biomedical-image-processing

There are 25 repositories under biomedical-image-processing topic.

pathml
Dana-Farber-AIOS / pathml
Tools for computational pathology
machine-learning digital-pathology computational-pathology biomedical-image-processing pathology histopathology spatial-transcriptomics image-analysis microscopy fluorescence-microscopy-imaging deep-learning python pytorch research pathml
Language:Python 438
seung-lab / connected-components-3d
Connected components on discrete and continuous multilabel 3D & 2D images. Handles 26, 18, and 6 connected variants; periodic boundaries (4, 8, & 6)
connected-components python numpy biomedical-image-processing cpp union-find image-processing cython 3d decision-tree 2d algorithm 3d-images neighborhood path-compression ccl cclabel labeling-algorithms surface-area periodic-boundary
Language:C++ 429
cambridgeltl / 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
Language:Python 391
jvanvugt / pytorch-unet
Tunable U-Net implementation in PyTorch
deep-neural-networks segmentation biomedical-image-processing pytorch unet
Language:Python 344
seung-lab / euclidean-distance-transform-3d
Euclidean distance & signed distance transform for multi-label 3D anisotropic images using marching parabolas.
cpp python distance-transform euclidean-distance 3d 2d 1d connectomics neuroscience algorithm biomedical-image-processing numpy anisotropy anisotropic parallel euclidean-distance-transform marching-parabolas signed-distance-field signed-distance-functions
Language:C++ 260
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
Language:Python 248
tkuanlun350 / 3DUnet-Tensorflow-Brats18
3D Unet biomedical segmentation model powered by tensorpack with fast io speed
deep-learning biomedical-image-processing unet segmentation brain-tumor-segmentation tensorflow
Language:Python 202
GaNDLF
mlcommons / GaNDLF
A generalizable application framework for segmentation, regression, and classification using PyTorch
deep-learning regression classification segmentation data-augmentation biomedical-image-processing medical-imaging framework clinical-workflow machine-learning medical-image-analysis medical-informatics pytorch
Language:Python 188
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
Language:Jupyter Notebook 185
zudi-lin / pytorch_connectomics
PyTorch Connectomics: segmentation toolbox for EM connectomics
computer-vision neuroscience connectomics pytorch segmentation biomedical-image-processing microscopy deep-learning
Language:Python 180
kimimaro
seung-lab / kimimaro
Skeletonize densely labeled 3D image segmentations with TEASAR. (Medial Axis Transform)
biomedical-image-processing teasar skeletonization connectomics python skeletons volumetric-data image-segmentation voxel centerline medial-axis-transform centerline-extraction computer-vision-algorithms cross-section cross-section-area
Language:C++ 179
anjanatiha / Pneumonia-Detection-from-Chest-X-Ray-Images-with-Deep-Learning
Detecting Pneumonia in Chest X-ray Images using Convolutional Neural Network and Pretrained Models
image-recognition image-detection convolutional-neural-networks keras keras-tensorflow tensorflow inception inceptionv3 imagenet deep-convolutional-networks pneumonia-detection chest-xray-images biomedical-image-processing biomedical-image-analysis biomedical-applications medical-imaging medical-image-processing medical-image-analysis medical-image-computing medical-application
Language:Jupyter Notebook 169
ELEKTRONN / elektronn3
A PyTorch-based library for working with 3D and 2D convolutional neural networks, with focus on semantic segmentation of volumetric biomedical image data
pytorch 3d-cnn convolutional-neural-networks biomedical-image-processing electron-microscopy 3d-convolutional-network semantic-segmentation
Language:Python 169
seung-lab / cloud-volume
Read and write Neuroglancer datasets programmatically.
neuroglancer volumetric-data python cloud numpy connectomics microscopy microscopy-images chunked-image biomedical-image-processing s3 gcs mesh skeletons serverless big-data electron-microscopy tensor matrix large-image
Language:Python 163
sacmehta / YNet
Y-Net: Joint Segmentation and Classification for Diagnosis of Breast Biopsy Images
deep-learning convolutional-neural-networks semantic-segmentation biomedical-image-processing
Language:Python 144
yuanqing811 / ISIC2018
ISIC 2018: Skin Lesion Analysis Towards Melanoma Detection
deep-learning computer-vision biomedical-image-processing melanoma-recognition
Language:Python 144
mattmacy / torchbiomed
Datasets, Transforms and Utilities specific to Biomedical Imaging
biomedical-image-processing pytorch
Language:Python 110
mirzaevinom / promise12_segmentation
Codes that I have written to complete promise12 prostate segmentation competition.
biomedical-image-processing deep-learning prostate-structures semantic-segmentation
Language:Python 101
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 mri mri-images nibabel python pytorch unet unet-image-segmentation monai
Language:Jupyter Notebook 96
seung-lab / dijkstra3d
Dijkstra's Shortest Path for 6, 18, and 26-Connected 3D (Volumetric) Image Volumes
