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Biologists who want to analyse their single-cell transcriptomics dataset must install and use specialist software via the command line. This is often impractical for non-bioinformaticians. Whilst the popular CELLxGENE software provides an…
Quantifying cell morphology using images and machine learning has proven to be a powerful tool to study the response of cells to treatments. However, models used to quantify cellular morphology are typically trained with a single microscopy…
In this paper we address the issue of photo galleries synchronization, where pictures related to the same event are collected by different users. Existing solutions to address the problem are usually based on unrealistic assumptions, like…
We introduce software for reading, writing and processing fluorescence single-molecule and image spectroscopy data and developing analysis pipelines that unifies various spectroscopic analysis tools. Our software can be used for processing…
Wide-field imaging Mueller polarimetry is a revolutionary, label-free, and non-invasive modality for computer-aided intervention: in neurosurgery it aims to provide visual feedback of white matter fibre bundle orientation from derived…
Any algorithm (in the sense of Gurevich's abstract-state-machine axiomatization of classical algorithms) operating over any arbitrary unordered domain can be simulated by a dynamic cellular automaton, that is, by a pattern-directed cellular…
Image processing holds immense potential for societal benefit, yet its full potential is often accessible only to tech-savvy experts. Bridging this knowledge gap and providing accessible tools for users of all backgrounds remains an…
Simulated microbial communities are used in benchmarking microbial abundance estimators and other bioinformatic utilities. To match current data scales, large simulated samples are needed, and many. The speed of current implementations…
Cellular image segmentation is essential for quantitative biology yet remains difficult due to heterogeneous modalities, morphological variability, and limited annotations. We present GenCellAgent, a training-free multi-agent framework that…
In this paper, the problem of classifying synthetic and natural texture images is addressed. To tackle this problem, an innovative method is proposed that combines concepts from corrosion modeling and cellular automata to generate a texture…
We introduce CellSegmenter, a structured deep generative model and an amortized inference framework for unsupervised representation learning and instance segmentation tasks. The proposed inference algorithm is convolutional and…
Photo Rater is a computer vision project that uses neural networks to help photographers select the best photo among those that are taken based on the same scene. This process is usually referred to as "culling" in photography, and it can…
Recent trends in cell segmentation have shifted towards universal models to handle diverse cell morphologies and imaging modalities. However, for continuously emerging cell types and imaging techniques, these models still require hundreds…
Biomedical research results are being published at a high rate, and with existing search engines, the vast amount of published work is usually easily accessible. However, reproducing published results, either experimental data or…
Advanced image segmentation and processing tools present an opportunity to study cell processes and their dynamics. However, image analysis is often routine and time-consuming. Nowadays, alternative data-driven approaches using deep…
In this paper, we describe a Graphical User Interface (GUI) designed to manage large quantities of image data of a biological system. After setting the design requirements for the system, we developed an ecology quantification GUI that…
Biomedical challenges have become the de facto standard for benchmarking biomedical image analysis algorithms. While the number of challenges is steadily increasing, surprisingly little effort has been invested in ensuring high quality…
Fully- or semi-automatic image enhancement software helps users to increase the visual appeal of photos and does not require in-depth knowledge of manual image editing. However, fully-automatic approaches usually enhance the image in a…
In this paper we propose a novel algorithm to combine two or more cellular complexes, providing a minimal fragmentation of the cells of the resulting complex. We introduce here the idea of arrangement generated by a collection of cellular…
This paper presents a smartphone-based imaging system capable of quantifying the concentration of an assortment of biological/chemical assay samples. The main objective is to construct an image database which characterizes the relationship…