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.

BioImage.IO Chatbot: A Personalized Assistant for BioImage Analysis Augmented by Community Knowledge Base

The rapidly expanding landscape of bioimage analysis tools presents a navigational challenge for both experts and newcomers. Traditional search methods often fall short in assisting users in this complex environment. To address this, we introduce the BioImage$.$IO Chatbot, an AI-driven conversational assistant tailored for the bioimage community. Built upon large language models, this chatbot provides personalized, context-aware answers by aggregating and interpreting information from diverse databases, tool-specific documentation, and structured data sources. Enhanced by a community-contributed knowledge base and fine-tuned retrieval methods, the BioImage$.$IO Chatbot offers not just a personalized interaction but also a knowledge-enriched, context-aware experience. It fundamentally transforms the way biologists, bioimage analysts, and developers navigate and utilize advanced bioimage analysis tools, setting a new standard for community-driven, accessible scientific research.

Roadmap on Deep Learning for Microscopy

Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep neural networks, and machine learning are all niche terms describing computational methods that have gained a pivotal role in microscopy-based research over the past decade. This Roadmap is written collectively by prominent researchers and encompasses selected aspects of how machine learning is applied to microscopy image data, with the aim of gaining scientific knowledge by improved image quality, automated detection, segmentation, classification and tracking of objects, and efficient merging of information from multiple imaging modalities. We aim to give the reader an overview of the key developments and an understanding of possibilities and limitations of machine learning for microscopy. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences.

ABANICCO: A New Color Space for Multi-Label Pixel Classification and Color Segmentation

In any computer vision task involving color images, a necessary step is classifying pixels according to color and segmenting the respective areas. However, the development of methods able to successfully complete this task has proven challenging, mainly due to the gap between human color perception, linguistic color terms, and digital representation. In this paper, we propose a novel method combining geometric analysis of color theory, fuzzy color spaces, and multi-label systems for the automatic classification of pixels according to 12 standard color categories (Green, Yellow, Light Orange, Deep Orange, Red, Pink, Purple, Ultramarine, Blue, Teal, Brown, and Neutral). Moreover, we present a robust, unsupervised, unbiased strategy for color naming based on statistics and color theory. ABANICCO was tested against the state of the art in color classification and with the standarized ISCC-NBS color system, providing accurate classification and a standard, easily understandable alternative for hue naming recognizable by humans and machines. We expect this solution to become the base to successfully tackle a myriad of problems in all fields of computer vision, such as region characterization, histopathology analysis, fire detection, product quality prediction, object description, and hyperspectral imaging.

From Nano to Macro: Overview of the IEEE Bio Image and Signal Processing Technical Committee

The Bio Image and Signal Processing (BISP) Technical Committee (TC) of the IEEE Signal Processing Society (SPS) promotes activities within the broad technical field of biomedical image and signal processing. Areas of interest include medical and biological imaging, digital pathology, molecular imaging, microscopy, and associated computational imaging, image analysis, and image-guided treatment, alongside physiological signal processing, computational biology, and bioinformatics. BISP has 40 members and covers a wide range of EDICS, including CIS-MI: Medical Imaging, BIO-MIA: Medical Image Analysis, BIO-BI: Biological Imaging, BIO: Biomedical Signal Processing, BIO-BCI: Brain/Human-Computer Interfaces, and BIO-INFR: Bioinformatics. BISP plays a central role in the organization of the IEEE International Symposium on Biomedical Imaging (ISBI) and contributes to the technical sessions at the IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), and the IEEE International Conference on Image Processing (ICIP). In this paper, we provide a brief history of the TC, review the technological and methodological contributions its community delivered, and highlight promising new directions we anticipate.

Translational Lung Imaging Analysis Through Disentangled Representations

The development of new treatments often requires clinical trials with translational animal models using (pre)-clinical imaging to characterize inter-species pathological processes. Deep Learning (DL) models are commonly used to automate retrieving relevant information from the images. Nevertheless, they typically suffer from low generability and explainability as a product of their entangled design, resulting in a specific DL model per animal model. Consequently, it is not possible to take advantage of the high capacity of DL to discover statistical relationships from inter-species images. To alleviate this problem, in this work, we present a model capable of extracting disentangled information from images of different animal models and the mechanisms that generate the images. Our method is located at the intersection between deep generative models, disentanglement and causal representation learning. It is optimized from images of pathological lung infected by Tuberculosis and is able: a) from an input slice, infer its position in a volume, the animal model to which it belongs, the damage present and even more, generate a mask covering the whole lung (similar overlap measures to the nnU-Net), b) generate realistic lung images by setting the above variables and c) generate counterfactual images, namely, healthy versions of a damaged input slice.

Deep learning based domain adaptation for mitochondria segmentation on EM volumes

Accurate segmentation of electron microscopy (EM) volumes of the brain is essential to characterize neuronal structures at a cell or organelle level. While supervised deep learning methods have led to major breakthroughs in that direction during the past years, they usually require large amounts of annotated data to be trained, and perform poorly on other data acquired under similar experimental and imaging conditions. This is a problem known as domain adaptation, since models that learned from a sample distribution (or source domain) struggle to maintain their performance on samples extracted from a different distribution or target domain. In this work, we address the complex case of deep learning based domain adaptation for mitochondria segmentation across EM datasets from different tissues and species. We present three unsupervised domain adaptation strategies to improve mitochondria segmentation in the target domain based on (1) state-of-the-art style transfer between images of both domains; (2) self-supervised learning to pre-train a model using unlabeled source and target images, and then fine-tune it only with the source labels; and (3) multi-task neural network architectures trained end-to-end with both labeled and unlabeled images. Additionally, we propose a new training stopping criterion based on morphological priors obtained exclusively in the source domain. We carried out all possible cross-dataset experiments using three publicly available EM datasets. We evaluated our proposed strategies on the mitochondria semantic labels predicted on the target datasets. The methods introduced here outperform the baseline methods and compare favorably to the state of the art. In the absence of validation labels, monitoring our proposed morphology-based metric is an intuitive and effective way to stop the training process and select in average optimal models.

Search for temporal cell segmentation robustness in phase-contrast microscopy videos

Studying cell morphology changes in time is critical to understanding cell migration mechanisms. In this work, we present a deep learning-based workflow to segment cancer cells embedded in 3D collagen matrices and imaged with phase-contrast microscopy. Our approach uses transfer learning and recurrent convolutional long-short term memory units to exploit the temporal information from the past and provide a consistent segmentation result. Lastly, we propose a geometrical-characterization approach to studying cancer cell morphology. Our approach provides stable results in time, and it is robust to the different weight initialization or training data sampling. We introduce a new annotated dataset for 2D cell segmentation and tracking, and an open-source implementation to replicate the experiments or adapt them to new image processing problems.