Projects in Awesome Lists tagged with biomedical-image-processing

https://github.com/dana-farber-aios/pathml

Tools for computational pathology

biomedical-image-processing computational-pathology deep-learning digital-pathology fluorescence-microscopy-imaging histopathology image-analysis machine-learning microscopy pathml pathology python pytorch research spatial-transcriptomics

Last synced: 16 Sep 2025

https://github.com/Dana-Farber-AIOS/pathml

Tools for computational pathology

biomedical-image-processing computational-pathology deep-learning digital-pathology fluorescence-microscopy-imaging histopathology image-analysis machine-learning microscopy pathml pathology python pytorch research spatial-transcriptomics

Last synced: 06 May 2025

https://cambridgeltl.github.io/visual-med-alpaca/

Visual Med-Alpaca is an open-source, multi-modal foundation model designed specifically for the biomedical domain, built on the LLaMa-7B.

biomedical biomedical-image-processing foundation-model large-language-models multimodal

Last synced: 12 May 2025

https://github.com/OpenEIT/OpenEIT

Python based dashboard for real-time Electrical Impedance Tomography including image reconstruction using Back Projection, Graz Consensus and Gauss Newton methods

biomedical-image-processing biomedical-instrumentation eit electrical-impedance-tomography image-reconstruction inverse-problems python tomography

Last synced: 15 Mar 2025

https://github.com/biapyx/biapy

Open source Python library for building bioimage analysis pipelines

biomedical-image-processing classification computer-vision convolutional-neural-networks deep-learning denoising image-processing image-segmentation instance-segmentation machine-learning medical-imaging object-detection python pytorch segmentation self-supervised-learning semantic-segmentation super-resolution

Last synced: 13 Mar 2026

https://github.com/mlcommons/gandlf

A generalizable application framework for segmentation, regression, and classification using PyTorch

biomedical-image-processing classification clinical-workflow data-augmentation deep-learning framework machine-learning medical-image-analysis medical-imaging medical-informatics pytorch regression segmentation

Last synced: 15 May 2025

https://github.com/mlcommons/GaNDLF

A generalizable application framework for segmentation, regression, and classification using PyTorch

biomedical-image-processing classification clinical-workflow data-augmentation deep-learning framework machine-learning medical-image-analysis medical-imaging medical-informatics pytorch regression segmentation

Last synced: 08 May 2025

https://github.com/zudi-lin/pytorch_connectomics

PyTorch Connectomics: segmentation toolbox for EM connectomics

biomedical-image-processing computer-vision connectomics deep-learning microscopy neuroscience pytorch segmentation

Last synced: 01 May 2025

https://github.com/seung-lab/kimimaro

Skeletonize densely labeled 3D image segmentations with TEASAR. (Medial Axis Transform)

biomedical-image-processing centerline centerline-extraction computer-vision-algorithms connectomics cross-section cross-section-area image-segmentation medial-axis-transform python skeletonization skeletons teasar volumetric-data voxel

Last synced: 15 May 2025

https://github.com/seung-lab/cloud-volume

Read and write Neuroglancer datasets programmatically.

big-data biomedical-image-processing chunked-image cloud connectomics electron-microscopy gcs large-image matrix mesh microscopy microscopy-images neuroglancer numpy python s3 serverless skeletons tensor volumetric-data

Last synced: 15 May 2025

https://github.com/amrzhd/mriskullstripping

Developing a UNet3D model for accurate MRI skull stripping using the Calgary Campinas 359 dataset, enhancing neuroimaging preprocessing workflows.

biomedical-image-processing image-segmentation monai mri mri-images nibabel python pytorch unet unet-image-segmentation

Last synced: 07 Apr 2025

https://github.com/seung-lab/dijkstra3d

Dijkstra's Shortest Path for 6, 18, and 26-Connected 3D (Volumetric) Image Volumes

2d 3d 3d-image-volumes a-star a-star-algorithm a-star-search bidirectional-dijkstra bidirectional-search biomedical-image-processing cpp dijkstra dijkstra-algorithm dijkstra-shortest-path path-planning pathfinding python shortest-path skeletonization unidirectional-search

Last synced: 07 Apr 2025

https://github.com/google-research/sofima

Scalable Optical Flow-based Image Montaging and Alignment

2d 3d 4d alignment-algorithm biomedical-image-processing connectomics electron-microscopy jax microscopy python3 stitching-algorithm

Last synced: 05 Apr 2025

https://github.com/seung-lab/fastremap

Remap, mask, renumber, unique, and in-place transposition of 3D labeled images. Point cloud too.

array-manipulations biomedical-image-processing cython in-place in-place-transposition looping masking numpy point-cloud python python3 remap remapping renumbering transpose unique

Last synced: 13 Apr 2025

https://github.com/fangq/mmc

Mesh-based Monte Carlo (MMC)

biomedical-image-processing matlab monte-carlo multi-threading parallel-computing photonics transport

Last synced: 07 Apr 2025

https://github.com/sondosaabed/biomedical-image-analysis-in-python

gaining essential skills for tasks like cardiac MRI segmentation and detecting Alzheimer's-related brain structure changes.

biomedical-image-processing image-analysis matplotlib python scipy

Last synced: 17 Jun 2025

https://github.com/seung-lab/microviewer

Multiplatform 3D numpy image browser based viewer with voxel painting.

