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Search results for microscopy
microscopy
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155 search results found
Deepslide
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449
Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.
Relion
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400
Image-processing software for cryo-electron microscopy
Pathml
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341
Tools for computational pathology
Cucim
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282
cuCIM - RAPIDS GPU-accelerated image processing library
Pycroscopy
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241
Scientific analysis of nanoscale materials imaging data
Aicsimageio
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177
Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python
Pyclesperanto_prototype
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173
GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data
Cellfinder
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170
Automated 3D cell detection in very large images
Atomai
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164
Deep and Machine Learning for Microscopy
Pytorch_connectomics
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151
PyTorch Connectomics: segmentation toolbox for EM connectomics
Cloud Volume
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120
Read and write Neuroglancer datasets programmatically.
Webknossos
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116
Visualize, share and annotate your large 3D images online
Axondeepseg
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112
Axon/Myelin segmentation using Deep Learning
Oad
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111
Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools and AI tools.
Brainreg
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103
Automated 3D brain registration with support for multiple species and atlases.
Bg Atlasapi
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97
A lightweight python module to interact with atlases for systems neuroscience
Picasso
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93
A collection of tools for painting super-resolution images
Cellvit
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82
CellViT: Vision Transformers for Precise Cell Segmentation and Classification
Awesome Biological Image Analysis
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74
A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.
Tensorflow Mil
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74
TF Implementation of Multiple Instance Learning FCN.
Decode
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65
This is the official implementation of our publication "Deep learning enables fast and dense single-molecule localization with high accuracy" (Nature Methods)
Pycytominer
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60
Python package for processing image-based profiling data
Fold_slice
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60
Electron/X-ray ptychography and tomography/laminography
Fpbase
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58
The Fluorescent Protein Database
Cytoself
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58
Self-supervised models for encoding protein localization patterns from microscopy images
Imswitch
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57
ImSwitch is a software solution in Python that aims at generalizing microscope control by providing a solution for flexible control of multiple microscope modalities.
Napari Micromanager
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54
GUI interface between napari and micromanager powered by pymmcore-plus and pymmcore-widgets
Gpim
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53
Gaussian processes and Bayesian optimization for images and hyperspectral data
Tif2blender
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50
Loading and handling microscopy data in blender
Planktoscope
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50
Open and Affordable Quantitative Imaging Platform
Minerva Story
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48
Minerva Story is an image viewer that is designed specifically to make it easy for non-expert users to interact with complex tissue images.
Deconvoptim.jl
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48
A multi-dimensional, high performance deconvolution framework written in Julia Lang for CPUs and GPUs.
Pyotf
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47
python functions for simulating optical transfer functions
Support
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46
Accurate denoising of voltage imaging data through statistically unbiased prediction, Nature Methods.
Libapr
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45
Library for producing and processing on the Adaptive Particle Representation (APR).
Sparse Sim
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45
Official MATLAB implementation of the "Sparse deconvolution" -v1.0.3
Nd2reader
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43
Pure Python library for reading NIS Elements ND2 images and metadata
Ome Types
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43
native Python dataclasses for the OME data model
Cytominer
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41
Methods for Image-Based Cell Profiling
Nd2
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41
Full-featured nd2 (Nikon NIS Elements) file reader for python. Outputs to numpy, dask, and xarray. Exhaustive metadata extraction
Sofima
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40
Scalable Optical Flow-based Image Montaging and Alignment
Cellseg_models.pytorch
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40
Encoder-Decoder Cell and Nuclei segmentation models
Odemis
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39
Open Delmic Microscope Software
Waveblocks
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39
Optimization framework developed in Pytorch, allowing calibration, and joint optimization of optics and deep learning models.
Nanoj Fluidics
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35
Manual, source-code and binaries for the NanoJ-Fluidics project
Spatialtranscriptomics
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34
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
Napari Aicsimageio
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32
Multiple file format reading directly into napari using pure Python
Segmentation
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29
Code for my master's thesis. Instance segmentation of fluorescence microscopy images with deep learning.
Zetastitcher
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29
ZetaStitcher is a tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.
Phd Thesis
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29
Experimental tech-demo for PhD thesis in Scientific Markdown; official:
Im2im Uq
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29
Image-to-image regression with uncertainty quantification in PyTorch. Take any dataset and train a model to regress images to images with rigorous, distribution-free uncertainty quantification.
Psfmodels
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28
Python bindings for scalar and vectorial models of the 3D microscope point spread function.
Threedeconv.jl
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25
A convex 3D deconvolution algorithm for low photon count fluorescence imaging
Sparse Deconv Py
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24
Official Python implementation of the 'Sparse deconvolution'-v0.3.0
Microscpsf Matlab
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24
Fast and Accurate 3D PSF Computation for Fluorescence Microscopy
Llspy
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23
Lattice light-sheet post-processing utility.
Focus_annotator
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23
This is a tool to annotate the focus plane of z-stacked images.
Flika
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20
An interactive image processing program for biologists written in Python.
