Python Microscopy Resources

SOFIMA SOFIMA (Scalable Optical Flow-based Image Montaging and Alignment) is a tool for stitching, aligning and warping large 2d, 3d and 4d microscopy

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.

Segment axon and myelin from microscopy data using deep learning. Written in Python. Using the TensorFlow framework. Based on a convolutional neural network architecture. Pixels are classified as either axon, myelin or background.

Deep Learning segmentation suite dessigned for 2D microscopy image segmentation This repository provides researchers with a code to try different enco

gACSON gACSON software is to visualize, segment, and analyze the morphology of neurons in three-dimensional electron microscopy images. If you use any

PyCellID (building...) Functions to analyze Cell-ID single-cell cytometry data using python language. Dependecies for this project. attrs(=21.1.0) fo

CIDRE About CIDRE is a retrospective illumination correction method for optical microscopy. It is designed to correct collections of images by buildin

BaSiC Matlab code accompanying A BaSiC Tool for Background and Shading Correction of Optical Microscopy Images by Tingying Peng, Kurt Thorn, Timm Schr

Introduction The field of connectomics aims to reconstruct the wiring diagram of the brain by mapping the neural connections at the level of individua

Cytokit Cytokit is a collection of tools for quantifying and analyzing properties of individual cells in large fluorescent microscopy datasets with a

Sparse deconvolution Python v0.3.0 Official Python implementation of the 'Sparse deconvolution', and the CPU (NumPy) and GPU (CuPy) calculation backen

AICSImageIO Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python Features Supports reading metadata and imaging

WobblyStitcher Introduction A scalable implementation of WobblyStitcher Dependencies $ python -m pip install numpy scikit-image Visualization ImageJ

Odemis Odemis (Open Delmic Microscope Software) is the open-source microscopy software of Delmic B.V. Odemis is used for controlling microscopes of De

EmbedSeg Introduction This repository hosts the version of the code used for the preprint Embedding-based Instance Segmentation of Microscopy Images.