With an increase in subject knowledge expertise required to solve specific biological questions, experts from different fields need to collaborate to address increasingly complex issues. To successfully collaborate, everyone involved in the collaboration must take steps to "". We thus present a guide on truly cross-disciplinary work using bioimage analysis as a showcase, where it is required that the expertise of biologists, microscopists, data analysts, clinicians, engineers, and physicists meet. We discuss considerations and best practices from the perspective of both users and technology developers, while offering suggestions for working together productively and how this can be supported by institutes and funders. Although this guide uses bioimage analysis as an example, the guiding principles of these perspectives are widely applicable to other cross-disciplinary work.
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http://dx.doi.org/10.3389/fbinf.2022.889755 | DOI Listing |
Biol Reprod
January 2025
Department of Anatomy and Cell Biology, Brody School of Medicine, East Carolina University, Greenville, NC USA.
The adult mammalian testis is filled with seminiferous tubules, which contain somatic Sertoli cells along with germ cells undergoing all phases of spermatogenesis. During spermatogenesis in postnatal mice, male germ cells undergo at least 17 different nomenclature changes as they proceed through mitosis as spermatogonia (=8), meiosis as spermatocytes (=6), and spermiogenesis as spermatids (=3) [1-6]. Adding to this complexity, combinations of germ cells at each of these stages of development are clumped together along the length of the seminiferous tubules.
View Article and Find Full Text PDFComput Struct Biotechnol J
December 2024
VISILAB Group, Universidad de Castilla-La Mancha, Av. Camilo José Cela, Ciudad Real, 13071, Ciudad Real, Spain.
The digitalization of traditional glass slide microscopy into whole slide images has opened up new opportunities for pathology, such as the application of artificial intelligence techniques. Specialized software is necessary to visualize and analyze these images. One of these applications is QuPath, a popular bioimage analysis tool.
View Article and Find Full Text PDFBiol Imaging
November 2024
Bioengineering Department[CMT1], Universidad Carlos III de Madrid, Leganes, Spain.
This manuscript showcases the latest advancements in deepImageJ, a pivotal Fiji/ImageJ plugin for bioimage analysis in life sciences. The plugin, known for its user-friendly interface, facilitates the application of diverse pre-trained convolutional neural networks to custom data. The manuscript demonstrates several deepImageJ capabilities, particularly in deploying complex pipelines, three-dimensional (3D) image analysis, and processing large images.
View Article and Find Full Text PDFJ Sleep Res
January 2025
Centre for Sleep and Vigilance Disorders, Department of Internal Medicine and Clinical Nutrition, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
Excessive daytime sleepiness (EDS) is a common complaint in the general population and is associated with cardiovascular disease and increased mortality. We aimed to investigate whether sleep duration is related to excessive daytime sleepiness in the general population, both in itself and in combination with other factors. We performed a cross-sectional analysis in the population-based Swedish CArdioPulmonary bioImage Study (SCAPIS) cohort (n = 27,976; 14,436 females; aged 50-64 years) to assess how sleep-related factors along with anthropometric, lifestyle, socioeconomic factors as well as somatic disease and psychological distress, were related with EDS assessed by the Epworth sleepiness scale (ESS).
View Article and Find Full Text PDFNat Methods
January 2025
Instituto Gulbenkian de Ciência, Oeiras, Portugal.
The expanding scale and complexity of microscopy image datasets require accelerated analytical workflows. NanoPyx meets this need through an adaptive framework enhanced for high-speed analysis. At the core of NanoPyx, the Liquid Engine dynamically generates optimized central processing unit and graphics processing unit code variations, learning and predicting the fastest based on input data and hardware.
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