Use Case: CSIRO Imaging Entomology Type Collections at Scale

Institution: CSIRO, National Research Collections of Australia 

Collaborators: David Yuan, Mei Yang, Merinda Campbell, Nicole Fisher

Collection Size: Australian National Insect Collection, 12+ million specimens

Type Collection Size: ~19,000

 

Multiple Magnify2 systems in use at CSIRO digitizing type specimens. Screenshot from SPNHC 2024 Presenation by David Yuan.

 

Background

CSIRO’s Australian National Insect Collection (ANIC) is one of the Southern Hemisphere’s largest entomology repositories, with ~12 million specimens and ~19,000 primary type specimens (holotypes, syntypes, lectotypes). To serve global taxonomy, biosecurity, and research communities, ANIC set out to systematically digitize its type specimens at publication-grade quality—reducing the need for physical loans and preserving fragile, often century-old material.

 

Challenge

  • High stakes, delicate material: Primary types require careful handling and exacting, reproducible imaging.
  • Heterogeneous subjects: From minute wasps (<1 mm) to large dragonflies and butterflies—some views require stitching + focus stacking.
  • Throughput vs. specificity: Researchers request multiple standardized views (dorsal, lateral) plus diagnostic views (wings, frontal/head), stressing both speed and precision.
  • Operational realities: Team size fluctuated post-COVID; software/policy constraints occasionally added friction; visibility and demand are growing in a new public-facing facility.

 

Solution

CSIRO operates two Magnify² systems dedicated to the Type Project:

  • Optics & lighting: Canon R-series bodies (R7), MP-E 65mm and 100mm macro lenses, dual off-camera flash moving with the camera for consistent, close-range lighting.
  • Multimode capture:
    • Focus stacking for all views to render full depth-of-field.
    • Tile stitching for larger insects (e.g., butterflies/dragonflies).
    • High-mag frontal views (5×/10×) for minute taxa, sometimes requiring hundreds of frames per view.
  • Repeatable SOPs: Three standard views per specimen (dorsal, lateral, diagnostic) with additional angles on request.
  • Data pipeline: Images flow to CSIRO’s public data portal (post-processing/QA) so researchers can remotely compare material without handling originals.

Overall type processing pipeline. Screenshot from SPNHC 2024 Presenation by David Yuan.

 

Results / Impact

  • ~11,000 type specimens completed (~50% of 19k target); remaining types in active progress.
  • Sustained throughput with small teams: Typical half-day sessions produce multiple fully stacked/stiched views per specimen; fragile or tiny subjects are accommodated with tailored runs.
  • Research access without loans: Taxonomists request specific diagnostic views (e.g wings, head) to compare other specimens against the Type specimen – fewer shipments, less risk.
  • Preservation & provenance: Publication-grade imagery of name-bearing specimens safeguards visual information prior to sub-sampling (e.g., DNA), and supports downstream biosecurity work.

  • Growing visibility & demand: In a new, glass-walled facility, digitization is more discoverable; requests are rising as the collection goes online.

    Examples of final images from a variety of type specimens. Screenshot from SPNHC 2024 Presenation by David Yuan.

 

What Changed vs. Before

  • Feasible precision at scale: Combining stacking + stitching makes previously impractical views routine.
  • Specimen-safe productivity: Repeatable lighting, motion control, and standardized views reduce handling while meeting research needs.
  • User-friendly operation: Visiting scientists and internal users can be trained quickly and still obtain publication-quality results.

 

Customer Quotes

“Without GIGAmacro, we wouldn’t have progressed the Type Project to this level—processing 10,000+ types in just a couple of years wouldn’t be realistic.”

“The stitching really sets it apart for large insects, while stacking gives us the fine diagnostic detail.”

“It’s user friendly—people can learn it quickly and get great results.”

 

Additional Information and Resources

CSIRO, National Research Collections of Australia 

 

GIGAmacro’s Role

GIGAmacro is honored to support CSIRO’s ambitious effort to image Australia’s name-bearing insects. The team at CSIRO has done fantastic work with the system and it is incredible to see the amount of throughput of images of the type specimens. We look forward to much more collaborative work in the future with CSIRO.