arXiv subjects

Florian Jug

Publications and source records attributed to Florian Jug.

At least 19 recordsLinked to original sources

arXiv2026

SWITi: Quantifying and Reducing Tiling Artifacts with Sliding Window Inner Tiling

SWITi is a test-time method for reducing artifacts in tiled predictions, particularly for neural networks that learn posterior distributions from which solutions are sampled at inference time. Tiled predictions are unavoidable for large image data, and artifacts arise whenever tiles are smaller than a network's receptive field and when tiles are independent posterior samples. SWITi averages overlapping sliding-window predictions, so discrepancies between neighboring samples are spread across shifted tile positions rather than accumulating at fixed seam coordinates. For posterior models, SWITi uses no more tile samples than an MMSE estimate requires and therefore incurs no additional forward passes. Additionally, we introduce two reference-free metrics, the Fraction of Rejected Tests (FRT) and Artifact Severity (ASV), for detecting and quantifying tiling artifacts from a per-tile permutation test that compares the distribution of pixel gradients across tile seams against the surrounding image content. On pre-trained and published image splitting models across three fluorescence microscopy datasets in 2D and 3D, we show that SWITi substantially attenuates stitching seams while also improving reconstruction fidelity and resolution. Since tiling artifacts in posterior predictions can easily be mistaken for biological structures or for boundaries between biological structures, removing or reducing them using SWITi will improve the downstream processing of large image predictions, which is particularly relevant for biomedical data.

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arXiv2026

{\lambda}Split: Self-Supervised Content-Aware Spectral Unmixing for Fluorescence Microscopy

In fluorescence microscopy, spectral unmixing aims to recover individual fluorophore concentrations from spectral images that capture mixed fluorophore emissions. Since classical methods operate pixel-wise and rely on least-squares fitting, their performance degrades with increasingly overlapping emission spectra and higher levels of noise, suggesting that a data-driven approach that can learn and utilize a structural prior might lead to improved results. Learning-based approaches for spectral imaging do exist, but they are either not optimized for microscopy data or are developed for very specific cases that are not applicable to fluorescence microscopy settings. To address this, we propose {\lambda}Split, a physics-informed deep generative model that learns a conditional distribution over concentration maps using a hierarchical Variational Autoencoder. A fully differentiable Spectral Mixer enforces consistency with the image formation process, while the learned structural priors enable state-of-the-art unmixing and implicit noise removal. We demonstrate {\lambda}Split on 3 real-world datasets that we synthetically cast into a total of 66 challenging spectral unmixing benchmarks. We compare our results against a total of 10 baseline methods, including classical methods and a range of learning-based methods. Our results consistently show competitive performance and improved robustness in high noise regimes, when spectra overlap considerably, or when the spectral dimensionality is lowered, making {\lambda}Split a new state-of-the-art for spectral unmixing of fluorescent microscopy data. Importantly, {\lambda}Split is compatible with spectral data produced by standard confocal microscopes, enabling immediate adoption without specialized hardware modifications.

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arXiv2026

MamaDino: A Hybrid Vision Model for Breast Cancer 3-Year Risk Prediction

Breast cancer screening programmes increasingly seek to move from one-size-fits-all interval to risk-adapted and personalized strategies. Deep learning (DL) has enabled image-based risk models with stronger 1- to 5-year prediction than traditional clinical models, but leading systems (e.g., Mirai) typically use convolutional backbones, very high-resolution inputs (>1M pixels) and simple multi-view fusion, with limited explicit modelling of contralateral asymmetry. We hypothesised that combining complementary inductive biases (convolutional and transformer-based) with explicit contralateral asymmetry modelling would allow us to match state-of-the-art 3-year risk prediction performance even when operating on substantially lower-resolution mammograms, indicating that using less detailed images in a more structured way can recover state-of-the-art accuracy. We present MamaDino, a mammography-aware multi-view attentional DINO model. MamaDino fuses frozen self-supervised DINOv3 ViT-S features with a trainable CNN encoder at 512x512 resolution, and aggregates bilateral breast information via a BilateralMixer to output a 3-year breast cancer risk score. We train on 53,883 women from OPTIMAM (UK) and evaluate on matched 3-year case-control cohorts: an in-distribution test set from four screening sites and an external out-of-distribution cohort from an unseen site. At breast-level, MamaDino matches Mirai on both internal and external tests while using ~13x fewer input pixels. Adding the BilateralMixer improves discrimination to AUC 0.736 (vs 0.713) in-distribution and 0.677 (vs 0.666) out-of-distribution, with consistent performance across age, ethnicity, scanner, tumour type and grade. These findings demonstrate that explicit contralateral modelling and complementary inductive biases enable predictions that match Mirai, despite operating on substantially lower-resolution mammograms.