dijkstra-shortest-path cpp biomedical-image-processing skeletonization shortest-path dijkstra-algorithm dijkstra 3d python 2d pathfinding path-planning bidirectional-dijkstra bidirectional-search a-star-algorithm unidirectional-search a-star-search a-star 3d-image-volumes
Language:C++ 83
google-research / sofima
Scalable Optical Flow-based Image Montaging and Alignment
connectomics stitching-algorithm alignment-algorithm 2d 3d 4d biomedical-image-processing electron-microscopy microscopy jax python3
Language:Jupyter Notebook 82
beasygo1ng / OCT-Retinal-Layer-Segmenter
UNet based model that segment retina to 8 layers in OCT images
biomedical-data-science biomedical-image-processing computer-vision-algorithms deep-learning deep-neural-networks image-segmentation images keras-tensorflow machine-learning neural-networks python retinal-layer-segmentation segmentation
Language:Jupyter Notebook 78
hoang-ho / Skin_Lesions_Classification_DCNNs
Transfer Learning with DCNNs (DenseNet, Inception V3, Inception-ResNet V2, VGG16) for skin lesions classification
computer-vision image-classification biomedical-image-processing densenet inceptionv3 inception-resnet vgg16 imagenet skin-cancer skin-lesion-classification transfer-learning fine-tuning ensemble-learning
Language:Jupyter Notebook 72
seung-lab / zmesh
Marching Cubes & Mesh Simplification on multi-label 3D images.
marching-cubes marching-cubes-algorithm connectomics biomedical-image-processing mesh-simplification volumetric-data meshing mesh-generation mesh-processing python
Language:C++ 68
seung-lab / fastremap
Remap, mask, renumber, unique, and in-place transposition of 3D labeled images. Point cloud too.
cython python python3 numpy remap remapping array-manipulations renumbering transpose in-place in-place-transposition looping masking biomedical-image-processing unique point-cloud
Language:C++ 63
aangelopoulos / im2im-uq
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.
unet uncertainty uncertainty-quantification uncertainty-estimation quantile-regression image-to-image-translation biomedical-image-processing biomedical-data-science computational-biology computational-imaging mri machine-learning microscopy pytorch
Language:Python 58
JiaxinZhuang / Skin-Lesion-Recognition.Pytorch
Rank3 Code for ISIC 2018: Skin Lesion Analysis Towards Melanoma Detection, Task 3
skin-lesion-analysis isic-2018 imbalanced-data miccai miccai2018-grandchanllage deep-learning computer-vision biomedical-image-processing melanoma-recognition pytorch classification isic2018
Language:Python 53
RuiyangJu / Bone_Fracture_Detection_YOLOv8
Scientific Reports 2023
biomedical-image-processing fracture-detection object-detection pytorch x-ray yolo yolov8
Language:Python 49
MuscleMap / MuscleMap
MuscleMap: An Open-Source, Community-Supported Consortium for Whole-Body Quantitative MRI of Muscle
3d-modeling artificial-intelligence automated biomedical-image-processing body-composition cnn computed-tomography computer-vision image-analysis-toolbox image-segmentation magnetic-resonance-imaging muscle muscle-model muscles open-science open-source pytorch segmentation segmentation-models python
Language:Python 48
fangq / mmc
Mesh-based Monte Carlo (MMC)
biomedical-image-processing matlab monte-carlo multi-threading parallel-computing photonics transport
Language:C 46
halleewong / MultiverSeg
[ICCV 2025] MultiverSeg: Scalable Interactive Segmentation of Biomedical Imaging Datasets with In-Context Guidance
biomedical-image-processing in-context-prompting in-context-segmentation interactive-segmentation medical-imaging segmentation
Language:Jupyter Notebook 46
SiyuanYan1 / Derm1M
[ICCV'25 Highlight] Derm1M: A Million‑Scale Vision‑Language Dataset Aligned with Clinical Ontology Knowledge for Dermatology
clip dataset dermatology dermatology-ai foundation-model medical-ai medical-image-analysis multi-modality vision-language-model vision-language-pretraining biomedical-image-processing
Language:Python 43
vaibhavshukla182 / Brain-MRI-Segmentation
Smart India Hackathon 2019 project given by the Department of Atomic Energy
deep-learning image-segmentation medical-imaging mri-images machine-learning brain-mri mri brain-imaging brain-tumor-segmentation keras-tensorflow brain-tumor segmentation biomedical-image-processing unet tensorflow
Language:Python 42
jvwilliams23 / pyssam
A Python library for biomedical statistical shape and appearance modelling.
biomedical-data-science biomedical-image-processing python statistical-shape-model
Language:Python 36
PathologyDataScience / HiPS
Histomic Prognostic Signature (HiPS): A population-level computational histologic signature for invasive breast cancer prognosis
biomarker-discovery biomedical-image-processing breast-cancer computational-pathology digital-pathology survival-prediction explainable-ai
Language:Python 32
anjanatiha / Cancer-Detection-from-Microscopic-Tissue-Images-with-Deep-Learning
Cancer Detection from Microscopic Images by Fine-tuning Pre-trained Models ("Inception") for new class labels
deep-learning microscopic-images cancer-detection biomedical-image-processing biomedical-image-analysis biomedical-applications medical-imaging medical-image-processing medical-image-computing medical-image-analysis medical-application nasnet nasnetmobile nasnet-models keras keras-tensorflow image-classification image-recognition convolutional-neural-network
Language:Jupyter Notebook 29

