A Python interface to access neuroanatomical atlases
- neuroscience
- python
- microscopy
- registration
Repository Index
47,133 repositories indexed
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Non-comprehensive list of projects and resources related to open microscopy.
Read and write Neuroglancer datasets programmatically.
- neuroglancer
- volumetric-data
- python
- cloud
Automated 3D brain registration with support for multiple species and atlases.
- registration
- atlases
- brain
- neuroscience
A collection of tools for painting super-resolution images
- microscopy
- super-resolution
- smlm
- dna-paint
Accurate and efficient spot detection for microscopy data
Python package for image-based profiling
- cytominer
- microscopy
- morphological-profiling
- python
micrOS - mini asynchronous automation OS for DIY projects.
- micropython
- iot-platform
- interrupts
- socket
Axon/Myelin segmentation using Deep Learning
- deep-learning
- machine-learning
- myelin
- axon
The python-microscopy environment - an open-source package for light microscopy
Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy
- biology
- fluorescence
- image-analysis
- image-processing
python functions for simulating optical transfer functions
- microscopy
- numpy
Gaussian processes and Bayesian optimization for images and hyperspectral data
- image-processing
- hyperspectral-images
- gaussian-processes
- bayesian-optimization
Pure Python library for reading NIS Elements ND2 images and metadata
- nd2
- pims
- nikon
- nis-elements
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
A foundation model-driven whole slide image-scale cell phenotyping method with QuPath integration Resources
- bioimage-analysis
- cell-classification
- computer-vision
- digital-pathology
Lattice light-sheet post-processing utility.
- microscopy
- light-sheet
- image-processing
- image-analysis
Noise Correction Algorithm for sCMOS cameras
- cmos
- imaging
- noise
- readout
Single-cell fluorescence microscopy data analysis
- microscopy
- fluorescence-microscopy-imaging
An interactive image processing program for biologists written in Python.
- biologists
- python
- imagej
- calcium
Accurate segmentation of bacterial microscope images using deep learning synthetically generated image data.
- microscopy
- image-processing
- segmentation
- biology
A mini SDI-12 implementation for getting sensor info over RS-485
- micropython
- sdi-12
- sensor
- pycom
A python package to analyze the matrix fiber orientation and intensity around cells in fiber matrices (as a proxy for cellular forces).
- imaging
- microscopy
- contractility
- collagen
[DEPRECATED] A package for storing morphological profiling data.