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arXiv2025

ResMatching: Noise-Resilient Computational Super-Resolution via Guided Conditional Flow Matching

Computational Super-Resolution (CSR) in fluorescence microscopy has, despite being an ill-posed problem, a long history. At its very core, CSR is about finding a prior that can be used to extrapolate frequencies in a micrograph that have never been imaged by the image-generating microscope. It stands to reason that, with the advent of better data-driven machine learning techniques, stronger prior can be learned and hence CSR can lead to better results. Here, we present ResMatching, a novel CSR method that uses guided conditional flow matching to learn such improved data-priors. We evaluate ResMatching on 4 diverse biological structures from the BioSR dataset and compare its results against 7 baselines. ResMatching consistently achieves competitive results, demonstrating in all cases the best trade-off between data fidelity and perceptual realism. We observe that CSR using ResMatching is particularly effective in cases where a strong prior is hard to learn, e.g. when the given low-resolution images contain a lot of noise. Additionally, we show that ResMatching can be used to sample from an implicitly learned posterior distribution and that this distribution is calibrated for all tested use-cases, enabling our method to deliver a pixel-wise data-uncertainty term that can guide future users to reject uncertain predictions.

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arXiv2025

{\epsilon}-Seg: Sparsely Supervised Semantic Segmentation of Microscopy Data

Semantic segmentation of electron microscopy (EM) images of biological samples remains a challenge in the life sciences. EM data captures details of biological structures, sometimes with such complexity that even human observers can find it overwhelming. We introduce {\epsilon}-Seg, a method based on hierarchical variational autoencoders (HVAEs), employing center-region masking, sparse label contrastive learning (CL), a Gaussian mixture model (GMM) prior, and clustering-free label prediction. Center-region masking and the inpainting loss encourage the model to learn robust and representative embeddings to distinguish the desired classes, even if training labels are sparse (0.05% of the total image data or less). For optimal performance, we employ CL and a GMM prior to shape the latent space of the HVAE such that encoded input patches tend to cluster wrt. the semantic classes we wish to distinguish. Finally, instead of clustering latent embeddings for semantic segmentation, we propose a MLP semantic segmentation head to directly predict class labels from latent embeddings. We show empirical results of {\epsilon}-Seg and baseline methods on 2 dense EM datasets of biological tissues and demonstrate the applicability of our method also on fluorescence microscopy data. Our results show that {\epsilon}-Seg is capable of achieving competitive sparsely-supervised segmentation results on complex biological image data, even if only limited amounts of training labels are available.

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arXiv2025

HazeMatching: Dehazing Light Microscopy Images with Guided Conditional Flow Matching

Fluorescence microscopy is a major driver of scientific progress in the life sciences. Although high-end confocal microscopes are capable of filtering out-of-focus light, cheaper and more accessible microscopy modalities, such as widefield microscopy, can not, which consequently leads to hazy image data. Computational dehazing is trying to combine the best of both worlds, leading to cheap microscopy but crisp-looking images. The perception-distortion trade-off tells us that we can optimize either for data fidelity, e.g. low MSE or high PSNR, or for data realism, measured by perceptual metrics such as LPIPS or FID. Existing methods either prioritize fidelity at the expense of realism, or produce perceptually convincing results that lack quantitative accuracy. In this work, we propose HazeMatching, a novel iterative method for dehazing light microscopy images, which effectively balances these objectives. Our goal was to find a balanced trade-off between the fidelity of the dehazing results and the realism of individual predictions (samples). We achieve this by adapting the conditional flow matching framework by guiding the generative process with a hazy observation in the conditional velocity field. We evaluate HazeMatching on 5 datasets, covering both synthetic and real data, assessing both distortion and perceptual quality. Our method is compared against 12 baselines, achieving a consistent balance between fidelity and realism on average. Additionally, with calibration analysis, we show that HazeMatching produces well-calibrated predictions. Note that our method does not need an explicit degradation operator to exist, making it easily applicable on real microscopy data. All data used for training and evaluation and our code will be publicly available under a permissive license.

