 days ago - Pushed: 8 days ago - Stars: 4 - Forks: 1

phasorpy/phasorpy

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

Language: Python - Size: 260 KB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 14 - Forks: 6

cgohlke/oiffile

Read Olympus image files (OIF and OIB)

Language: Python - Size: 216 KB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 10 - Forks: 1

Canadian-Light-Source/sgmdata

Helper module for working with data from the SGM Beamline

Language: Python - Size: 1000 KB - Last synced: 22 days ago - Pushed: 22 days ago - Stars: 2 - Forks: 1

aglowacki/XRF-Maps Fork of AdvancedPhotonSource/XRF-Maps

XRF-Maps is a C++ open source software package that implements these functions to provide a tool set for the analysis of XRF data sets

Language: C++ - Size: 5.49 MB - Last synced: 27 days ago - Pushed: 28 days ago - Stars: 1 - Forks: 1

cgohlke/psf

Point Spread Function calculations for fluorescence microscopy

Language: Python - Size: 141 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 29 - Forks: 4

cgohlke/lfdfiles

Laboratory for Fluorescence Dynamics (LFD) file formats

Language: Python - Size: 1010 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 5 - Forks: 2

cgohlke/chebyfit

Fit exponential and harmonic functions using Chebyshev polynomials

Language: C - Size: 79.1 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 2 - Forks: 1

Fluorescence-Tools/tttrlib

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

Language: C++ - Size: 904 MB - Last synced: 3 days ago - Pushed: about 1 month ago - Stars: 18 - Forks: 0

cgohlke/sdtfile

Read Becker & Hickl SDT files

Language: Python - Size: 80.1 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 10 - Forks: 6

wisstock/domb-napari

napari plugin for analyzing fluorescence-labeled proteins redistribution

Language: Python - Size: 18.3 MB - Last synced: 9 days ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

shibarjun/napari-findaureus

napari-findaureus: A tool designed to identify bacteria in infected bone tissue images obtained via Confocal Laser Scanning Microscopy (CLSM).

Language: Python - Size: 111 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

BBQuercus/eFISHent

RNA smFISH oligos/probes design tool

Language: Python - Size: 12.8 MB - Last synced: about 1 month ago - Pushed: 7 months ago - Stars: 10 - Forks: 0

lens-biophotonics/ZetaStitcher

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

Language: Python - Size: 3.15 MB - Last synced: 23 days ago - Pushed: 5 months ago - Stars: 37 - Forks: 6

JacobHanimann/scDINO

Self-Supervised Vision Transformers for multiplexed imaging datasets

Language: Python - Size: 19.2 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 30 - Forks: 8

cgohlke/icsdll

Interface to the image correlation spectroscopy library ICSx64.dll

Language: C++ - Size: 177 KB - Last synced: about 2 months ago - Pushed: 5 months ago - Stars: 1 - Forks: 0

zaman13/Photobleaching-Analysis

A python code for analyzing photobleaching in fluorescence microscopy from a time series TIF image stack

Language: Python - Size: 2.05 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 0

GiacomoGiacomelli/Cell-Profiles-and-Demographs

R-Scripts and Fiji-macro used for the construction of kymographs based on fluorescence profiles

Language: R - Size: 8.4 MB - Last synced: 3 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

DavidStirling/QuantiFish

Zebrafish embryo fluorescence quantification

Language: Python - Size: 195 KB - Last synced: about 15 hours ago - Pushed: about 18 hours ago - Stars: 3 - Forks: 1

alexblaessle/PyFRAP

PyFRAP: A Python based FRAP analysis tool box

Language: Python - Size: 8.9 MB - Last synced: 29 days ago - Pushed: over 3 years ago - Stars: 17 - Forks: 8

Jhsmit/ColiCoords

Single-cell fluorescence microscopy data analysis

Language: Python - Size: 84.3 MB - Last synced: about 1 month ago - Pushed: almost 3 years ago - Stars: 24 - Forks: 8

WeisongZhao/Sparse-SIM

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

Language: MATLAB - Size: 15.1 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 61 - Forks: 14

shanizu/FUSE

FUSE toolkit supports fluorescent cell image alignment and analysis.

Language: HTML - Size: 106 MB - Last synced: 25 days ago - Pushed: 3 months ago - Stars: 0 - Forks: 1

SayantanDutta95/QAB-PnP-ADMM-Deconvolution

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

Language: MATLAB - Size: 142 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 5 - Forks: 1

Anivader/HoloScreen-onco

High-throughput detection and enumeration of tumor cells in blood using Digital Holographic Microscopy (DHM) and Deep Learning.

