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.

Unlocking the Potential of Digital Pathology: Novel Baselines for Compression

Digital pathology offers a groundbreaking opportunity to transform clinical practice in histopathological image analysis, yet faces a significant hurdle: the substantial file sizes of pathological Whole Slide Images (WSI). While current digital pathology solutions rely on lossy JPEG compression to address this issue, lossy compression can introduce color and texture disparities, potentially impacting clinical decision-making. While prior research addresses perceptual image quality and downstream performance independently of each other, we jointly evaluate compression schemes for perceptual and downstream task quality on four different datasets. In addition, we collect an initially uncompressed dataset for an unbiased perceptual evaluation of compression schemes. Our results show that deep learning models fine-tuned for perceptual quality outperform conventional compression schemes like JPEG-XL or WebP for further compression of WSI. However, they exhibit a significant bias towards the compression artifacts present in the training data and struggle to generalize across various compression schemes. We introduce a novel evaluation metric based on feature similarity between original files and compressed files that aligns very well with the actual downstream performance on the compressed WSI. Our metric allows for a general and standardized evaluation of lossy compression schemes and mitigates the requirement to independently assess different downstream tasks. Our study provides novel insights for the assessment of lossy compression schemes for WSI and encourages a unified evaluation of lossy compression schemes to accelerate the clinical uptake of digital pathology.

Comparative Analysis of nnUNet and MedNeXt for Head and Neck Tumor Segmentation in MRI-guided Radiotherapy

Radiation therapy (RT) is essential in treating head and neck cancer (HNC), with magnetic resonance imaging(MRI)-guided RT offering superior soft tissue contrast and functional imaging. However, manual tumor segmentation is time-consuming and complex, and therfore remains a challenge. In this study, we present our solution as team TUMOR to the HNTS-MRG24 MICCAI Challenge which is focused on automated segmentation of primary gross tumor volumes (GTVp) and metastatic lymph node gross tumor volume (GTVn) in pre-RT and mid-RT MRI images. We utilized the HNTS-MRG2024 dataset, which consists of 150 MRI scans from patients diagnosed with HNC, including original and registered pre-RT and mid-RT T2-weighted images with corresponding segmentation masks for GTVp and GTVn. We employed two state-of-the-art models in deep learning, nnUNet and MedNeXt. For Task 1, we pretrained models on pre-RT registered and mid-RT images, followed by fine-tuning on original pre-RT images. For Task 2, we combined registered pre-RT images, registered pre-RT segmentation masks, and mid-RT data as a multi-channel input for training. Our solution for Task 1 achieved 1st place in the final test phase with an aggregated Dice Similarity Coefficient of 0.8254, and our solution for Task 2 ranked 8th with a score of 0.7005. The proposed solution is publicly available at Github Repository.

Improved Multi-Task Brain Tumour Segmentation with Synthetic Data Augmentation

This paper presents the winning solution of task 1 and the third-placed solution of task 3 of the BraTS challenge. The use of automated tools in clinical practice has increased due to the development of more and more sophisticated and reliable algorithms. However, achieving clinical standards and developing tools for real-life scenarios is a major challenge. To this end, BraTS has organised tasks to find the most advanced solutions for specific purposes. In this paper, we propose the use of synthetic data to train state-of-the-art frameworks in order to improve the segmentation of adult gliomas in a post-treatment scenario, and the segmentation of meningioma for radiotherapy planning. Our results suggest that the use of synthetic data leads to more robust algorithms, although the synthetic data generation pipeline is not directly suited to the meningioma task. The code for these tasks is available at https://github.com/ShadowTwin41/BraTS_2023_2024_solutions.

Brain Tumour Removing and Missing Modality Generation using 3D WDM

This paper presents the second-placed solution for task 8 and the participation solution for task 7 of BraTS 2024. The adoption of automated brain analysis algorithms to support clinical practice is increasing. However, many of these algorithms struggle with the presence of brain lesions or the absence of certain MRI modalities. The alterations in the brain's morphology leads to high variability and thus poor performance of predictive models that were trained only on healthy brains. The lack of information that is usually provided by some of the missing MRI modalities also reduces the reliability of the prediction models trained with all modalities. In order to improve the performance of these models, we propose the use of conditional 3D wavelet diffusion models. The wavelet transform enabled full-resolution image training and prediction on a GPU with 48 GB VRAM, without patching or downsampling, preserving all information for prediction. For the inpainting task of BraTS 2024, the use of a large and variable number of healthy masks and the stability and efficiency of the 3D wavelet diffusion model resulted in 0.007, 22.61 and 0.842 in the validation set and 0.07 , 22.8 and 0.91 in the testing set (MSE, PSNR and SSIM respectively). The code for these tasks is available at https://github.com/ShadowTwin41/BraTS_2023_2024_solutions.

