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A New Dataset and Versatile Multi-Task Surgical Workflow Analysis Framework for Thoracoscopic Mitral Valvuloplasty

By Meng Lan, Xinjian Yan, Weixin Si, Xiaomeng Li.

Introduction

  • The official implementation for our paper "A New Dataset and Versatile Multi-Task Surgical Workflow Analysis Framework for Thoracoscopic Mitral Valvuloplasty".

Abstract. Surgical Workflow Analysis (SWA) on videos is critical for AI-assisted intelligent surgery. Existing SWA methods primarily focus on laparoscopic surgeries, while research on complex thoracoscopy-assisted cardiac surgery remains largely unexplored. In this paper, we introduce TMVP-SurVideo, the first SWA video dataset for Thoracoscopic cardiac Mitral ValvuloPlasty (TMVP). TMVP-SurVideo comprises 57 independent long-form surgical videos and over 429K annotated frames, covering four key tasks, namely phase and instrument recognitions, and phase and instrument anticipations. To achieve a comprehensive SWA system for TMVP and overcome the limitations of current SWA methods, we propose SurgFormer, the first query-based Transformer framework that simultaneously performs recognition and anticipation of surgical phases and instruments. SurgFormer uses four low-dimensional learnable task embeddings to independently decode representation embeddings for the predictions of the four tasks. During the decoding process, an information interaction module that contains the intra-frame task-level information interaction layer and the inter-frame temporal correlation learning layer is devised to operate on the task embeddings, enabling the information collaboration between tasks within each frame and temporal correlation learning of each task across frames. Besides, SurgFormer's unique architecture allows it to perform both offline and online inferences using a dynamic memory bank without model modification. Our proposed SurgFormer is evaluated on the TMVP-SurVideo and existing Cholec80 datasets to demonstrate its effectiveness on SWA

TMVP-SurVideo Dataset

TMVP-SurVideo is the first large-scale surgical video dataset for TMVP, with frame-level annotations for four tasks: phase recognition, instrument recognition, phase anticipation and instrument anticipation.

Comparson bwtween TMVP-SurVideo and existing SWA datasets
Overview of the phases and instruments in TMVP-SurVideo dataset.

Installation

Requirements

  • Python>=3.7

    We recommend you to use miniconda to create a conda environment:

    conda create -n swa python=3.7 pip

    Then, activate the environment:

    conda activate swa

  • PyTorch>=2.1.0, torchvision>=0.6.1 (following instructions here)

    For example, if your CUDA version is 11.8, you could install pytorch and torchvision as following:

    conda install pytorch=2.1.0 torchvision=0.16.0 cudatoolkit=11.8 -c pytorch

Compiling CUDA operators

cd ./models/ops
sh ./make.sh
# unit test (should see all checking is True)
python test.py

Usage

Dataset preparation

Five test demo videos and the annotaions could be download at here

The whole TMVP-SurVideo dataset will be released at here

  • The structure of data folder is arranged as follows:
(root folder)
├── data
|  ├── TMVP-SurVideo
|  |  ├── frames
|  |  |  ├── 001
|  |  |  ├── 002
|  |  |  ├── 003
|  |  |  ├── ......
|  |  ├── phase_annotations
|  |  |  ├── 001.txt
|  |  |  ├── 002.txt
|  |  |  ├── ......
|  |  ├── instrument_annotations
|  |  |  ├── 001.txt
|  |  |  ├── 002.txt
|  |  |  ├── ......
|  |  ├── phase_anticipation_annotations
|  |  |  ├── 001.txt
|  |  |  ├── 002.txt
|  |  |  ├── ......
|  |  ├── instrument_anticipation_annotations
|  |  |  ├── 001.txt
|  |  |  ├── 002.txt
|  |  |  ├── ......
├── code
|  ├── ......

Generate data path information files needed for the training

  • Run $ get_path_labels.py and $ get_path_labels_2.py to generate the files needed for the training

Training

The model is trained in a distribued manner.

sh train.sh

Inference

The trained weights of SurgFormer could be download at here.

sh test.sh