Language: MATLAB - Size: 75.2 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

SPerrott22/Deepcell-to-QuPath

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

Language: Jupyter Notebook - Size: 37 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

WeisongZhao/sparse-deconv-py

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

Language: Python - Size: 67.4 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 32 - Forks: 14

stevexniu/fishprobe

FISHprobe: DNA Probe Design Pipeline

Language: HTML - Size: 87.6 MB - Last synced: 5 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

cgohlke/ipcf.ipynb

Tutorial on pair correlation function analysis of fluorescence fluctuations in big image time series

Language: HTML - Size: 2.98 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 10 - Forks: 1

FranckLab/single-layer-3D-TFM

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

Language: MATLAB - Size: 162 KB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 6 - Forks: 1

peterhpark/neuroclear

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.

Language: Jupyter Notebook - Size: 28.8 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 14 - Forks: 1

shalinshah1993/temporalDNAbarcodes

A MATLAB suite implementing computer vision pipeline to extract information from the noisy TIRF microscopy data (image stack)

Language: MATLAB - Size: 81.5 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 2

JoachimGoedhart/Quantify-Intensity-from-Timelapse

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

Size: 15.2 MB - Last synced: 7 months ago - Pushed: almost 5 years ago - Stars: 8 - Forks: 0

dpscience/DDRS4PALS

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

Language: C++ - Size: 31.7 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 10 - Forks: 5

atakehiro/GUI_ROI_tool

the GUI tool for taking a region of interest (ROI) from a fluorescence image

Language: MATLAB - Size: 14.6 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 1 - Forks: 0

yzhang34/two-step-SOS-sim

Super-resolution fluorescence microscopy by stepwise optical saturation

Language: MATLAB - Size: 471 KB - Last synced: 7 months ago - Pushed: about 5 years ago - Stars: 1 - Forks: 1

yzhang34/saturation-compensated-FLIM

Saturation-compensated measurements for fluorescence lifetime imaging microscopy

Language: MATLAB - Size: 657 KB - Last synced: 7 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

dpscience/DQuickLTFit

DQuickLTFit - A least-square fitting tool for the analysis of positron lifetime spectra using the Levenberg-Marquardt algorithm

Language: C++ - Size: 4.14 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 4 - Forks: 1

yzhang34/MPM-FD-FLIM-SNR

Investigation of signal-to-noise ratio in frequency-domain multiphoton fluorescence lifetime imaging microscopy

Language: MATLAB - Size: 2.1 MB - Last synced: 7 months ago - Pushed: about 5 years ago - Stars: 2 - Forks: 0

sanger-matteo/Memb_2_Cyto

This program perform automated analysis of fluorescence foci and their location in bacterial cells. The program defines the membrane and cytosol compartments and it measures several attributes of the fluorescence signal within these compartments, such as the ratio of signal between cytosol and membrane and the signal profile along the cell width in bacteria.

Language: MATLAB - Size: 4.31 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

yzhang34/Kmeans-FLIM-Phasors

Automatic segmentation of intravital fluorescence microscopy images by K-means clustering of FLIM phasors

Language: MATLAB - Size: 140 MB - Last synced: 7 months ago - Pushed: almost 5 years ago - Stars: 3 - Forks: 2

computational-imaging/ThreeDeconv.jl

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

Language: Julia - Size: 531 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 30 - Forks: 5

hansenjn/NuclQ

NuclQ - an ImageJ plugin to quantify intensity levels by distance to the nuclear membrane.

Language: Java - Size: 106 KB - Last synced: 4 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

hansenjn/CiliaQ

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

Language: Java - Size: 20.4 MB - Last synced: 7 months ago - Pushed: 9 months ago - Stars: 6 - Forks: 2

caticoa3/ImageJ_Semi-auto

ImageJ Scripts for Microscope Images of Florescently Labled Cells

Size: 1.54 MB - Last synced: 10 months ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

KerosuoLab/Shapemetrics

Language: MATLAB - Size: 7.6 MB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 3 - Forks: 1

bmandracchia/MIRO Fork of ShuJiaLab/MIRO

Multiscale Image Restoration for fluorescence microscopy

Language: MATLAB - Size: 32.2 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 1 - Forks: 0

hansenjn/MotiQ

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

Language: Java - Size: 7.93 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 6 - Forks: 1

midesjardins/Widefield-Imaging-Acquisition

A program designed to acquire brain imaging data using intrinsic, GCaMP fluorescence and IR laser speckle optical imaging in awake mice.

Language: Python - Size: 4.93 MB - Last synced: 9 months ago - Pushed: 10 months ago - Stars: 2 - Forks: 0

malj390/FISH_spot_selection

This tool is meant for the manual intensity extraction of FISH spots

Language: Jupyter Notebook - Size: 1.33 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

hansenjn/AdipoQ

A simple toolbox of ImageJ plugins for quantifying adipocyte morphology and function in tissues and in vitro.

Size: 95.9 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 2 - Forks: 0

maroiliop/Enrichment-Analysis

FIJI macros for Enrichment Analysis

Size: 444 KB - Last synced: 12 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

akabago/ZeroCostDL4Mic-VirtualMultiplexing

This

Language: Jupyter Notebook - Size: 1.06 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

AlexSath/prodivis

A tool to accurately normalize and visualize protein distribution in 3D structures imaged with confocal microscopy using z-stacks.