Pymmcore Plus
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20
Extensions for pymmcore (micro-manager) providing improved python UX and pure python acquisition engine
Deconvolutionlab2
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19
Java (ImageJ/Fiji) software package for 3D deconvolution microscopy
Microscopy Tools
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19
Tools for microscopic captures and focus stackshots (beta)
Zstackdepthcolorcode
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19
Z-stack Depth Colorcode ImageJ FIJI plugin
Cellfinder Core
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19
Standalone cellfinder cell detection algorithm
Ricom_cpp
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18
riCOM (real time centre of mass) application for 4D STEM
Scripts
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18
🔬🍸 Home of the ImageJ BAR: A collection of Broadly Applicable Routines for ImageJ
Microscpsf Py
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18
Fast and Accurate 3D PSF Computation for Fluorescence Microscopy
Symbac
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18
Accurate segmentation of bacterial microscope images using synthetically generated image data.
Smartphone_fpm
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17
A Smartphone-based Fourier Ptychographic Microscope Using the Display Screen for Illumination
Sitk Ibex
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16
Aligning images acquired with the IBEX microscopy imaging technique
Stitchit
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16
Stitching of large tiled datasets
Micromanager Samples
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15
Python samples for Micro-Manager: image acquisition and microscope control system
Biom3d
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15
Easy Volumetric Segmentation with Deep Learning
Microfpga
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14
Electronic control of microscope elements (camera/laser triggering, TTL, PWM, servos, analog i/o) based on affordable FPGAs, integrated with Micro-Manager, Java, Python and LabView.
Pyapr
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14
Content-adaptive storage and processing of large volumetric microscopy data using the Adaptive Particle Representation (APR)
Remote_refocus
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14
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/remote_refocus/
Ncs
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14
Noise Correction Algorithm for sCMOS cameras
Amfinder
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14
The Automatic Mycorrhiza Finder (AMFinder) allows for automatic computer vision-based identification and quantification of AM fungal colonisation and intraradical hyphal structures on ink-stained root images using convolutional neural networks.
Useq Schema
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13
An implementation agnostic schema for describing a sequence of events during a multi-dimensional imaging acquisition.
Geome
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13
Rapidstorm
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12
rapidSTORM open-source localization microscopy software
Bioformatslink
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12
Package for interacting with Bio-Formats library in the Wolfram Language
Cryosparc2_public
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12
CryoSPARC is the state-of-the-art platform used globally for obtaining 3D structural information from single particle cryo-EM data. The cryoSPARC platform enables automated, high quality and high-throughput structure discovery of proteins, viruses and molecular complexes for research and drug discovery.
Exllsm Circuit Reconstruction
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12
Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery
Deep Learning Super Resolution Image Reconstruction Dsir
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12
Deep-Learning convolutional auto-encoders applied to super-resolution microscopy data to localization image reconstruction.
Ngff Zarr
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12
A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.
Simple_sim_fusion_demo
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12
Simple demo of structured illumination microscopy image fusion via Richardson-Lucy deconvolution
Shampoo
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12
An open source digital holographic microscopy toolkit in Python.
Cset
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12
CSET (Compressed Sensing Electron Tomography)-toolbox is a three-dimensional TV-based compressed sensing reconstruction toolbox that consists of algebraic iterative algorithms (SART and SIRT) with total variation (TV) based CS. In addition, it integrates a Fast Iterative Shrinkage-Thresholding Algorithm (FISTA) that is an acceleration method to speed up the algorithm convergence.
Colicoords
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12
Single-cell fluorescence microscopy data analysis
Nbomicroscopymetadataspecs
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12
The 4DN + BINA Tiered System of Microscopy Metadata Guidelines was developed by the 4DN Imaging Standards Working Group in collaboration with the BINA Data Management and Quality Control Working Group (https://www.bioimagingna.org/qc-dm-wg) for documenting microscopy experiments and assessing the quality of image data.
Brighteyes Ttm
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12
BrightEyes Time-tagging module: open-source hardware, a time to digital converter, multi channels, with a resolution of 30 ps designed for fluorescence scanning laser microscopy.
Comdet
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12
ImageJ plugin detecting and colocalizing particles of given size (vesicles, dots, etc on biological microscopy images)
Brainreg Napari
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11
Automated 3D brain registration in napari with support for multiple species and atlases.
Vvdviewer
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11
3D/4D volumetric rendering of microscopy data
Atomai
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11
Deep and machine learning for atomic-scale and mesoscale data
Napari_lattice
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11
Napari plugin for custom analysis and visualization of lattice lightsheet and Oblique Plane Microscopy data. The plugin is optimized for data from the Zeiss lattice lightsheet microscope.
Flute
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11
Fluorescence Lifetime Ultimate Explorer (FLUTE) is a GUI for exploring and analyzing Fluorescence Lifetime Microscopy (FLIM) data
Sacd
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11
Source code of SACD(Super-resolution with Auto-Correlation two-step Deconvolution)
Actk
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11
Automated Cell Toolkit
Neuro
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11
Visualisation and analysis of brain imaging data
1-100 of 155 search results
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