Few-Shot Adaptation of Training-Free Foundation Model for 3D Medical Image Segmentation

Vision foundation models have achieved remarkable progress across various image analysis tasks. In the image segmentation task, foundation models like the Segment Anything Model (SAM) enable generalizable zero-shot segmentation through user-provided prompts. However, SAM primarily trained on natural images, lacks the domain-specific expertise of medical imaging. This limitation poses challenges when applying SAM to medical image segmentation, including the need for extensive fine-tuning on specialized medical datasets and a dependency on manual prompts, which are both labor-intensive and require intervention from medical experts. This work introduces the Few-shot Adaptation of Training-frEe SAM (FATE-SAM), a novel method designed to adapt the advanced Segment Anything Model 2 (SAM2) for 3D medical image segmentation. FATE-SAM reassembles pre-trained modules of SAM2 to enable few-shot adaptation, leveraging a small number of support examples to capture anatomical knowledge and perform prompt-free segmentation, without requiring model fine-tuning. To handle the volumetric nature of medical images, we incorporate a Volumetric Consistency mechanism that enhances spatial coherence across 3D slices. We evaluate FATE-SAM on multiple medical imaging datasets and compare it with supervised learning methods, zero-shot SAM approaches, and fine-tuned medical SAM methods. Results show that FATE-SAM delivers robust and accurate segmentation while eliminating the need for large annotated datasets and expert intervention. FATE-SAM provides a practical, efficient solution for medical image segmentation, making it more accessible for clinical applications.

FLAVARS: A Multimodal Foundational Language and Vision Alignment Model for Remote Sensing

Remote sensing imagery is dense with objects and contextual visual information. There is a recent trend to combine paired satellite images and text captions for pretraining performant encoders for downstream tasks. However, while contrastive image-text methods like CLIP enable vision-language alignment and zero-shot classification ability, vision-only downstream performance tends to degrade compared to image-only pretraining, such as MAE. In this paper, we propose FLAVARS, a pretraining method that combines the best of both contrastive learning and masked modeling, along with geospatial alignment via contrastive location encoding. We find that FLAVARS significantly outperforms a baseline of SkyCLIP for vision-only tasks such as KNN classification and semantic segmentation, +6\% mIOU on SpaceNet1, while retaining the ability to perform zero-shot classification, unlike MAE pretrained methods.

Towards Zero-Shot & Explainable Video Description by Reasoning over Graphs of Events in Space and Time

In the current era of Machine Learning, Transformers have become the de facto approach across a variety of domains, such as computer vision and natural language processing. Transformer-based solutions are the backbone of current state-of-the-art methods for language generation, image and video classification, segmentation, action and object recognition, among many others. Interestingly enough, while these state-of-the-art methods produce impressive results in their respective domains, the problem of understanding the relationship between vision and language is still beyond our reach. In this work, we propose a common ground between vision and language based on events in space and time in an explainable and programmatic way, to connect learning-based vision and language state of the art models and provide a solution to the long standing problem of describing videos in natural language. We validate that our algorithmic approach is able to generate coherent, rich and relevant textual descriptions on videos collected from a variety of datasets, using both standard metrics (e.g. Bleu, ROUGE) and the modern LLM-as-a-Jury approach.

CellViT++: Energy-Efficient and Adaptive Cell Segmentation and Classification Using Foundation Models

