# SAF-IS: a Spatial Annotation Free Framework for Instance Segmentation of Surgical Tools

arXiv: https://arxiv.org/abs/2309.01723 · HTML: https://mlsanity.com/paper/2309.01723/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 36 of its 58 references that are in the map.
- First posted on arXiv 4 Sep 2023.

## Builds on (most cited first, 30 of 36)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [End-to-End Object Detection with Transformers](https://mlsanity.com/paper/2005.12872/) (2020)
- [Mask R-CNN](https://mlsanity.com/paper/1703.06870/) (2017)
- [SegFormer: Simple and Efficient Design for Semantic Segmentation with Transformers](https://mlsanity.com/paper/2105.15203/) (2021)
- [Supervised Contrastive Learning](https://mlsanity.com/paper/2004.11362/) (2020)
- [RAFT: Recurrent All-Pairs Field Transforms for Optical Flow](https://mlsanity.com/paper/2003.12039/) (2020)
- [A Survey on Contrastive Self-supervised Learning](https://mlsanity.com/paper/2011.00362/) (2020)
- [TrackFormer: Multi-Object Tracking with Transformers](https://mlsanity.com/paper/2101.02702/) (2021)
- [EndoNet: A Deep Architecture for Recognition Tasks on Laparoscopic Videos](https://mlsanity.com/paper/1602.03012/) (2016)
- [Pruning and Quantization for Deep Neural Network Acceleration: A Survey](https://mlsanity.com/paper/2101.09671/) (2021)
- [2017 Robotic Instrument Segmentation Challenge](https://mlsanity.com/paper/1902.06426/) (2019)
- [2018 Robotic Scene Segmentation Challenge](https://mlsanity.com/paper/2001.11190/) (2020)
- [Neural Rendering for Stereo 3D Reconstruction of Deformable Tissues in Robotic Surgery](https://mlsanity.com/paper/2206.15255/) (2022)
- [Automatic Instrument Segmentation in Robot-Assisted Surgery Using Deep Learning](https://mlsanity.com/paper/1803.01207/) (2018)
- [ISINet: An Instance-Based Approach for Surgical Instrument Segmentation](https://mlsanity.com/paper/2007.05533/) (2020)
- [Incorporating Temporal Prior from Motion Flow for Instrument Segmentation in Minimally Invasive Surgery Video](https://mlsanity.com/paper/1907.07899/) (2019)
- [Dissecting Self-Supervised Learning Methods for Surgical Computer Vision](https://mlsanity.com/paper/2207.00449/) (2022)
- [TraSeTR: Track-to-Segment Transformer with Contrastive Query for Instance-level Instrument Segmentation in Robotic Surgery](https://mlsanity.com/paper/2202.08453/) (2022)
- [Weakly Supervised Convolutional LSTM Approach for Tool Tracking in Laparoscopic Videos](https://mlsanity.com/paper/1812.01366/) (2018)
- [Learning Motion Flows for Semi-supervised Instrument Segmentation from Robotic Surgical Video](https://mlsanity.com/paper/2007.02501/) (2020)
- [Exploiting the potential of unlabeled endoscopic video data with self-supervised learning](https://mlsanity.com/paper/1711.09726/) (2017)
- [ToolNet: Holistically-Nested Real-Time Segmentation of Robotic Surgical Tools](https://mlsanity.com/paper/1706.08126/) (2017)
- [Concurrent Segmentation and Localization for Tracking of Surgical Instruments](https://mlsanity.com/paper/1703.10701/) (2017)
- [U-NetPlus: A Modified Encoder-Decoder U-Net Architecture for Semantic and Instance Segmentation of Surgical Instrument](https://mlsanity.com/paper/1902.08994/) (2019)
- [Deep Residual Learning for Instrument Segmentation in Robotic Surgery](https://mlsanity.com/paper/1703.08580/) (2017)
- [Weakly-Supervised Learning for Tool Localization in Laparoscopic Videos](https://mlsanity.com/paper/1806.05573/) (2018)
- [Endo-Sim2Real: Consistency learning-based domain adaptation for instrument segmentation](https://mlsanity.com/paper/2007.11514/) (2020)
- [ST-MTL: Spatio-Temporal Multitask Learning Model to Predict Scanpath While Tracking Instruments in Robotic Surgery](https://mlsanity.com/paper/2112.08189/) (2021)
- [FUN-SIS: a Fully UNsupervised approach for Surgical Instrument Segmentation](https://mlsanity.com/paper/2202.08141/) (2022)
- [CaRTS: Causality-driven Robot Tool Segmentation from Vision and Kinematics Data](https://mlsanity.com/paper/2203.09475/) (2022)

## Built on by (most cited first, 2 of 2)

- [Hierarchical Prototype-Memory Adaptation of SAM for Surgical Instrument Segmentation](https://mlsanity.com/paper/2608.24541/) (2026)
- [SurgiATM: A Physics-Guided Plug-and-Play Model for Deep Learning-Based Smoke Removal in Laparoscopic Surgery](https://mlsanity.com/paper/2511.05059/) (2025)

## Abstract (arXiv)

Instance segmentation of surgical instruments is a long-standing research problem, crucial for the development of many applications for computer-assisted surgery. This problem is commonly tackled via fully-supervised training of deep learning models, requiring expensive pixel-level annotations to train. In this work, we develop a framework for instance segmentation not relying on spatial annotations for training. Instead, our solution only requires binary tool masks, obtainable using recent unsupervised approaches, and binary tool presence labels, freely obtainable in robot-assisted surgery. Based on the binary mask information, our solution learns to extract individual tool instances from single frames, and to encode each instance into a compact vector representation, capturing its semantic features. Such representations guide the automatic selection of a tiny number of instances (8 only in our experiments), displayed to a human operator for tool-type labelling. The gathered information is finally used to match each training instance with a binary tool presence label, providing an effective supervision signal to train a tool instance classifier. We validate our framework on the EndoVis 2017 and 2018 segmentation datasets. We provide results using binary masks obtained either by manual annotation or as predictions of an unsupervised binary segmentation model. The latter solution yields an instance segmentation approach completely free from spatial annotations, outperforming several state-of-the-art fully-supervised segmentation approaches.