FAIMED 3D

use fastai to quickly train fully three-dimensional models on radiological data

Classification

from faimed3d.all import *

Load data in various medical formats (DICOM, NIfTI, NRRD) or even videos as simple as in fastai.

d = pd.read_csv('../data/radiopaedia_cases.csv')
dls = ImageDataLoaders3D.from_df(d,
                                 item_tfms = Resize3D((20, 112, 112)),
                                 batch_tfms = aug_transforms_3d(), 
                                 bs = 2, val_bs = 2)

Faimed3d provides multiple model architectures, pretrained on the UCF101 dataset for action recoginiton, which can be used for transfer learning.

Model	3-fold accuracy	duration/epoch	model size
efficientnet b0	92.5 %	9M:35S	48.8 MB
efficientnet b1	90.1 %	13M:20S	80.5 MB
resnet 18	87.6 %	6M:57S	339.1 MB
resnet 50	94.8 %	12M:16S	561.2 MB
resnet 101	96.0 %	17M:20S	1,030 MB

# slow
learn = cnn_learner_3d(dls, efficientnet_b0)

# slow
learn.lr_find()

SuggestedLRs(lr_min=0.014454397559165954, lr_steep=6.309573450380412e-07)

Click here for a more in-depth classification example.

Segmentation

dls = SegmentationDataLoaders3D.from_df(d,
                                 item_tfms = Resize3D((20, 112, 112)),
                                 batch_tfms = aug_transforms_3d(), 
                                 bs = 2, val_bs = 2)

All models in faimed3d can be used as a backbone for U-Nets, even with pre-trained weights.

# slow
learn = unet_learner_3d(dls, efficientnet_b0, n_out = 2)

# slow 
learn.lr_find()

SuggestedLRs(lr_min=0.33113112449646, lr_steep=0.10000000149011612)

Click here for a more in-depth segmentation example.

Extension to fastai for volumetric medical data

Related tags

Overview

FAIMED 3D

Classification

Segmentation

Owner

Keno

TGRNet: A Table Graph Reconstruction Network for Table Structure Recognition

Out-of-boundary View Synthesis towards Full-frame Video Stabilization

DeepLearning Anomalies Detection with Bluetooth Sensor Data

The pytorch implementation of DG-Font: Deformable Generative Networks for Unsupervised Font Generation

Lorien: A Unified Infrastructure for Efficient Deep Learning Workloads Delivery

Code repo for "FASA: Feature Augmentation and Sampling Adaptation for Long-Tailed Instance Segmentation" (ICCV 2021)

Repository for training material for the 2022 SDSC HPC/CI User Training Course

prior-based-losses-for-medical-image-segmentation

Camera-caps - Examine the camera capabilities for V4l2 cameras

VLGrammar: Grounded Grammar Induction of Vision and Language

Code base for "On-the-Fly Test-time Adaptation for Medical Image Segmentation"

NeurIPS workshop paper 'Counter-Strike Deathmatch with Large-Scale Behavioural Cloning'

sssegmentation is a general framework for our research on strongly supervised semantic segmentation.

Example scripts for the detection of lanes using the ultra fast lane detection model in Tensorflow Lite.

masscan + nmap + Finger

Classify the disease status of a plant given an image of a passion fruit

Code for the SIGGRAPH 2022 paper "DeltaConv: Anisotropic Operators for Geometric Deep Learning on Point Clouds."

It is an open dataset for object detection in remote sensing images.

Facilitating Database Tuning with Hyper-ParameterOptimization: A Comprehensive Experimental Evaluation

Repositório da disciplina de APC, no segundo semestre de 2021