Volumetric parameterization of the placenta to a flattened template

Related tags

Deep Learningplacenta-flattening
Overview

placenta-flattening

A MATLAB algorithm for volumetric mesh parameterization. Developed for mapping a placenta segmentation derived from an MRI image to a flattened template for visualization. The code can work on NIFTI images or MATLAB matrices containing imaging information.

Requirements

Add the MATLAB packages to the working path.

Usage

main(grayImage, segImage): input a grayscale MRI image and the corresponding binary segmentation, where voxels labeled '1' correspond to the placenta. The inputs grayImage, segImage can either be full path locations of NIFTI image files, or image matrices. The grayImage input can be a 3D MRI volume, or a 4D series of MRI volumes. The script outputs the flattened meshes and images containing the mapped intensities.

Development

Please contact Mazdak Abulnaga, [email protected].

Citing and Paper

Please consider citing our paper

@inproceedings{abulnaga2019placenta,
title={Placental Flattening via Volumetric Parameterization},
author={Abulnaga, S. Mazdak and Abaci Turk, Esra and Bessmeltsev, Mikhail and Grant, P. Ellen and Solomon, Justin and Golland, Polina},
booktitle={Medical Image Computing and Computer Assisted Intervention -- MICCAI 2019},
year={2019},
pages={39--47},
}
You might also like...
This project uses Template Matching technique for object detecting by detection of template image over base image
This project uses Template Matching technique for object detecting by detection of template image over base image

Object Detection Project Using OpenCV This project uses Template Matching technique for object detecting by detection the template image over base ima

Pratham Bhatnagar 4 Nov 16, 2021
Generic template to bootstrap your PyTorch project with PyTorch Lightning, Hydra, W&B, and DVC.

NN Template Generic template to bootstrap your PyTorch project. Click on Use this Template and avoid writing boilerplate code for: PyTorch Lightning,

Luca Moschella 520 Dec 30, 2022
All the essential resources and template code needed to understand and practice data structures and algorithms in python with few small projects to demonstrate their practical application.

Data Structures and Algorithms Python INDEX 1. Resources - Books Data Structures - Reema Thareja competitiveCoding Big-O Cheat Sheet DAA Syllabus Inte

Shushrut Kumar 129 Dec 15, 2022
Grammar Induction using a Template Tree Approach

Gitta Gitta ("Grammar Induction using a Template Tree Approach") is a method for inducing context-free grammars. It performs particularly well on data

Thomas Winters 36 Nov 15, 2022
A template repository for submitting a job to the Slurm Cluster installed at the DISI - University of Bologna

Cluster di HPC con GPU per esperimenti di calcolo (draft version 1.0) Per poter utilizzare il cluster il primo passo è abilitare l'account istituziona

null 20 Dec 16, 2022
This is a template for the Non-autoregressive Deep Learning-Based TTS model (in PyTorch).

Non-autoregressive Deep Learning-Based TTS Template This is a template for the Non-autoregressive TTS model. It contains Data Preprocessing Pipeline D

Keon Lee 13 Dec 5, 2022
STMTrack: Template-free Visual Tracking with Space-time Memory Networks

STMTrack This is the official implementation of the paper: STMTrack: Template-free Visual Tracking with Space-time Memory Networks. Setup Prepare Anac

Zhihong Fu 62 Dec 21, 2022
A modified version of DeepMind's Alphafold2 to divide CPU part (MSA and template searching) and GPU part (prediction model)

ParallelFold Author: Bozitao Zhong This is a modified version of DeepMind's Alphafold2 to divide CPU part (MSA and template searching) and GPU part (p

Bozitao Zhong 77 Dec 22, 2022
Source Code For Template-Based Named Entity Recognition Using BART

Template-Based NER Source Code For Template-Based Named Entity Recognition Using BART Training Training train.py Inference inference.py Corpus ATIS (h

null 174 Dec 19, 2022
Comments
  • Is it possible to provide public input data?

    Is it possible to provide public input data?

    Hello, I am a master student majoring in computer science. I am very interested in your work and hope to reproduce the results, but because there is no MRI scan data, I cannot successfully run the program to observe the effect. If you can provide the program input data, I will really appreciate.

    opened by yuemos 3
  • 4d

    4d

    Now accepts 4D input grayscale images as input. Implemented by adding a loop when mapping the MRI images to the flattened space. I've tested with 4D nifti input, but not 4D image matrices.

    opened by PaddySlator 0
Releases(v1.0.0)
Owner
Mazdak Abulnaga
CS PhD student at MIT
Mazdak Abulnaga
GitHub Repository
PyTorch implementation of DUL (Data Uncertainty Learning in Face Recognition, CVPR2020)

PyTorch implementation of DUL (Data Uncertainty Learning in Face Recognition, CVPR2020)

Mouxiao Huang 20 Nov 15, 2022
Modified fork of Xuebin Qin's U-2-Net Repository. Used for demonstration purposes.