Language: Python - Size: 6.12 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 2 - Forks: 0

swharden/PrairieView-Quick-Loader

ImageJ plugin to quickly load multiphoton imaging data from PrairieView folders

Language: Java - Size: 66.4 KB - Last synced: 2 days ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

Isaac-Jardin/CaImAn

Calcium Imaging Analyzer (CaImAn) consists of a bunch of scripts written in python and put together to speed the analysis of calcium imaging experiments performed with the NIS-Elements Advanced Research software from Nikon.

Language: Python - Size: 88.9 KB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 0

UU-cellbiology/rods-detection-in-noisy-images

Detection of straight line segments (rods) in noisy images

Language: MATLAB - Size: 3.97 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 3 - Forks: 3

canfkoyuncu/ObjectOrientedSegmentation

Object Oriented Segmentation of Cell Nuclei in Fluorescence Microscopy Images

Language: MATLAB - Size: 117 KB - Last synced: over 1 year ago - Pushed: over 4 years ago - Stars: 1 - Forks: 2

jonnew/cyclops

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

Language: C++ - Size: 428 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 38 - Forks: 22

dpscience/DLTPulseGenerator

DLTPulseGenerator - A library for the simulation of lifetime spectra based on realistically modelled detector-output pulses

Language: C++ - Size: 2.47 MB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 2

SarthakJariwala/Python_GUI_apps

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

Language: Python - Size: 2.21 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 12 - Forks: 6

donal-s/roi-trace-selector

ROI Trace Selection

Language: TypeScript - Size: 5.17 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

QBioLab/CountmRNA.jl

Tracking cell and count mRNA inside each cell

Language: Jupyter Notebook - Size: 2.4 MB - Last synced: 6 months ago - Pushed: about 2 years ago - Stars: 1 - Forks: 0

imrahilias/biophysics

All this is part of my Projektarbeit (student project) @ TU Wien 2021

Language: Jupyter Notebook - Size: 149 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

garcia-nacho/DFSanalyzer

R package to analyze microscopic images of Double-Fluorescence Systems

Language: Roff - Size: 276 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

subhamoymahajan/in-silico-microscopy

This open-source software package allows in-silico microscopy of molecular simulations such as molecular dynamics, monte carlo, etc.

Language: Python - Size: 200 MB - Last synced: over 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 2

zoccoler/metroid

Computational tool to filter subcellular transmembrane potential signals from noisy single cell fluorescence videos

Language: Jupyter Notebook - Size: 334 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0

christophmark/imagej-interactive-thresholding

ImageJ macros that automate the workflow of thresholding and analyzing the size and intensity of objects/regions in microscope images.

Size: 9.77 KB - Last synced: about 1 year ago - Pushed: about 7 years ago - Stars: 1 - Forks: 1

lowrank/fumot-rte

fluorescence ultrasound modulated optical tomography with radiative transport equation.

Language: C - Size: 183 KB - Last synced: 4 months ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0

AndrewGYork/split_wrmscarlet

A scientific publication that describes a new red fluorophore, along with a set of strains, reagents and protocols, to make it faster and easier to label endogenous C. elegans proteins with fluorescent tags. Read the publication here: https://andrewgyork.github.io/split_wrmscarlet

Language: HTML - Size: 40.5 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 1

rsenft1/Fiji-Figure-Generator

Useful scripts for saving multichannel fluorescence images for use in figures and saving relevant metadata

Size: 2.1 MB - Last synced: 6 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 1

ssiddhantsharma/Mosquito-Haemolymph

Haemolymph Circulation in Mosquito larvae

Size: 363 KB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 1 - Forks: 0

mueller-lab/PyFDAP Fork of alexblaessle/PyFDAP

PyFDAP is a Python-based analysis framework for Fluorescence Decay After Photoconversion (FDAP) experiments.

Language: Python - Size: 3.88 MB - Last synced: about 1 year ago - Pushed: over 7 years ago - Stars: 1 - Forks: 0

ver228/bacteria-loci-tracker

Bacterial chromosmal foci tracker.

Language: MATLAB - Size: 79.7 MB - Last synced: over 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

gkoulouras/easyFRAP-web

A web tool for the analysis of Fluorescence Recovery After Photobleaching (FRAP) data.

Language: JavaScript - Size: 3.42 MB - Last synced: 7 months ago - Pushed: about 5 years ago - Stars: 2 - Forks: 0

chepo92/legoscope

Lego based fluorescence microscope

Language: Python - Size: 157 MB - Last synced: 11 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

DavidStirling/SpotMeasure

Quantitation of migration of fluorescent spots into regions of interest.

Language: Python - Size: 321 KB - Last synced: 10 months ago - Pushed: about 6 years ago - Stars: 1 - Forks: 0

uw-loci/SpectralAnalysis

Code for spectral separation for Fiber based spectral FLIM project

Language: Matlab - Size: 32.7 MB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0