Set of models for classifcation of 3D volumes

Overview

Classification models 3D Zoo - Keras and TF.Keras

This repository contains 3D variants of popular CNN models for classification like ResNets, DenseNets, VGG, etc. It also contains weights obtained by converting ImageNet weights from the same 2D models.

This repository is based on great classification_models repo by @qubvel

Architectures:

Installation

pip install classification-models-3D

Examples

Loading model with imagenet weights:
# for keras
from classification_models_3D.keras import Classifiers

# for tensorflow.keras
# from classification_models_3D.tfkeras import Classifiers

ResNet18, preprocess_input = Classifiers.get('resnet18')
model = ResNet18(input_shape=(128, 128, 128, 3), weights='imagenet')

All possible nets for Classifiers.get() method: 'resnet18, 'resnet34', 'resnet50', 'resnet101', 'resnet152', 'seresnet18', 'seresnet34', 'seresnet50', 'seresnet101', 'seresnet152', 'seresnext50', 'seresnext101', 'senet154', 'resnext50', 'resnext101', 'vgg16', 'vgg19', 'densenet121', 'densenet169', 'densenet201', 'inceptionresnetv2', 'inceptionv3', 'mobilenet', 'mobilenetv2'

Convert imagenet weights (2D -> 3D)

Code to convert 2D imagenet weights to 3D variant is available here: convert_imagenet_weights_to_3D_models.py. Weights were obtained with TF2, but works OK with Keras + TF1 as well.

How to choose input shape

If initial 2D model had shape (512, 512, 3) then you can use shape (D, H, W, 3) where D * H * W ~= 512*512, so something like (64, 64, 64, 3) will be ok.

Training with single NVIDIA 1080Ti (11 GB) worked with:

  • DenseNet121, DenseNet169 and ResNet50 with shape (96, 128, 128, 3) and batch size 6
  • DenseNet201 with shape (96, 128, 128, 3) and batch size 5
  • ResNet18 with shape (128, 160, 160, 3) and batch size 6

Related repositories

Unresolved problems

  • There is no DepthwiseConv3D layer in keras, so repo used custom layer from this repo by @alexandrosstergiou which can be slower than native implementation.
  • There is no imagenet weights for 'inceptionresnetv2' and 'inceptionv3'.

Description

This code was used to get 1st place in DrivenData: Advance Alzheimer’s Research with Stall Catchers competition.

More details on ArXiv: https://arxiv.org/abs/2104.01687

Citation

If you find this code useful, please cite it as:

@InProceedings{RSolovyev_2021_stalled,
  author = {Solovyev, Roman and Kalinin, Alexandr A. and Gabruseva, Tatiana},
  title = {3D Convolutional Neural Networks for Stalled Brain Capillary Detection},
  booktitle = {Arxiv: 2104.01687},
  month = {April},
  year = {2021}
}
Comments
  • Update __init__.py

    Update __init__.py

    Using keras 2.9.0, import keras_applications as ka gives the following error:- ModuleNotFoundError: No module named 'keras_applications'

    Instead using from keras import applications as ka works!

    opened by msmuskan 0
  • Pushing current version to PyPI

    Pushing current version to PyPI

    Hello @ZFTurbo,

    if you have time, please push the current updated status (with ConvNeXt) of this repo to PyPI. :)

    Thanks again for the great work and your time!

    Cheers, Dominik

    opened by muellerdo 0
  • Grad cam issue

    Grad cam issue

    Hello ,

    base_model, preprocess_input = Classifiers.get('seresnext50') model = base_model(input_shape=(512, 512, 20, 1 ), weights=None , include_top = False ) x = Flatten()(model.output) x = Dense(1024, activation= 'sigmoid')(x) x = Dense(2, activation= 'sigmoid')(x)

    Trying to train a model , the accuracy is everything resides upto expectation, but the gradcam are quite off from the region of the focus - how the accuracy is good but the grad cam is off the focus of targeted area .