Digital Pathology is a cornerstone in the diagnosis and treatment of diseases. A key task in this field is the identification and segmentation of cells in hematoxylin and eosin-stained images. Existing methods for cell segmentation often require extensive annotated datasets for training and are limited to a predefined cell classification scheme. To overcome these limitations, we propose $\text{CellViT}^{{\scriptscriptstyle ++}}$, a framework for generalized cell segmentation in digital pathology. $\text{CellViT}^{{\scriptscriptstyle ++}}$ utilizes Vision Transformers with foundation models as encoders to compute deep cell features and segmentation masks simultaneously. To adapt to unseen cell types, we rely on a computationally efficient approach. It requires minimal data for training and leads to a drastically reduced carbon footprint. We demonstrate excellent performance on seven different datasets, covering a broad spectrum of cell types, organs, and clinical settings. The framework achieves remarkable zero-shot segmentation and data-efficient cell-type classification. Furthermore, we show that $\text{CellViT}^{{\scriptscriptstyle ++}}$ can leverage immunofluorescence stainings to generate training datasets without the need for pathologist annotations. The automated dataset generation approach surpasses the performance of networks trained on manually labeled data, demonstrating its effectiveness in creating high-quality training datasets without expert annotations. To advance digital pathology, $\text{CellViT}^{{\scriptscriptstyle ++}}$ is available as an open-source framework featuring a user-friendly, web-based interface for visualization and annotation. The code is available under https://github.com/TIO-IKIM/CellViT-plus-plus.

Test-Time Optimization for Domain Adaptive Open Vocabulary Segmentation

We present Seg-TTO, a novel framework for zero-shot, open-vocabulary semantic segmentation (OVSS), designed to excel in specialized domain tasks. While current open vocabulary approaches show impressive performance on standard segmentation benchmarks under zero-shot settings, they fall short of supervised counterparts on highly domain-specific datasets. We focus on segmentation-specific test-time optimization to address this gap. Segmentation requires an understanding of multiple concepts within a single image while retaining the locality and spatial structure of representations. We propose a novel self-supervised objective adhering to these requirements and use it to align the model parameters with input images at test time. In the textual modality, we learn multiple embeddings for each category to capture diverse concepts within an image, while in the visual modality, we calculate pixel-level losses followed by embedding aggregation operations specific to preserving spatial structure. Our resulting framework termed Seg-TTO is a plug-in-play module. We integrate Seg-TTO with three state-of-the-art OVSS approaches and evaluate across 22 challenging OVSS tasks covering a range of specialized domains. Our Seg-TTO demonstrates clear performance improvements across these establishing new state-of-the-art. Code: https://github.com/UlinduP/SegTTO.

Zero-shot Shark Tracking and Biometrics from Aerial Imagery

The recent widespread adoption of drones for studying marine animals provides opportunities for deriving biological information from aerial imagery. The large scale of imagery data acquired from drones is well suited for machine learning (ML) analysis. Development of ML models for analyzing marine animal aerial imagery has followed the classical paradigm of training, testing, and deploying a new model for each dataset, requiring significant time, human effort, and ML expertise. We introduce Frame Level ALIgment and tRacking (FLAIR), which leverages the video understanding of Segment Anything Model 2 (SAM2) and the vision-language capabilities of Contrastive Language-Image Pre-training (CLIP). FLAIR takes a drone video as input and outputs segmentation masks of the species of interest across the video. Notably, FLAIR leverages a zero-shot approach, eliminating the need for labeled data, training a new model, or fine-tuning an existing model to generalize to other species. With a dataset of 18,000 drone images of Pacific nurse sharks, we trained state-of-the-art object detection models to compare against FLAIR. We show that FLAIR massively outperforms these object detectors and performs competitively against two human-in-the-loop methods for prompting SAM2, achieving a Dice score of 0.81. FLAIR readily generalizes to other shark species without additional human effort and can be combined with novel heuristics to automatically extract relevant information including length and tailbeat frequency. FLAIR has significant potential to accelerate aerial imagery analysis workflows, requiring markedly less human effort and expertise than traditional machine learning workflows, while achieving superior accuracy. By reducing the effort required for aerial imagery analysis, FLAIR allows scientists to spend more time interpreting results and deriving insights about marine ecosystems.