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arXiv2025

scSplit: Bringing Severity Cognizance to Image Decomposition in Fluorescence Microscopy

Fluorescence microscopy, while being a key driver for progress in the life sciences, is also subject to technical limitations. To overcome them, computational multiplexing techniques have recently been proposed, which allow multiple cellular structures to be captured in a single image and later be unmixed. Existing image decomposition methods are trained on a set of superimposed input images and the respective unmixed target images. It is critical to note that the relative strength (mixing ratio) of the superimposed images for a given input is a priori unknown. However, existing methods are trained on a fixed intensity ratio of superimposed inputs, making them not cognizant of the range of relative intensities that can occur in fluorescence microscopy. In this work, we propose a novel method called scSplit that is cognizant of the severity of the above-mentioned mixing ratio. Our idea is based on InDI , a popular iterative method for image restoration, and an ideal starting point to embrace the unknown mixing ratio in any given input. We introduce (i) a suitably trained regressor network that predicts the degradation level (mixing ratio) of a given input image and (ii) a degradation-specific normalization module, enabling degradation-aware inference across all mixing ratios. We show that this method solves two relevant tasks in fluorescence microscopy, namely image splitting and bleedthrough removal, and empirically demonstrate the applicability of scSplit on 5 public datasets. The source code with pre-trained models is hosted at https://github.com/juglab/scSplit/.

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arXiv2024

MicroSSIM: Improved Structural Similarity for Comparing Microscopy Data

Microscopy is routinely used to image biological structures of interest. Due to imaging constraints, acquired images, also called as micrographs, are typically low-SNR and contain noise. Over the last few years, regression-based tasks like unsupervised denoising and splitting have found utility in working with such noisy micrographs. For evaluation, Structural Similarity (SSIM) is one of the most popular measures used in the field. For such tasks, the best evaluation would be when both low-SNR noisy images and corresponding high-SNR clean images are obtained directly from a microscope. However, due to the following three peculiar properties of the microscopy data, we observe that SSIM is not well suited to this data regime: (a) high-SNR micrographs have higher intensity pixels as compared to low-SNR micrographs, (b) high-SNR micrographs have higher intensity pixels than found in natural images, images for which SSIM was developed, and (c) a digitally configurable offset is added by the detector present inside the microscope which affects the SSIM value. We show that SSIM components behave unexpectedly when the prediction generated from low-SNR input is compared with the corresponding high-SNR data. We explain this by introducing the phenomenon of saturation, where SSIM components become less sensitive to (dis)similarity between the images. We propose an intuitive way to quantify this, which explains the observed SSIM behavior. We introduce MicroSSIM, a variant of SSIM, which overcomes the above-discussed issues. We justify the soundness and utility of MicroSSIM using theoretical and empirical arguments and show the utility of MicroSSIM on two tasks: unsupervised denoising and joint image splitting with unsupervised denoising. Since our formulation can be applied to a broad family of SSIM-based measures, we also introduce MicroMS3IM, a microscopy-specific variation of MS-SSIM.

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arXiv2024

denoiSplit: a method for joint microscopy image splitting and unsupervised denoising

In this work, we present denoiSplit, a method to tackle a new analysis task, i.e. the challenge of joint semantic image splitting and unsupervised denoising. This dual approach has important applications in fluorescence microscopy, where semantic image splitting has important applications but noise does generally hinder the downstream analysis of image content. Image splitting involves dissecting an image into its distinguishable semantic structures. We show that the current state-of-the-art method for this task struggles in the presence of image noise, inadvertently also distributing the noise across the predicted outputs. The method we present here can deal with image noise by integrating an unsupervised denoising subtask. This integration results in improved semantic image unmixing, even in the presence of notable and realistic levels of imaging noise. A key innovation in denoiSplit is the use of specifically formulated noise models and the suitable adjustment of KL-divergence loss for the high-dimensional hierarchical latent space we are training. We showcase the performance of denoiSplit across multiple tasks on real-world microscopy images. Additionally, we perform qualitative and quantitative evaluations and compare the results to existing benchmarks, demonstrating the effectiveness of using denoiSplit: a single Variational Splitting Encoder-Decoder (VSE) Network using two suitable noise models to jointly perform semantic splitting and denoising.

