The rapid pace of innovation in biological imaging and the diversity of its applications have prevented the establishment of a community-agreed standardized data format. We propose that complementing established open formats such as OME-TIFF and HDF5 with a next-generation file format such as Zarr will satisfy the majority of use cases in bioimaging. Critically, a common metadata format used in all these vessels can deliver truly findable, accessible, interoperable and reusable bioimaging data.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8648559PMC
http://dx.doi.org/10.1038/s41592-021-01326-wDOI Listing

Publication Analysis

Top Keywords

next-generation file
8
file format
8
ome-ngff next-generation
4
format
4
format expanding
4
expanding bioimaging
4
bioimaging data-access
4
data-access strategies
4
strategies rapid
4
rapid pace
4

Similar Publications

Background: Central nervous system tumors are among the most lethal types of cancer. A critical factor for tailored neurosurgical resection strategies depends on specific tumor types. However, it is uncommon to have a preoperative tumor diagnosis, and intraoperative morphology-based diagnosis remains challenging.

View Article and Find Full Text PDF

Robust discrimination between closely related species of salmon based on DNA fragments.

Anal Bioanal Chem

January 2025

Statistical Engineering Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899-8980, USA.

Closely related species of Salmonidae, including Pacific and Atlantic salmon, can be distinguished from one another based on nucleotide sequences from the cytochrome c oxidase sub-unit 1 mitochondrial gene (COI), using ensembles of fragments aligned to genetic barcodes that serve as digital proxies for the relevant species. This is accomplished by exploiting both the nucleotide sequences and their quality scores recorded in a FASTQ file obtained via Next Generation (NextGen) Sequencing of mitochondrial DNA extracted from Coho salmon caught with hook and line in the Gulf of Alaska. The alignment is done using MUSCLE (Muscle 5.

View Article and Find Full Text PDF

The need for smart microalgal bioprospecting.

Nat Prod Bioprospect

January 2025

Faculty of Science, Climate Change Cluster (C3), Algal Biotechnology & Biosystems, University of Technology Sydney, Sydney, NSW, 2007, Australia.

Microalgae's adaptability and resilience to Earth's diverse environments have evolved these photosynthetic microorganisms into a biotechnological source of industrially relevant physiological functions and biometabolites. Despite this, microalgae-based industries only exploit a handful of species. This lack of biodiversity hinders the expansion of the microalgal industry.

View Article and Find Full Text PDF

High-grade B-cell lymphoma with 11q aberration (HGBCL-11q) is a rare germi-nal centre lymphoma characterised by a typical gain/loss pattern on chromo-some 11q but without MYC translocation. It shares some features with Burkitt lymphoma (BL), HGBCLs and germinal centre-derived diffuse large B-cell lym-phoma, not otherwise specified (GCB-DLBCL-NOS). Since microRNA expression in HGBCL-11q remains unknown, we aimed to identify and compare the mi-croRNA expression profiles in HGBCL-11q, BL and in GCB-DLBCL-NOS.

View Article and Find Full Text PDF

Lossless and reference-free compression of FASTQ/A files using GeneSqueeze.

Sci Rep

January 2025

Rajant Health Incorporated, 200 Chesterfield Parkway, Malvern, PA, 19355PA, USA.

As sequencing becomes more accessible, there is an acute need for novel compression methods to efficiently store sequencing files. Omics analytics can leverage sequencing technologies to enhance biomedical research and individualize patient care, but sequencing files demand immense storage capabilities, particularly when sequencing is utilized for longitudinal studies. Addressing the storage challenges posed by these technologies is crucial for omics analytics to achieve their full potential.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!