Discover haesleinhuepf/benchmarking_DoG Open Source project

BIA Bob is a Jupyter+LLM-based assistant for interacting with image data and for working on Bio-image Analysis tasks.

bia-bob

blablado is an extensible Assistant that listens to your voice and can execute custom Python functions you provided. It can speak as well.

blablado

Accelerated Pixel and Object Classifiers (APOC)

apoc

Feature extraction for labeled objects in images using regionprops from scikit-image

napari-skimage-regionprops

GPU-accelerated, OpenCL-based Random Forest Classifiers for pixel and labeled object classification in napari.

napari-accelerated-pixel-and-object-classification

devbio-napari

napari-assistant

Process and analyze surfaces using vedo in napari.

napari-process-points-and-surfaces

Generate markdown notebooks from ImageJ Macro

imagejmacromarkdown

Benchmarking Large Language Models for Bio-Image Analysis Code Generation

human-eval-bia

awesome-napari-plugins-that-are-not-on-the-napari-hub-yet

An AI-based story writer and Python library which uses OpenAI's chatGPT and Dall-E to generate PDFs with a story and a picture from a prompt and writes them into a PDF.

story-writer

napari-cupy-image-processing

A plugin based on scikit-image for segmenting nuclei and cells based on fluorescent microscopy images with high intensity in nuclei and/or membranes.

napari-segment-blobs-and-things-with-membranes

Process images using SimpleITK in napari

napari-simpleitk-image-processing

napari-plot-profile

Gamified image segmentation quality estimation

the-segmentation-game

Optimize image processing workflows in napari

napari-workflow-optimizer

natari

Napari gaming

I2K2022-napari-workshop

git-bob uses AI to solve Github-issues. It runs inside the Github CI, no need to install anything on your computer.

git-bob

napari-workflows

A python script editor plugin for napari

napari-script-editor

napari-brightness-contrast

napari-tools-menu

Transfer surface layers between Napari and Blender.

napari-blender-bridge

Inspect relationships between napari-plugins in active workflows.

napari-workflow-inspector

Blog post: How to develop ImageJ Java plugins and Jythons scripts simultaneously from your IDE

run_jython_scripts_from_ide

An implementation of retrieval-augmented-generation (RAG) using numpy and OpenAI embeddings, with no clutter, for academic purposes

simple-rag

processing_imagej

napari-folder-browser

bia-tischi

Tracking particles in Napari, using the LapTrack library

napari-laptrack

A napari plugin for pixel classification using XGBoost.

napari-xgboost

napari-curtain

napari-pypistats

napari-manual-split-and-merge-labels

Browse folders and images in owncloud/nextcloud servers and open them using just a double-click!

napari-owncloud

NEUBIAS_TS11

napari-minimal-plugin

Open and save 3D image stacks as animated gifs in napari

napari-animated-gif-io

beetlesafari

label_neighbor_filters

A meta plugin for processing timelapse data timepoint by timepoint in napari

napari-time-slicer

Auto-generate python code from within napari to make napari-assistant compatible plugins

napari-assistant-plugin-generator

Generate PowerPoint files using chatGPT and Dall-E

git-bob-bioimage-analysis-example

prompting-pptx

napari-layer-details-display

A Jupyter kernel for communicating with large language models

ipy-llm-kernel

A library for feature extraction from 3D label images

spheri

looping_vision_and_image_generation

A simple Chat interface based on voila, OpenAI and llama-index that allows you to query information from documents using human language.

simple-chat-with-docs

Report of efforts in the Project "Seamless Integration of Quantitative Bio-Image Analysis Plugins"

napari-mahotas-image-processing

napari-oclrfc

hip_clij

napari-webcam

ptd

napari-plugin-integration

napari-generalized-histogram-thresholding

Control zoom, slicing and contrast windowing with mouse and touch screen

napari-mouse-controls

Use pyFAST's CPU/GPU-accelerated image processing from within napari.

napari-pyfast-image-processing