Every Component Counts: Rethinking the Measure of Success for Medical Semantic Segmentation in Multi-Instance Segmentation Tasks

We present Connected-Component~(CC)-Metrics, a novel semantic segmentation evaluation protocol, targeted to align existing semantic segmentation metrics to a multi-instance detection scenario in which each connected component matters. We motivate this setup in the common medical scenario of semantic metastases segmentation in a full-body PET/CT. We show how existing semantic segmentation metrics suffer from a bias towards larger connected components contradicting the clinical assessment of scans in which tumor size and clinical relevance are uncorrelated. To rebalance existing segmentation metrics, we propose to evaluate them on a per-component basis thus giving each tumor the same weight irrespective of its size. To match predictions to ground-truth segments, we employ a proximity-based matching criterion, evaluating common metrics locally at the component of interest. Using this approach, we break free of biases introduced by large metastasis for overlap-based metrics such as Dice or Surface Dice. CC-Metrics also improves distance-based metrics such as Hausdorff Distances which are uninformative for small changes that do not influence the maximum or 95th percentile, and avoids pitfalls introduced by directly combining counting-based metrics with overlap-based metrics as it is done in Panoptic Quality.

LIMIS: Towards Language-based Interactive Medical Image Segmentation

Within this work, we introduce LIMIS: The first purely language-based interactive medical image segmentation model. We achieve this by adapting Grounded SAM to the medical domain and designing a language-based model interaction strategy that allows radiologists to incorporate their knowledge into the segmentation process. LIMIS produces high-quality initial segmentation masks by leveraging medical foundation models and allows users to adapt segmentation masks using only language, opening up interactive segmentation to scenarios where physicians require using their hands for other tasks. We evaluate LIMIS on three publicly available medical datasets in terms of performance and usability with experts from the medical domain confirming its high-quality segmentation masks and its interactive usability.

De-Identification of Medical Imaging Data: A Comprehensive Tool for Ensuring Patient Privacy

Medical data employed in research frequently comprises sensitive patient health information (PHI), which is subject to rigorous legal frameworks such as the General Data Protection Regulation (GDPR) or the Health Insurance Portability and Accountability Act (HIPAA). Consequently, these types of data must be pseudonymized prior to utilisation, which presents a significant challenge for many researchers. Given the vast array of medical data, it is necessary to employ a variety of de-identification techniques. To facilitate the anonymization process for medical imaging data, we have developed an open-source tool that can be used to de-identify DICOM magnetic resonance images, computer tomography images, whole slide images and magnetic resonance twix raw data. Furthermore, the implementation of a neural network enables the removal of text within the images. The proposed tool automates an elaborate anonymization pipeline for multiple types of inputs, reducing the need for additional tools used for de-identification of imaging data. We make our code publicly available at https://github.com/code-lukas/medical_image_deidentification.

Spacewalker: Traversing Representation Spaces for Fast Interactive Exploration and Annotation of Unstructured Data

Unstructured data in industries such as healthcare, finance, and manufacturing presents significant challenges for efficient analysis and decision making. Detecting patterns within this data and understanding their impact is critical but complex without the right tools. Traditionally, these tasks relied on the expertise of data analysts or labor-intensive manual reviews. In response, we introduce Spacewalker, an interactive tool designed to explore and annotate data across multiple modalities. Spacewalker allows users to extract data representations and visualize them in low-dimensional spaces, enabling the detection of semantic similarities. Through extensive user studies, we assess Spacewalker's effectiveness in data annotation and integrity verification. Results show that the tool's ability to traverse latent spaces and perform multi-modal queries significantly enhances the user's capacity to quickly identify relevant data. Moreover, Spacewalker allows for annotation speed-ups far superior to conventional methods, making it a promising tool for efficiently navigating unstructured data and improving decision making processes. The code of this work is open-source and can be found at: https://github.com/code-lukas/Spacewalker

Towards Synthetic Data Generation for Improved Pain Recognition in Videos under Patient Constraints

Recognizing pain in video is crucial for improving patient-computer interaction systems, yet traditional data collection in this domain raises significant ethical and logistical challenges. This study introduces a novel approach that leverages synthetic data to enhance video-based pain recognition models, providing an ethical and scalable alternative. We present a pipeline that synthesizes realistic 3D facial models by capturing nuanced facial movements from a small participant pool, and mapping these onto diverse synthetic avatars. This process generates 8,600 synthetic faces, accurately reflecting genuine pain expressions from varied angles and perspectives. Utilizing advanced facial capture techniques, and leveraging public datasets like CelebV-HQ and FFHQ-UV for demographic diversity, our new synthetic dataset significantly enhances model training while ensuring privacy by anonymizing identities through facial replacements. Experimental results demonstrate that models trained on combinations of synthetic data paired with a small amount of real participants achieve superior performance in pain recognition, effectively bridging the gap between synthetic simulations and real-world applications. Our approach addresses data scarcity and ethical concerns, offering a new solution for pain detection and opening new avenues for research in privacy-preserving dataset generation. All resources are publicly available to encourage further innovation in this field.