Repository Index

Brian is a free, open source simulator for spiking neural networks.

• python
• neuroscience
• science
• differential-equations

Segment Anything for Microscopy

• microscopy-images
• segment-anything
• segmentation
• cell-segmentation

ZeroCostDL4Mic: A Google Colab based no-cost toolbox to explore Deep-Learning in Microscopy

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.

• histopathology-images
• microscopy
• sliding-windows
• medical-image-analysis

CAI NEURAL API - Pascal based deep learning neural network API optimized for AVX, AVX2 and AVX512 instruction sets plus OpenCL capable devices including AMD, Intel and NVIDIA.

• pascal
• lazarus
• delphi
• free-pascal

CellViT: Vision Transformers for Precise Cell Segmentation and Classification

• ai
• cell
• digitalpathology
• microscopy

Translated[iFlytek Simultaneous Interpretation] free alternative — local system audio real-time translation and transcription for international conferences, foreign-language podcasts, game voice chat, and raw (unsubtitled) films and shows, with on-screen floating window, live subtitles, and offline recognition. Offline real‑time Language transcription, floating live subtitles.

• audio-transcription
• audio2text
• cross-platform
• offline-first

Deep and Machine Learning for Microscopy

• microscopy
• materials
• machine-learning
• materials-science

Usiigaci: stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning

• tensorflow
• python3
• keras
• resnet-101

A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data

PyTorch Connectomics: segmentation toolbox for EM connectomics

• computer-vision
• neuroscience
• connectomics
• pytorch

TSPS is a cross platform Toolkit for Sensing People in Spaces. It performs openCV operations on live video (Kinect, web camera, etc) and sends it to clients as JSON (via WebSockets), OSC, TUIO, or TCP.

Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools and AI tools.

• python
• microscopy
• scripting
• automation

A dataset of 2D imagery, 3D point cloud data, and 3D vehicle bounding box labels all generated using the Grand Theft Auto 5 game engine.

Axon/Myelin segmentation using Deep Learning

• deep-learning
• machine-learning
• myelin
• axon

Go Scoring API for PMML

• golang
• pmml
• random-forest
• classification

Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy

• biology
• fluorescence
• image-analysis
• image-processing

A foundation model-driven whole slide image-scale cell phenotyping method with QuPath integration Resources

• bioimage-analysis
• cell-classification
• computer-vision
• digital-pathology

Accurate segmentation of bacterial microscope images using deep learning synthetically generated image data.

• microscopy
• image-processing
• segmentation
• biology

DetecDiv provides a comprehensive set of tools to analyze time microscopy images using deep learning methods. The software structure is such that data can be processed either at the command line or using a graphical user-interface. Detecdiv classification models include : image classification and regression, semantic segmentation, LSTM networks to analyze data and image timeseries.

Panoptic segmentation algorithms for 2D and 3D electron microscopy images

• deep-learning
• semantic-segmentation
• segmentation
• pytorch