Fluorescent Neuronal Cells v2: multi-task, multi-format annotations for deep learning in microscopy.

Fluorescent Neuronal Cells v2 is a collection of fluorescence microscopy images and the corresponding ground-truth annotations, designed to foster innovative research in the domains of Life Sciences and Deep Learning. This dataset encompasses three image collections wherein rodent neuronal cell nuclei and cytoplasm are stained with diverse markers to highlight their anatomical or functional characteristics. Specifically, we release 1874 high-resolution images alongside 750 corresponding ground-truth annotations for several learning tasks, including semantic segmentation, object detection and counting. The contribution is two-fold. First, thanks to the variety of annotations and their accessible formats, we anticipate our work will facilitate methodological advancements in computer vision approaches for segmentation, detection, feature extraction, unsupervised and self-supervised learning, transfer learning, and related areas. Second, by enabling extensive exploration and benchmarking, we hope Fluorescent Neuronal Cells v2 will catalyze breakthroughs in fluorescence microscopy analysis and promote cutting-edge discoveries in life sciences.

How big is Big Data? A comprehensive survey of data production, storage, and streaming in science and industry.

The contemporary surge in data production is fueled by diverse factors, with contributions from numerous stakeholders across various sectors. Comparing the volumes at play among different big data entities is challenging due to the scarcity of publicly available data. This survey aims to offer a comprehensive perspective on the orders of magnitude involved in yearly data generation by some public and private leading organizations, using an array of online sources for estimation. These estimates are based on meaningful, individual data production metrics and plausible per-unit sizes. The primary objective is to offer insights into the comparative scales of major big data players, their sources, and data production flows, rather than striving for precise measurements or incorporating the latest updates. The results are succinctly conveyed through a visual representation of the relative data generation volumes across these entities.

Automating cell counting in fluorescent microscopy through deep learning with c-ResUnet.

Counting cells in fluorescent microscopy is a tedious, time-consuming task that researchers have to accomplish to assess the effects of different experimental conditions on biological structures of interest. Although such objects are generally easy to identify, the process of manually annotating cells is sometimes subject to fatigue errors and suffers from arbitrariness due to the operator's interpretation of the borderline cases. We propose a Deep Learning approach that exploits a fully-convolutional network in a binary segmentation fashion to localize the objects of interest. Counts are then retrieved as the number of detected items. Specifically, we introduce a Unet-like architecture, cell ResUnet (c-ResUnet), and compare its performance against 3 similar architectures. In addition, we evaluate through ablation studies the impact of two design choices, (i) artifacts oversampling and (ii) weight maps that penalize the errors on cells boundaries increasingly with overcrowding. In summary, the c-ResUnet outperforms the competitors with respect to both detection and counting metrics (respectively, [Formula: see text] score = 0.81 and MAE = 3.09). Also, the introduction of weight maps contribute to enhance performances, especially in presence of clumping cells, artifacts and confounding biological structures. Posterior qualitative assessment by domain experts corroborates previous results, suggesting human-level performance inasmuch even erroneous predictions seem to fall within the limits of operator interpretation. Finally, we release the pre-trained model and the annotated dataset to foster research in this and related fields.

Preparing Distributed Computing Operations for the HL-LHC Era With Operational Intelligence.

As a joint effort from various communities involved in the Worldwide LHC Computing Grid, the Operational Intelligence project aims at increasing the level of automation in computing operations and reducing human interventions. The distributed computing systems currently deployed by the LHC experiments have proven to be mature and capable of meeting the experimental goals, by allowing timely delivery of scientific results. However, a substantial number of interventions from software developers, shifters, and operational teams is needed to efficiently manage such heterogenous infrastructures. Under the scope of the Operational Intelligence project, experts from several areas have gathered to propose and work on "smart" solutions. Machine learning, data mining, log analysis, and anomaly detection are only some of the tools we have evaluated for our use cases. In this community study contribution, we report on the development of a suite of operational intelligence services to cover various use cases: workload management, data management, and site operations.