    Using the layer - 'activation-161' as output ref - https://github.com/fitushar/3D-Grad-CAM/blob/master/3DGrad-CAM.ipynb for the gradcam generation code , the results are always at the border of the image.

    opened by ntirupathirao18 0
  • ImportError: cannot import name 'VersionAwareLayers' from 'keras.layers'

    ImportError: cannot import name 'VersionAwareLayers' from 'keras.layers'

    Thank you for the great work.

    I am experiencing the following error over and over, even though I created a brand new tensorflow environment and installed all the necessary libraries in it. Could you please have a look on it and guide me how do I solve this problem? Thank you.

    ImportError: Unable to import 'VersionAwareLayers' from 'keras.layers' (/home/ubuntu/anaconda3/envs/cm_3d/lib/python3.7/site-packages/keras/layers/init.py)

    opened by nasir3843 2
  • 3D DenseNet

    3D DenseNet

    Hello and sorry to bother you beforehand,

    I am currently conducting my master thesis project and I am trying to implement a 3D DenseNet-121 with knee MRIs as input data. While I was searching on how to implement a 3D version of the DenseNet I came across your repository and tried to change it for my application.

    I have some issues regarding my try and I didn't know where else to ask about it and again I am sorry if I am completely of topic asking them here.

    Firstly, my input shapes are (250,320,18,1) and when I give them as input to the 3D DenseNet I developed with stride_size=1 for my Conv_block and pooling_size=(2,2,2) and strides=(2,2,1) for my AveragePooling3D layer in the transition block, the model is constructed properly with the specific input_size, while when I am trying to load a DenseNet121 from classification_models_3d.tfkeras classifiers I am unable to construct it with input_shape(250,320,18,1), stride_size=1 and kernel_size=2. It gives as an error "Negative dimension size... for node pool4_pool/AvgPool3D". Is there a way to specifically define the strides for AvgPool3D layer in the transition block?

    And secondly, I was thinking to load the 3D weights to my 3D DenseNet 121, is there a folder in your repository where I can find your pre-trained weights on imagenet??

    Again thank you for having this repository publicly available and sorry if I am completely of topic asking such things here.

    I look forward for you answer, Kind regards, Anastasis

    opened by alexopoulosanastasis 4
  • What are the limitations on Inceptionv3 input shape?

    What are the limitations on Inceptionv3 input shape?

    I seem to always get this error when I try to create InceptionV3 model no matter what input_shape. What are the limitations on input shape there?

    InvalidArgumentError: Negative dimension size caused by subtracting 3 from 2 for '{{node conv3d_314/Conv3D}} = 
    Conv3D[T=DT_FLOAT, data_format="NDHWC", dilations=[1, 1, 1, 1, 1], padding="VALID", strides=[1, 2, 2, 2, 1]](Placeholder, 
    conv3d_314/Conv3D/ReadVariableOp)' with input shapes: [?,2,17,17,192], [3,3,3,192,320].
    
    opened by mazatov 0
Releases(v1.0.4)
Instant Real-Time Example-Based Style Transfer to Facial Videos

FaceBlit: Instant Real-Time Example-Based Style Transfer to Facial Videos The official implementation of FaceBlit: Instant Real-Time Example-Based Sty

Aneta Texler 131 Dec 19, 2022
Ian Covert 130 Jan 01, 2023
UniLM AI - Large-scale Self-supervised Pre-training across Tasks, Languages, and Modalities

Pre-trained (foundation) models across tasks (understanding, generation and translation), languages (100+ languages), and modalities (language, image, audio, vision + language, audio + language, etc.