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arXiv2024

Enabling Global Image Data Sharing in the Life Sciences

Coordinated collaboration is essential to realize the added value of and infrastructure requirements for global image data sharing in the life sciences. In this White Paper, we take a first step at presenting some of the most common use cases as well as critical/emerging use cases of (including the use of artificial intelligence for) biological and medical image data, which would benefit tremendously from better frameworks for sharing (including technical, resourcing, legal, and ethical aspects). In the second half of this paper, we paint an ideal world scenario for how global image data sharing could work and benefit all life sciences and beyond. As this is still a long way off, we conclude by suggesting several concrete measures directed toward our institutions, existing imaging communities and data initiatives, and national funders, as well as publishers. Our vision is that within the next ten years, most researchers in the world will be able to make their datasets openly available and use quality image data of interest to them for their research and benefit. This paper is published in parallel with a companion White Paper entitled Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data, which addresses challenges and opportunities related to producing well-documented and high-quality image data that is ready to be shared. The driving goal is to address remaining challenges and democratize access to everyday practices and tools for a spectrum of biomedical researchers, regardless of their expertise, access to resources, and geographical location.

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arXiv2024

Live-cell imaging powered by computation

The proliferation of microscopy methods for live-cell imaging offers many new possibilities for users but can also be challenging to navigate. We focus here on computational methods that promise to boost live-cell fluorescence microscopy, where intra-cellular dynamics and cell viability constrain measurements considerably. Considering the tradeoffs between signal-to-noise ratio (SNR), spatial resolution, temporal resolution, and multi-color and multi-channel capacity, we review computational methods that can be layered on top of commonly used existing microscopies, as well as hybrid methods that integrate computation and microscope hardware.

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arXiv2023

MIFA: Metadata, Incentives, Formats, and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis

Artificial Intelligence methods are powerful tools for biological image analysis and processing. High-quality annotated images are key to training and developing new methods, but access to such data is often hindered by the lack of standards for sharing datasets. We brought together community experts in a workshop to develop guidelines to improve the reuse of bioimages and annotations for AI applications. These include standards on data formats, metadata, data presentation and sharing, and incentives to generate new datasets. We are positive that the MIFA (Metadata, Incentives, Formats, and Accessibility) recommendations will accelerate the development of AI tools for bioimage analysis by facilitating access to high quality training data.

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arXiv2023

Community-developed checklists for publishing images and image analysis

Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging in particular is currently undergoing rapid technological advancements. However for scientists wishing to publish the obtained images and image analyses results, there are to date no unified guidelines. Consequently, microscopy images and image data in publications may be unclear or difficult to interpret. Here we present community-developed checklists for preparing light microscopy images and image analysis for publications. These checklists offer authors, readers, and publishers key recommendations for image formatting and annotation, color selection, data availability, and for reporting image analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby heighten the quality of microscopy data is in publications.

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arXiv2023

μSplit: efficient image decomposition for microscopy data

We present μSplit, a dedicated approach for trained image decomposition in the context of fluorescence microscopy images. We find that best results using regular deep architectures are achieved when large image patches are used during training, making memory consumption the limiting factor to further improving performance. We therefore introduce lateral contextualization (LC), a novel meta-architecture that enables the memory efficient incorporation of large image-context, which we observe is a key ingredient to solving the image decomposition task at hand. We integrate LC with U-Nets, Hierarchical AEs, and Hierarchical VAEs, for which we formulate a modified ELBO loss. Additionally, LC enables training deeper hierarchical models than otherwise possible and, interestingly, helps to reduce tiling artefacts that are inherently impossible to avoid when using tiled VAE predictions. We apply μSplit to five decomposition tasks, one on a synthetic dataset, four others derived from real microscopy data. Our method consistently achieves best results (average improvements to the best baseline of 2.25 dB PSNR), while simultaneously requiring considerably less GPU memory. Our code and datasets can be found at https://github.com/juglab/uSplit.

