fluorescence-microscopy-imaging

There are 5 repositories under fluorescence-microscopy-imaging topic.

pathml
Dana-Farber-AIOS / pathml
Tools for computational pathology
biomedical-image-processing computational-pathology deep-learning digital-pathology fluorescence-microscopy-imaging histopathology image-analysis machine-learning microscopy pathml pathology python pytorch research spatial-transcriptomics
Language:Python 368
Sparse-SIM
WeisongZhao / Sparse-SIM
Official MATLAB implementation of the "Sparse deconvolution" -v1.0.3
microscopy deconvolution matlab-gui super-resolution image-processing image-restoration fluorescence-microscopy-imaging
Language:MATLAB 70
jonnew / cyclops
Precision current source, with optional optical feedback, for driving LEDs and laser diodes
neuroscience optogenetics fluorescence fluorescence-microscopy-imaging arduino hardware led biology
Language:AGS Script 43
WeisongZhao / sparse-deconv-py
Official Python implementation of the 'Sparse deconvolution'-v0.3.0
fluorescence-microscopy-imaging image-processing image-restoration microscopy python3 super-resolution
Language:Python 40
lens-biophotonics / ZetaStitcher
ZetaStitcher is a tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.
stitching microscopy microscopy-images fluorescence-microscopy-imaging volumetric-images
Language:Python 37
JacobHanimann / scDINO
Self-Supervised Vision Transformers for multiplexed imaging datasets
high-content-screening self-supervised-learning single-cell fluorescence-microscopy-imaging greyscale-image morphology multi-channel multi-head-attention phenotyping vision-transformer unsupervised
Language:Python 34
cxm12 / UNiFMIR
Pretraining a foundation model for generalizable fluorescence microscopy-based image restoration
deep-learning fluorescence-microscopy-imaging image-processing
Language:Python 33
cgohlke / psf
Point Spread Function calculations for fluorescence microscopy
fluorescence-microscopy-imaging point-spread-function python
Language:Python 30
computational-imaging / ThreeDeconv.jl
A convex 3D deconvolution algorithm for low photon count fluorescence imaging
julia deconvolution-microscopy fluorescence-microscopy-imaging microscopy image-processing
Language:Julia 30
ColiCoords
Jhsmit / ColiCoords
Single-cell fluorescence microscopy data analysis
microscopy fluorescence-microscopy-imaging
Language:Python 24
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.
microscopy fluorescence-microscopy-imaging deep-learning
Language:Jupyter Notebook 19
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
ptu flim becker picoquant python single-molecule fluorescence fluorescence-correlation fluorescence-microscopy-imaging imaging
Language:C++ 18
alexblaessle / PyFRAP
PyFRAP: A Python based FRAP analysis tool box
data-fitting fluorescence-microscopy-imaging frap frap-analysis frap-experiment gui pde python
Language:Python 17
SarthakJariwala / Python_GUI_apps
GLabViz - Interactive Analysis and Visualization Application for Scientific Data written in Python using Qt and pyqtrgaph
python data-analysis data-visualization fluorescence-decays-analysis spectral-analysis fluorescence-microscopy-analysis uv-vis qt-gui fluorescence fluorescence-microscopy-imaging spectroscopy spectrum-analyzer qt image-analysis spectra-analysis python-gui-apps databrowser lifetime-analysis pyqtgraph
Language:Python 17
phasorpy / phasorpy
An open-source Python library for the analysis of fluorescence lifetime and hyperspectral images using the phasor approach
fluorescence-microscopy-imaging image-analysis python flim phasor
Language:Python 14
delunapaolo / calipy
Real-time, interactive exploration of 3D image stacks
calcium-imaging gui python numpy pyqtgraph pyqt microscopy live-microscopy exploratory-data-analysis exploratory-data-visualizations interactive-analysis segmentation cell-segmentation fluorescence-microscopy-imaging fluorescence-data fluorescence-traces
Language:Python 12
dpscience / DDRS4PALS
DDRS4PALS - A software for the acquisition and simulation of positron lifetime spectra (PALS) using the DRS4 evaluation board.
