Python Electron-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

bluetooth-battery-electron An electron application to check battery of bluetooth devices connected to linux devices. This project provides an electron

PyElecCL Python program to perform second checks for electron Monte Carlo radiat

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.

CoulombGas This code implements the neural canonical transformation approach to the thermodynamic properties of uniform electron gas. Building on JAX,

CoulombGas This code implements the neural canonical transformation approach to the thermodynamic properties of uniform electron gas. Building on JAX,

Run python scripts and pass data between multiple python and node processes using this npm module. process-communication has a event based architecture for interacting with python data and errors inside nodejs.

WARNING This is still very much a work in progress and nothing can be assumed stable in any way Temp notes: Two types of created installer, based on w

Create standalone, installable R Shiny apps using Electron

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

AITom Introduction AITom is an open-source platform for AI driven cellular electron cryo-tomography analysis. AITom is originated from the tomominer l

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

Discord-Netflix A updated version from the original Discord-Netflix from nirewen A Netflix wrapper that uses Discord RPC to show what you're watching

Angular Desktop UI This is a collection for native desktop like user interface components in Angular, especially useful for Electron apps. It starts w

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

OpenSEM Project Status: Preliminary The purpose of this project is to create a modern and open-source hardware and software platform for using vintage

napari-subboxer A napari plugin for visualising and interacting with electron cryotomograms. Installation You can install napari-subboxer via pip: pip

neopo A lightweight solution for local Particle development. Features Builds Particle projects locally without any overhead. Compatible with Particle

ElectriPy ⚡ Visualize the electric field of a point charges network. 🔌 Installation Install ElectriPy package: $ pip install electripy You are all d

Aurora Aurora is a Django web application that can receive, virus check and validate transfers of digital archival records, and allows archivists to a

napari-tomoslice A napari plugin for visualising and interacting with electron cryotomograms. Installation You can install napari-tomoslice via pip: p

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

kikuchipy is an open-source Python library for processing and analysis of electron backscatter diffraction (EBSD) patterns. The library builds on the

Dazzler is a Python async UI/Web framework built with aiohttp and react. Create dazzling fast pages with a layout of Python components and bindings to update from the backend.

A desktop application for JupyterLab, based on Electron.

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

The JavaScript Database Embedded persistent or in memory database for Node.js, nw.js, Electron and browsers, 100% JavaScript, no binary dependency. AP

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

Zulip overview Zulip is a powerful, open source group chat application that combines the immediacy of real-time chat with the productivity benefits of

Python Desktop App Learn how to make a desktop GUI application using Python, JavaScript, HTML, & CSS all thanks to pywebview. pywebview is essentially

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

Mockoon Mockoon is the easiest and quickest way to run mock APIs locally. No remote deployment, no account required, open source. It has been built wi

Eel Eel is a little Python library for making simple Electron-like offline HTML/JS GUI apps, with full access to Python capabilities and libraries. Ee