3d-reconstruction biomedical-image-processing voxel-painting

Last synced: 26 Oct 2025

https://github.com/seung-lab/tinybrain

Image pyramid generation for grayscale and segmentation image resize.

average-pooling biomedical-image-processing countless cython downsample image-hierarchy image-processing image-pyramid image-pyramids image-segmentation mode-pooling python resize resize-images volumetric-data

Last synced: 16 Aug 2025

https://github.com/luisvalesilva/wsipre

Handling whole-slide images with region-level annotations.

biomedical-image-analysis biomedical-image-processing python-library virtual-slide whole-slide-imaging

Last synced: 02 Apr 2026

https://github.com/kyegomez/simpleunet

An simple implementation of Unet because all the implementations i've seen are wayy tooo complicated.

artificial-intelligence biomedical biomedical-image-processing computer-vision gpt4 image image-classification image-segmentation texttovide unet vllm

Last synced: 07 May 2025

https://github.com/borda/pybpdl

Binary Pattern Dictionary Learning for gene activation in microscopy images

atlas biomedical-image-processing decomposition dictionary-learning drosophila-imaginal-discs gene-activation image-analysis image-decomposition image-segmentation ovary patterns

Last synced: 07 May 2025

https://github.com/sondosaabed/datacamp-image-processing-track

This track covers the fundamentals, from image pre-processing to deep learning. Began with image enhancement, restoration, biomedical images to convolutional neural nets, build powerful deep learning image classifiers.

biomedical-image-processing image-analysis image-processing keras matplotlib python scipy

Last synced: 12 Mar 2026

https://github.com/elektronn/elektronn2

A highly configurable toolkit for training 3D/2D CNNs and general Neural Networks, based on Theano

3d-cnn 3d-convolutional-network biomedical-image-processing cnn convolutional-neural-networks electron-microscopy theano

Last synced: 21 Feb 2026

https://github.com/brainlife/abcd-spec

Application for Big Computational Data Specification (v1.1). This specification provide information on how to write an Application that can run on the open platform

biomedical-image-processing brain cloud-computing cyberinfrastructure hcp specification

Last synced: 23 Feb 2026

https://github.com/adrianbzg/muscular-dystrophy-diagnosis

Code for "A Convolutional Neural Network for the automatic diagnosis of collagen VI-related muscular dystrophies" (Applied Soft Computing, 2019)

biomedical-image-processing convolutional-neural-networks deep-learning image-analysis

Last synced: 11 Sep 2025

https://github.com/fitushar/quantification-of-trabeculae-inside-the-heart-from-mri-using-fractal-analysis

In this project, we demonstrate the fractal dimension (FD) and manual segmentation of the Magnetic Resonance Imaging (MRI) of the heart that quantify amount of trabeculae inside the heart.

biomedical-image-processing compaction fractal-algorithms fractal-analysis heart mri quantification trabeculae-inside

Last synced: 15 Apr 2026

https://github.com/sweetpand/tensorflow_best_practices

Biomedical Image Analysis with TensorFlow and DLTK

biomedical-engineering biomedical-image-analysis biomedical-image-processing biomedical-signal-processing dltk tensorflow tensorflow-experiments tensorflow-lite tensorflow-models tensorflow-mri

Last synced: 02 Apr 2025

https://github.com/tyleradammartinez/body-signals-filtering

BMEN 3311 (Biomedical Signal Analysis): Reads in biomedical data from a patient’s files into a script and plots the data. Then take the discrete Fourier transforms of each signal then plot the frequency Spectrums. In addition, create a digital notch filter to remove the noise coming from mains power in the ECG signal without creating a phase shift due to filtering (zero-phase filtering), determine if the patient was tired during the recording of the EMG signal based on the frequency spectrum of the EMG signal, and determine the mental state of the patient during the recording of the EEG signal based on the frequency spectrum of the EEG signal. Finally, break down how much of the EEG signal is comprised of the four EEG wave components (Delta, Theta, Alpha and Beta), and display it in a bar graph.

biomedical-image-processing ecg-signal eeg emg-signal signal-processing

Last synced: 28 Jul 2025

https://github.com/reshalfahsi/msgnet

Modified MobileNet-ShuffleNet-GhostNet Network for Lightweight Retinal Vessel Segmentation

biomedical-engineering biomedical-image-analysis biomedical-image-processing image-segmentation medical-image-segmentation pytorch

Last synced: 19 May 2026

https://github.com/emogooo/biomedical-data-processing-with-image-filters

Processing biomedical data using LBP, HOG, and Gabor filters for enhanced analysis and feature extraction.

biomedical-image-processing gabor-filters hog-features lbp

Last synced: 14 Mar 2025

https://github.com/amirhosein2c/mip-ddpm

How To Segment in 3D Using 2D Models: Automated 3D Segmentation of Prostate Cancer Metastatic Lesions on PET Volumes Using Multi-Angle Maximum Intensity Projections and Diffusion Models

biomedical-image-processing biomedical-image-segmentation ddpm diffusion-models metastatic-cancer-detection pet-imaging psma python pytorch