Related Experiment Video
Updated: Dec 12, 2025

Using Light Sheet Fluorescence Microscopy to Image Zebrafish Eye Development
Published on: April 10, 2016
BD5: An open HDF5-based data format to represent quantitative biological dynamics data
Koji Kyoda1,2, Kenneth H L Ho1,2, Yukako Tohsato1,2,3
1Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
Abstract:
BD5 is a new binary data format based on HDF5 (hierarchical data format version 5). It can be used for representing quantitative biological dynamics data obtained from bioimage informatics techniques and mechanobiological simulations. Biological Dynamics Markup Language (BDML) is an XML (Extensible Markup Language)-based open format that is also used to represent such data; however, it becomes difficult to access quantitative data in BDML files when the file size is large because parsing XML-based files requires large computational resources to first read the whole file sequentially into computer memory. BD5 enables fast random (i.e., direct) access to quantitative data on disk without parsing the entire file. Therefore, it allows practical reuse of data for understanding biological mechanisms underlying the dynamics.
Related Concept Videos
Globular and Fibrous Proteins
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
Gene Families
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Biostatistics: Overview
Discrete variables are...
Protein Families

