Digitising slide collections

A project to create workflows and data pipelines for high-throughput, digitisation of the museum’s diverse slide collections.

We are using state-of-the-art equipment to capture images and extract data from a selection of our microscopic slides collection.

The pilot is to design workflows for 2 microscope slide digitisation workflows:

  • Broad and thin mass digitisation for all 100,000 slides being imaged 
  • High magnification imagery for 20% of these slides including transcription needed for specific research projects


The pilot project is split into 2 main workflows:

High throughput

This is the broad and thin high-throughput approach to digitisation.  We have digitised 100,000 slides using the SatScan 

A unique identifier (barcode) was attached to each slide  a taxonomy and location record was  in the Museum's collections management system with Using Inselect 

High resolution

Images needed for research on the actual specimen not just the data. Approx 20% of the slides will go through the high resolution Axioscan at 5x magnification and be fully transcribed by a digitiser.

Project summary

  • Focus: To develop workflows for the digitisation of microscope slides within our collections
  • Funding: NERC / Natural History Museum
  • Start date: 2015 
  • End date: 2016 

Project team


Digital Museum

We are digitising 80 million specimens from our collections to an online data portal.

Digital collections programme

Establishing high-throughput digital capture workflows for collection types.


The Museum's 80 million specimens form the world’s most important natural history collection.