Segment Anything Model for Zero-shot Single Particle Tracking in Liquid Phase Transmission Electron Microscopy

Liquid phase transmission electron microscopy (LPTEM) offers an unparalleled combination of spatial and temporal resolution, making it a promising tool for single particle tracking at the nanoscale. However, the absence of a standardized framework for identifying and tracking nanoparticles in noisy LPTEM videos has impeded progress in the field to develop this technique as a single particle tracking tool. To address this, we leveraged Segment Anything Model 2 (SAM 2), released by Meta, which is a foundation model developed for segmenting videos and images. Here, we demonstrate that SAM 2 can successfully segment LPTEM videos in a zero-shot manner and without requiring fine-tuning. Building on this capability, we introduce SAM4EM, a comprehensive framework that integrates promptable video segmentation with particle tracking and statistical analysis, providing an end-to-end LPTEM analysis framework for single particle tracking. SAM4EM achieves nearly 50-fold higher accuracy in segmenting and analyzing LPTEM videos compared to state-of-the-art methods, paving the way for broader applications of LPTEM in nanoscale imaging.

Gaussian Masked Autoencoders

This paper explores Masked Autoencoders (MAE) with Gaussian Splatting. While reconstructive self-supervised learning frameworks such as MAE learns good semantic abstractions, it is not trained for explicit spatial awareness. Our approach, named Gaussian Masked Autoencoder, or GMAE, aims to learn semantic abstractions and spatial understanding jointly. Like MAE, it reconstructs the image end-to-end in the pixel space, but beyond MAE, it also introduces an intermediate, 3D Gaussian-based representation and renders images via splatting. We show that GMAE can enable various zero-shot learning capabilities of spatial understanding (e.g., figure-ground segmentation, image layering, edge detection, etc.) while preserving the high-level semantics of self-supervised representation quality from MAE. To our knowledge, we are the first to employ Gaussian primitives in an image representation learning framework beyond optimization-based single-scene reconstructions. We believe GMAE will inspire further research in this direction and contribute to developing next-generation techniques for modeling high-fidelity visual data. More details at https://brjathu.github.io/gmae

KAnoCLIP: Zero-Shot Anomaly Detection through Knowledge-Driven Prompt Learning and Enhanced Cross-Modal Integration

Zero-shot anomaly detection (ZSAD) identifies anomalies without needing training samples from the target dataset, essential for scenarios with privacy concerns or limited data. Vision-language models like CLIP show potential in ZSAD but have limitations: relying on manually crafted fixed textual descriptions or anomaly prompts is time-consuming and prone to semantic ambiguity, and CLIP struggles with pixel-level anomaly segmentation, focusing more on global semantics than local details. To address these limitations, We introduce KAnoCLIP, a novel ZSAD framework that leverages vision-language models. KAnoCLIP combines general knowledge from a Large Language Model (GPT-3.5) and fine-grained, image-specific knowledge from a Visual Question Answering system (Llama3) via Knowledge-Driven Prompt Learning (KnPL). KnPL uses a knowledge-driven (KD) loss function to create learnable anomaly prompts, removing the need for fixed text prompts and enhancing generalization. KAnoCLIP includes the CLIP visual encoder with V-V attention (CLIP-VV), Bi-Directional Cross-Attention for Multi-Level Cross-Modal Interaction (Bi-CMCI), and Conv-Adapter. These components preserve local visual semantics, improve local cross-modal fusion, and align global visual features with textual information, enhancing pixel-level anomaly detection. KAnoCLIP achieves state-of-the-art performance in ZSAD across 12 industrial and medical datasets, demonstrating superior generalization compared to existing methods.

Is Segment Anything Model 2 All You Need for Surgery Video Segmentation? A Systematic Evaluation

Surgery video segmentation is an important topic in the surgical AI field. It allows the AI model to understand the spatial information of a surgical scene. Meanwhile, due to the lack of annotated surgical data, surgery segmentation models suffer from limited performance. With the emergence of SAM2 model, a large foundation model for video segmentation trained on natural videos, zero-shot surgical video segmentation became more realistic but meanwhile remains to be explored. In this paper, we systematically evaluate the performance of SAM2 model in zero-shot surgery video segmentation task. We conducted experiments under different configurations, including different prompting strategies, robustness, etc. Moreover, we conducted an empirical evaluation over the performance, including 9 datasets with 17 different types of surgeries.