Microsoft 7.6k Jan 01, 2023
Makes patches from huge resolution .svs slide files using openslide

openslide_patcher Makes patches from huge resolution .svs slide files using openslide Example collage I made from outputs:

2 Dec 23, 2021
Put blind watermark into a text with python

text_blind_watermark Put blind watermark into a text. Can be used in Wechat dingding ... How to Use install pip install text_blind_watermark Alice Pu

郭飞 164 Dec 30, 2022
On the Complementarity between Pre-Training and Back-Translation for Neural Machine Translation (Findings of EMNLP 2021))

PTvsBT On the Complementarity between Pre-Training and Back-Translation for Neural Machine Translation (Findings of EMNLP 2021) Citation Please cite a

Sunbow Liu 10 Nov 25, 2022
PromptDet: Expand Your Detector Vocabulary with Uncurated Images

PromptDet: Expand Your Detector Vocabulary with Uncurated Images Paper Website Introduction The goal of this work is to establish a scalable pipeline

103 Dec 20, 2022
Code to reproduce the results for Statistically Robust Neural Network Classification, published in UAI 2021

Code to reproduce the results for Statistically Robust Neural Network Classification, published in UAI 2021

1 Jun 02, 2022
Code for Massive-scale Decoding for Text Generation using Lattices

Massive-scale Decoding for Text Generation using Lattices Jiacheng Xu, Greg Durrett TL;DR: a new search algorithm to construct lattices encoding many

Jiacheng Xu 37 Dec 18, 2022
PyKale is a PyTorch library for multimodal learning and transfer learning as well as deep learning and dimensionality reduction on graphs, images, texts, and videos

PyKale is a PyTorch library for multimodal learning and transfer learning as well as deep learning and dimensionality reduction on graphs, images, texts, and videos. By adopting a unified pipeline-ba

PyKale 370 Dec 27, 2022
PyTorch implementation of "A Simple Baseline for Low-Budget Active Learning".

A Simple Baseline for Low-Budget Active Learning This repository is the implementation of A Simple Baseline for Low-Budget Active Learning. In this pa

10 Nov 14, 2022
On-device speech-to-intent engine powered by deep learning

Rhino Made in Vancouver, Canada by Picovoice Rhino is Picovoice's Speech-to-Intent engine. It directly infers intent from spoken commands within a giv

Picovoice 510 Dec 30, 2022
Simple renderer for use with MuJoCo (>=2.1.2) Python Bindings.

Viewer for MuJoCo in Python Interactive renderer to use with the official Python bindings for MuJoCo. Starting with version 2.1.2, MuJoCo comes with n

Rohan P. Singh 62 Dec 30, 2022
[NeurIPS-2021] Mosaicking to Distill: Knowledge Distillation from Out-of-Domain Data

MosaicKD Code for NeurIPS-21 paper "Mosaicking to Distill: Knowledge Distillation from Out-of-Domain Data" 1. Motivation Natural images share common l

ZJU-VIPA 37 Nov 10, 2022
Official code for UnICORNN (ICML 2021)

UnICORNN (Undamped Independent Controlled Oscillatory RNN) [ICML 2021] This repository contains the implementation to reproduce the numerical experime

Konstantin Rusch 21 Dec 22, 2022
Examples of using f2py to get high-speed Fortran integrated with Python easily

f2py Examples Simple examples of using f2py to get high-speed Fortran integrated with Python easily. These examples are also useful to troubleshoot pr

Michael 35 Aug 21, 2022
Neon-erc20-example - Example of creating SPL token and wrapping it with ERC20 interface in Neon EVM

Example of wrapping SPL token by ERC2-20 interface in Neon Requirements Install

7 Mar 28, 2022
Official implementation of "StyleCariGAN: Caricature Generation via StyleGAN Feature Map Modulation" (SIGGRAPH 2021)

StyleCariGAN in PyTorch Official implementation of StyleCariGAN:Caricature Generation via StyleGAN Feature Map Modulation in PyTorch Requirements PyTo

PeterZhouSZ 49 Oct 31, 2022
clustering moroccan stocks time series data using k-means with dtw (dynamic time warping)

Moroccan Stocks Clustering Context Hey! we don't always have to forecast time series am I right ? We use k-means to cluster about 70 moroccan stock pr

Ayman Lafaz 7 Oct 18, 2022
PFENet: Prior Guided Feature Enrichment Network for Few-shot Segmentation (TPAMI).

PFENet This is the implementation of our paper PFENet: Prior Guided Feature Enrichment Network for Few-shot Segmentation that has been accepted to IEE

DV Lab 230 Dec 31, 2022