BioimageAIpub: a toolbox for AI-ready bioimaging data publishing

TL;DR

BioimageAIpub is a workflow that simplifies converting and sharing bioimaging data, facilitating easier access for AI analysis by integrating with HuggingFace platform.

Contribution

It introduces a streamlined process for converting bioimaging data into AI-ready formats and uploading them to HuggingFace, reducing data preparation time.

Findings

Enables seamless conversion of bioimaging data.

Facilitates sharing datasets on HuggingFace.

Reduces time for data wrangling in bioimaging.

Abstract

Modern bioimage analysis approaches are data hungry, making it necessary for researchers to scavenge data beyond those collected within their (bio)imaging facilities. In addition to scale, bioimaging datasets must be accompanied with suitable, high-quality annotations and metadata. Although established data repositories such as the Image Data Resource (IDR) and BioImage Archive offer rich metadata, their contents typically cannot be directly consumed by image analysis tools without substantial data wrangling. Such a tedious assembly and conversion of (meta)data can account for a dedicated amount of time investment for researchers, hindering the development of more powerful analysis tools. Here, we introduce BioimageAIpub, a workflow that streamlines bioimaging data conversion, enabling a seamless upload to HuggingFace, a widely used platform for sharing machine learning datasets and models.