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arXiv2023

DeepContrast: Deep Tissue Contrast Enhancement using Synthetic Data Degradations and OOD Model Predictions

Microscopy images are crucial for life science research, allowing detailed inspection and characterization of cellular and tissue-level structures and functions. However, microscopy data are unavoidably affected by image degradations, such as noise, blur, or others. Many such degradations also contribute to a loss of image contrast, which becomes especially pronounced in deeper regions of thick samples. Today, best performing methods to increase the quality of images are based on Deep Learning approaches, which typically require ground truth (GT) data during training. Our inability to counteract blurring and contrast loss when imaging deep into samples prevents the acquisition of such clean GT data. The fact that the forward process of blurring and contrast loss deep into tissue can be modeled, allowed us to propose a new method that can circumvent the problem of unobtainable GT data. To this end, we first synthetically degraded the quality of microscopy images even further by using an approximate forward model for deep tissue image degradations. Then we trained a neural network that learned the inverse of this degradation function from our generated pairs of raw and degraded images. We demonstrated that networks trained in this way can be used out-of-distribution (OOD) to improve the quality of less severely degraded images, e.g. the raw data imaged in a microscope. Since the absolute level of degradation in such microscopy images can be stronger than the additional degradation introduced by our forward model, we also explored the effect of iterative predictions. Here, we observed that in each iteration the measured image contrast kept improving while detailed structures in the images got increasingly removed. Therefore, dependent on the desired downstream analysis, a balance between contrast improvement and retention of image details has to be found.

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arXiv2023

Better Research Software Tools to Elevate the Rate of Scientific Discovery -- or why we need to invest in research software engineering

In the past decade, enormous progress has been made in advancing the state-of-the-art in bioimage analysis - a young computational field that works in close collaboration with the life sciences on the quantitative analysis of scientific image data. In many cases, tremendous effort has been spent to package these new advances into usable software tools and, as a result, users can nowadays routinely apply cutting-edge methods to their analysis problems using software tools such as ilastik [1], cellprofiler [2], Fiji/ImageJ2 [3,4] and its many modern plugins that build on the BigDataViewer ecosystem [5], and many others. Such software tools have now become part of a critical infrastructure for science [6]. Unfortunately, overshadowed by the few exceptions that have had long-lasting impact, many other potentially useful tools fail to find their way into the hands of users. While there are many reasons for this, we believe that at least some of the underlying problems, which we discuss in more detail below, can be mitigated. In this opinion piece, we specifically argue that embedding teams of research software engineers (RSEs) within imaging and image analysis core facilities would be a major step towards sustainable bioimage analysis software.

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arXiv2023

bAIoimage analysis: elevating the rate of scientific discovery -- as a community

The future of bioimage analysis is increasingly defined by the development and use of tools that rely on deep learning and artificial intelligence (AI). For this trend to continue in a way most useful for stimulating scientific progress, it will require our multidisciplinary community to work together, establish FAIR data sharing and deliver usable, reproducible analytical tools.

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arXiv2022

N2V2 -- Fixing Noise2Void Checkerboard Artifacts with Modified Sampling Strategies and a Tweaked Network Architecture

In recent years, neural network based image denoising approaches have revolutionized the analysis of biomedical microscopy data. Self-supervised methods, such as Noise2Void (N2V), are applicable to virtually all noisy datasets, even without dedicated training data being available. Arguably, this facilitated the fast and widespread adoption of N2V throughout the life sciences. Unfortunately, the blind-spot training underlying N2V can lead to rather visible checkerboard artifacts, thereby reducing the quality of final predictions considerably. In this work, we present two modifications to the vanilla N2V setup that both help to reduce the unwanted artifacts considerably. Firstly, we propose a modified network architecture, i.e., using BlurPool instead of MaxPool layers throughout the used U-Net, rolling back the residual U-Net to a non-residual U-Net, and eliminating the skip connections at the uppermost U-Net level. Additionally, we propose new replacement strategies to determine the pixel intensity values that fill in the elected blind-spot pixels. We validate our modifications on a range of microscopy and natural image data. Based on added synthetic noise from multiple noise types and at varying amplitudes, we show that both proposed modifications push the current state-of-the-art for fully self-supervised image denoising.

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