biomedical-image-processing

Dana-Farber-AIOS / pathml

seung-lab / connected-components-3d

cambridgeltl / visual-med-alpaca

jvanvugt / pytorch-unet

seung-lab / euclidean-distance-transform-3d

OpenEIT / OpenEIT

tkuanlun350 / 3DUnet-Tensorflow-Brats18

mlcommons / GaNDLF

BiaPyX / BiaPy

zudi-lin / pytorch_connectomics

seung-lab / kimimaro

anjanatiha / Pneumonia-Detection-from-Chest-X-Ray-Images-with-Deep-Learning

ELEKTRONN / elektronn3

seung-lab / cloud-volume

sacmehta / YNet

yuanqing811 / ISIC2018

mattmacy / torchbiomed

mirzaevinom / promise12_segmentation

amrzhd / MRISkullStripping

seung-lab / dijkstra3d

google-research / sofima

beasygo1ng / OCT-Retinal-Layer-Segmenter

hoang-ho / Skin_Lesions_Classification_DCNNs

seung-lab / zmesh

seung-lab / fastremap

aangelopoulos / im2im-uq

JiaxinZhuang / Skin-Lesion-Recognition.Pytorch

RuiyangJu / Bone_Fracture_Detection_YOLOv8

MuscleMap / MuscleMap

fangq / mmc

halleewong / MultiverSeg

SiyuanYan1 / Derm1M

vaibhavshukla182 / Brain-MRI-Segmentation

jvwilliams23 / pyssam

PathologyDataScience / HiPS

anjanatiha / Cancer-Detection-from-Microscopic-Tissue-Images-with-Deep-Learning