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Search results for python microscopy
microscopy
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python
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83 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.
Pathml
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341
Tools for computational pathology
Aicsimageio
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177
Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python
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.
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
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
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
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.
Ome Types
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43
native Python dataclasses for the OME data model
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
Cellseg_models.pytorch
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40
Encoder-Decoder Cell and Nuclei segmentation models
Sofima
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40
Scalable Optical Flow-based Image Montaging and Alignment
Odemis
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39
Open Delmic Microscope Software
Napari Aicsimageio
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32
Multiple file format reading directly into napari using pure Python
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.
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.
Sparse Deconv Py
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24
Official Python implementation of the 'Sparse deconvolution'-v0.3.0
Llspy
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23
Lattice light-sheet post-processing utility.
Pymmcore Plus
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20
Extensions for pymmcore (micro-manager) providing improved python UX and pure python acquisition engine
Flika
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20
An interactive image processing program for biologists written in Python.
Cellfinder Core
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19
Standalone cellfinder cell detection algorithm
Scripts
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18
🔬🍸 Home of the ImageJ BAR: A collection of Broadly Applicable Routines for ImageJ
Symbac
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18
Accurate segmentation of bacterial microscope images using synthetically generated image data.
Microscpsf Py
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18
Fast and Accurate 3D PSF Computation for Fluorescence Microscopy
Sitk Ibex
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16
Aligning images acquired with the IBEX microscopy imaging technique
Biom3d
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15
Easy Volumetric Segmentation with Deep Learning
Micromanager Samples
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15
Python samples for Micro-Manager: image acquisition and microscope control system
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/
Pyapr
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14
Content-adaptive storage and processing of large volumetric microscopy data using the Adaptive Particle Representation (APR)
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
Colicoords
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12
Single-cell fluorescence microscopy data analysis
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.
Simple_sim_fusion_demo
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12
Simple demo of structured illumination microscopy image fusion via Richardson-Lucy deconvolution
Ngff Zarr
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12
A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.
Shampoo
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12
An open source digital holographic microscopy toolkit in Python.
Actk
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11
Automated Cell Toolkit
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.
Neuro
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11
Visualisation and analysis of brain imaging data
Flute
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11
Fluorescence Lifetime Ultimate Explorer (FLUTE) is a GUI for exploring and analyzing Fluorescence Lifetime Microscopy (FLIM) data
Brainreg Napari
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11
Automated 3D brain registration in napari with support for multiple species and atlases.
Extrack
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10
ExTrack MLE for diffusive noisy single-particle tracks
Nanomesh
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9
Python workflow tool for generating meshes from 2D and 3D image data
Bioio
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8
Image reading, metadata management, and image writing for Microscopy images in Python
Brightfield Drift Correction 3d
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8
Acquire bright field images along with the super resolution data and use it to track drift in 3D with nanometer precision!
Ps_decomp
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8
Periodic plus smooth image decomposition, as described by Moisan (http://www.math-info.univ-paris5.fr/~moisan/paper
Simplipytem
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7
Package to make analysis of transmission electron microscopy images simple.
Cytominer Database
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7
A package for storing morphological profiling data.
Pymontecarlo
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7
Python interface for Monte Carlo simulation programs
Navigate
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7
navigate - open source light-sheet microscope controls
Rf Ulm
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7
Radio-Frequency Ultrasound Localization Microscopy
Nrefocus
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7
python library for numerical focusing (refocusing, autofocusing) of complex wave fields
Napari Czann Segment
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7
Semantic Segmention and Image2Image using DeepLearning ONNX models packaged as *.czann files.
Dicomslide
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6
Python library for reading whole slide images in DICOM format
Cellocity
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6
Scientific software for analysis of confluent cell dynamics.
Optics
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6
A toolbox for optical simulation. The implementation of phase-retrieval algorithm is included.
Napari Psf Analysis
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6
A napari plugin to analysis point spread functions.
Compactionanalyzer
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6
Evaluates the fiber orientation and intensity around cells that compact collagen tissue as measure of contractile strength.
Pydhm
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6
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.
Anystar
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6
[WACV 2024] Reference implementation of "AnyStar: Domain randomized universal star-convex 3D instance segmentation"
Lucyd Deconvolution
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5
A Feature-Driven Richardson-Lucy Deconvolution Network
Pycudasirecon
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5
CUDA-accelerated reconstruction for 3D-structured-illumination
Napari Apr Viewer
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5
Create and view APR images in napari
Rescan_line_sted
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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
Czitools
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5
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.
Inline_holo
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5
Python code for inline holography using through-focus image series.
Vectorial Light Sheet Simulation
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5
Vectorial ray tracing software for light-sheet microscopes
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