U^2-Net (U square net) Modified version of U2Net used for demonstation purposes. Paper: U^2-Net: Going Deeper with Nested U-Structure for Salient Obje

Shreyas Bhat Kera 13 Aug 28, 2022
code for "Feature Importance-aware Transferable Adversarial Attacks"

Feature Importance-aware Attack(FIA) This repository contains the code for the paper: Feature Importance-aware Transferable Adversarial Attacks (ICCV

Hengchang Guo 44 Nov 24, 2022
Model-based reinforcement learning in TensorFlow

Bellman Website | Twitter | Documentation (latest) What does Bellman do? Bellman is a package for model-based reinforcement learning (MBRL) in Python,

46 Nov 09, 2022
Safe Policy Optimization with Local Features

Safe Policy Optimization with Local Feature (SPO-LF) This is the source-code for implementing the algorithms in the paper "Safe Policy Optimization wi

Akifumi Wachi 6 Jun 05, 2022
A Dataset for Direct Quotation Extraction and Attribution in News Articles.

DirectQuote - A Dataset for Direct Quotation Extraction and Attribution in News Articles DirectQuote is a corpus containing 19,760 paragraphs and 10,3

THUNLP-MT 9 Sep 23, 2022
nanodet_plus,yolov5_v6.0

OAK_Detection OAK设备上适配nanodet_plus,yolov5_v6.0 Environment pytorch = 1.7.0

炼丹去了 1 Feb 18, 2022
Tools for computational pathology

A toolkit for computational pathology and machine learning. View documentation Please cite our paper Installation There are several ways to install Pa

254 Dec 12, 2022
A High-Performance Distributed Library for Large-Scale Bundle Adjustment

MegBA: A High-Performance and Distributed Library for Large-Scale Bundle Adjustment This repo contains an official implementation of MegBA. MegBA is a

旷视研究院 3D 组 336 Dec 27, 2022
A benchmark dataset for emulating atmospheric radiative transfer in weather and climate models with machine learning (NeurIPS 2021 Datasets and Benchmarks Track)

ClimART - A Benchmark Dataset for Emulating Atmospheric Radiative Transfer in Weather and Climate Models Official PyTorch Implementation Using deep le

21 Dec 31, 2022
Collection of TensorFlow2 implementations of Generative Adversarial Network varieties presented in research papers.

TensorFlow2-GAN Collection of tf2.0 implementations of Generative Adversarial Network varieties presented in research papers. Model architectures will

41 Apr 28, 2022
Simple Dynamic Batching Inference

Simple Dynamic Batching Inference 解决了什么问题？ 众所周知，Batch对于GPU上深度学习模型的运行效率影响很大。。。 是在Inference时。搜索、推荐等场景自带比较大的batch，问题不大。但更多场景面临的往往是稀碎的请求(比如图片服务里一次一张图)。 如果

116 Jan 01, 2023
A Human-in-the-Loop workflow for creating HD images from text

A Human-in-the-Loop? workflow for creating HD images from text DALL·E Flow is an interactive workflow for generating high-definition images from text

Jina AI 2.5k Jan 02, 2023
Official implementation of "StyleCariGAN: Caricature Generation via StyleGAN Feature Map Modulation" (SIGGRAPH 2021)

StyleCariGAN: Caricature Generation via StyleGAN Feature Map Modulation This repository contains the official PyTorch implementation of the following

Wonjong Jang 270 Dec 30, 2022
Convert game ISO and archives to CD CHD for emulation on Linux.

tochd Convert game ISO and archives to CD CHD for emulation. Author: Tuncay D. Source: https://github.com/thingsiplay/tochd Releases: https://github.c

Tuncay 20 Jan 02, 2023
Code for "MetaMorph: Learning Universal Controllers with Transformers", Gupta et al, ICLR 2022

MetaMorph: Learning Universal Controllers with Transformers This is the code for the paper MetaMorph: Learning Universal Controllers with Transformers

Agrim Gupta 50 Jan 03, 2023
[NeurIPS 2021] Well-tuned Simple Nets Excel on Tabular Datasets

[NeurIPS 2021] Well-tuned Simple Nets Excel on Tabular Datasets Introduction This repo contains the source code accompanying the paper: Well-tuned Sim

52 Jan 04, 2023
DecoupledNet is semantic segmentation system which using heterogeneous annotations

DecoupledNet: Decoupled Deep Neural Network for Semi-supervised Semantic Segmentation Created by Seunghoon Hong, Hyeonwoo Noh and Bohyung Han at POSTE

Hyeonwoo Noh 74 Sep 22, 2021
Official implement of "CAT: Cross Attention in Vision Transformer".

CAT: Cross Attention in Vision Transformer This is official implement of "CAT: Cross Attention in Vision Transformer". Abstract Since Transformer has

100 Dec 15, 2022
Benchmark VAE - Library for Variational Autoencoder benchmarking

Documentation pythae This library implements some of the most common (Variational) Autoencoder models. In particular it provides the possibility to pe

1.1k Jan 02, 2023