Digitization and Utilization of Natural History Collections

The digitization of natural history collections has transformed centuries-old cabinets of specimens into dynamic digital archives that underpin modern biodiversity science. By converting physical specimens, labels and field notes into high-resolution images and structured metadata, museums and herbaria worldwide have created interoperable databases accessible to researchers, policymakers and the public. This process encompasses a sequence of tasks—specimen curation and staging, imaging, image processing, metadata capture and georeferencing—that together form a comprehensive digitization pipeline. Advances in automation, machine learning and cloud-based infrastructures have accelerated mass digitization, while citizen-science platforms have harnessed public participation to transcribe legacy records at scale.

Digitized collections serve as foundational resources for ecological modelling, conservation planning and historical biogeography. Aggregated data portals facilitate novel analyses of species distributions, phenological shifts and responses to environmental change. Three-dimensional imaging and virtual reality applications have enhanced morphological studies and public engagement, while distributed networks of biorepositories now contribute to global pathogen surveillance. Integration with environmental and genomic databases further extends the utility of collections, enabling interdisciplinary research into climate adaptation, food security and emerging diseases. As collections become increasingly digital and connected, they reinforce the role of natural history institutions as critical infrastructure for both fundamental science and evidence-based decision-making.

Research from Nature Portfolio

No recent Nature Portfolio content available.

Digitization and Utilization of Natural History Collections publication trend

The graph below shows the total number of articles in digitization and utilization of natural history collections across all publications each year (not limited to Nature Index journals).

Technical terms

Digitization pipeline: A sequence of coordinated tasks—from specimen preparation to image capture and metadata encoding—required to convert physical collections into digital form.

Metadata: Structured information describing specimen attributes such as taxonomy, collection date, locality and preparator, which enables data discovery and reuse.

Georeferencing: The process of assigning precise geographic coordinates to collection localities based on label information or gazetteers, facilitating spatial analyses.

Persistent identifier: A stable, unique code (such as a DOI or UUID) assigned to a digital record or specimen image to ensure long-term accessibility and unambiguous citation.

Biorepository: An organised facility that stores and curates biological specimens and associated data, often including frozen tissues, vouchers and digital surrogates, for research and reference.

References

1. Five task clusters that enable efficient and effective digitization of biological collections. ZooKeys (2012).
2. The notes from nature tool for unlocking biodiversity records from museum records through citizen science. ZooKeys (2012).
3. Inselect: Automating the Digitization of Natural History Collections. PLOS ONE (2015).
4. VertNet: A New Model for Biodiversity Data Sharing. PLOS Biology (2010).
5. Leveraging natural history biorepositories as a global, decentralized, pathogen surveillance network. PLOS Pathogens (2021).
6. The next generation of natural history collections. PLOS Biology (2018).
7. A global approach for natural history museum collections. Science (2023).
8. Whole-drawer imaging for digital management and curation of a large entomological collection. ZooKeys (2012).
9. The Global Museum: natural history collections and the future of evolutionary science and public education. PeerJ (2020).
10. More Than Just Records: Analysing Natural History Collections for Biodiversity Planning. PLOS ONE (2012).