positrons pals lifetime-spectroscopy switched-capacitor-array drs4 domino-ring-sampler dltpulsegenerator simulation acquisition drs4-evaluation-board detector pulse photomultiplier antimatter positron-lifetime-spectra qt-framework mpfit alglib lifetime-spectra fluorescence-microscopy-imaging
Language:C++ 11
BBQuercus / eFISHent
RNA smFISH oligos/probes design tool
bioinformatics cli fluorescence-microscopy-imaging
Language:Python 10
cgohlke / ipcf.ipynb
Pair correlation function analysis of fluorescence fluctuations in big image time series
python jupyter-notebook fluorescence-fluctuations tutorial pair-correlation fluorescence-microscopy-imaging
Language:HTML 10
cgohlke / oiffile
Read Olympus image files (OIF and OIB)
fluorescence-microscopy-imaging format-reader image olympus python
Language:Python 10
cgohlke / sdtfile
Read Becker & Hickl SDT files
fluorescence-lifetime-spectroscopy fluorescence-microscopy-imaging format-reader photon-counting python
Language:Python 10
JoachimGoedhart / Quantify-Intensity-from-Timelapse
Step-by-step instruction to quantify fluorescence intensities from timelapse imaging experiments
imagej fluorescence-intensity fluorescence-microscopy-imaging time-series-analysis
8
single-layer-3D-TFM
FranckLab / single-layer-3D-TFM
Repository for single-layer 3D TFM for measuring cellular displacements and tractions with epifluorescence microscopy
tfm traction microscopy traction-force-microscopy matlab fenics neutrophil fluorescence-microscopy-imaging epifluorescence
Language:MATLAB 7
SayantanDutta95 / QAB-PnP-ADMM-Deconvolution
Plug-and-Play ADMM scheme based on an adaptive denoiser using the Schroedinger equation's solutions of quantum physics.
deconvolution quantum-computing adaptive-transformation admm admm-algorithm deblurring deblurring-algorithm fluorescence-microscopy-imaging image image-processing image-restoration plug-and-play-priors plugandplay quantum-image-processing quantum-denoiser adaptive-denoiser quantum quantum-mechanics inverse-problem inverse-problems
Language:MATLAB 7
CiliaQ
hansenjn / CiliaQ
An ImageJ plugin to quantify ciliary shape, length, and fluorescence.
ciliaq-workflow imagej-plugin cilium cilia primary-cilia cilium-length ciliary-fluorescence time-lapse-imaging confocal-images fluorescence-microscopy-imaging imagej-plugins
Language:Java 6
cgohlke / lfdfiles
Laboratory for Fluorescence Dynamics (LFD) file formats
file-format fluorescence-lifetime-spectroscopy fluorescence-microscopy-imaging format-reader python
Language:Python 5
GuanqiaoDing / fraptrack
Track Fluorescent Protein in Live Cell images with OpenCV
fluorescence-microscopy-imaging opencv-python
Language:Python 5
MotiQ
hansenjn / MotiQ
A set of ImageJ plugins to quantify dynamics, morphology, and fluorescence of microglial cells.
imagej-plugins microglia microglial-morphology cell-migration image-analysis-workflows morphology morphology-analysis morphology-metrics motility microglial-motility morphology-reconstruction motility-analysis fluorescence-microscopy-analysis fluorescence-microscopy-imaging timelapse-image
Language:Java 5
Sam-Freitas / LightSaver
Fluorescent analysis of individualized C. elegans
caenorhabditis-elegans data-science fluorescence fluorescence-microscopy-imaging matlab
Language:MATLAB 5
cgohlke / ptufile
Read PicoQuant PTU and related files
python format-reader life-sciences-image tttr picoquant ptu flim fluorescence-microscopy-imaging photon-counting fluorescence-lifetime-spectroscopy
Language:Python 4
dpscience / DQuickLTFit
DQuickLTFit - A least-square fitting tool for the analysis of positron lifetime spectra using the Levenberg-Marquardt algorithm
analysis annihilation antimatter decay-spectrum exponential-distributions fitting fls fluorescence-microscopy-imaging least-square-regression levenberg-marquardt levenberg-marquardt-algorithm lifetime-spectroscopy mpfit multi-exponential pals positron-lifetime-spectra positrons qt-framework
Language:C++ 4
hansenjn / AdipoQ
A simple toolbox of ImageJ plugins for quantifying adipocyte morphology and function in tissues and in vitro.
adipocyte-differentiation adipocytes adipose-tissue adipose-tissue-segmentation cell-biology fluorescence-microscopy-imaging image-analysis imagej-plugin immunohistochemical-images droplet-analysis droplets-detection lipid-droplets
4
UU-cellbiology / rods-detection-in-noisy-images
Detection of straight line segments (rods) in noisy images
detection fluorescence-microscopy-imaging imagej-macro matlab-script tracking utrecht-university
Language:MATLAB 4
AlexSath / prodivis
A tool to accurately normalize and visualize protein distribution in 3D structures imaged with confocal microscopy using z-stacks.
python fluorescence-microscopy-imaging biology-images biochemistry proteins confocal-microscopy confocal-images fluorescence-intensity normalization 3d-models 3d
Language:Python 3
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.
calcium-imaging fluorescence-microscopy-imaging calcium-homeostasis
Language:Python 3
KerosuoLab / Shapemetrics
single-cell machine-learning spatial-analysis volumetric-calculations fluorescence-microscopy-imaging matlab ilastik 3d-segmentation fluorescent-signals label-matrix heat-map pixel-values membrane-staining-image shapemetrics
Language:MATLAB 3