1. Rapid, industrial scale
digitization of the NHM
microscope slide collection
Ben Price & Vladimir Blagoderov

3. Outline
•
The NHM slide collection
•
What is Digitization?
•
The NHM workflow
•
Psyllid collection
•
Future prospects

4. The NHM slide collection
•
~ 2 million slides (60 : 40 vertical : horizontal storage)

5. The NHM slide collection
•
Mix of slide sizes, mounts, storage cabinets

6. What is Digitization?
?

7. What is Digitization?
Label data:
–
Quick to image
•
5000 per day
–
Slow to transcribe (crowdsourcing)
–
Slow to georeference (crowdsourcing)

8. What is Digitization?
Specimen:
–
Slow to image
•
–
Data storage
•
–
100,000 per year
GB images
Image delivery
•
Proprietery software

9. The NHM workflow*
Data Capture
Handling
* Work in progress
Imaging
Preparation
Post Processing

10. Preparation
Handling
Imaging
Post Processing
•
Datamatrix Labels (4.5mm)
•
Processing Scripts (GIMP, Barcodefiler)
•
Computing Facilities (64bit, 16GB RAM)
•
Storage & Retrieval (Ke-EMu)
–
•
What is a slide?
Delivery (NHM data portal)
Data Capture

11. Preparation
Handling
Imaging
Post Processing
•
Horizontal vs Vertical storage
•
Card Slide covers!
•
Labelling & Handling = up to 90% of the time
Data Capture

12. Preparation
Handling
Imaging
Post Processing
Data Capture
•
Scanner – SLR – Mamiya Leaf – SatScanner
•
Balance slides per image vs label resolution (PPI)
•
Single slide imaging?

13. Preparation
Handling
Imaging
Horizontal Storage:
•
Less handling
–
•
Tray fits A3 scanner / SLR
Can be autocropped
Post Processing
Data Capture

14. Preparation
Handling
Imaging
Horizontal Storage:
•
Less handling
–
•
Tray fits A3 scanner / SLR
Manual cropping
–
Crowd cropping?
Post Processing
Data Capture

15. Preparation
Handling
Imaging
Post Processing
Vertical storage:
•
Single type of template (post processing)
•
High contrast (scripts)
•
Cheap (foam, card)
•
More Handling
•
Autocropping
Data Capture

16. Preparation
•
Imaging
Post Processing
Data Capture
Resolution tests (PPI)
–
PPI
Handling
Canon 650D (18MP sensor) + 50mm Macro
250
Slides 72
300
450
600
45
18
10

17. Preparation
•
Handling
Imaging
Post Processing
Data Capture
Resolution tests (PPI)
–
Mamiya Leaf (80MP sensor) + 80mm lens
PPI
300
450
600
Slides
180
72
50

18. Preparation
•
Handling
Imaging
Post Processing
Data Capture
Resolution tests (PPI)
–
HerbScanner (EPSON A3 size)
PPI
300
450
600
Slides
50
50
50

19. Preparation
•
Handling
Imaging
Post Processing
Resolution tests (PPI)
–
Slides
SatScanner (0.16x lens, low resolution ~1000 PPI)
72 - 100
Data Capture

20. Preparation
Handling
Imaging
Post Processing
Data Capture

21. Preparation
Handling
Imaging
Post Processing
Data Capture

22. Preparation
Handling
Imaging
Post Processing
Data Capture

23. Preparation
Handling
Imaging
Post Processing
Data Capture

24. Progress to date
•
Psyllidae slide collection (4000 slides)
•
Two digitizers + SatScanner = 4 days
•
Handling (not Imaging) is the bottleneck
•
Solutions:
–
–
More digitizers

25. Progress to date
•
Theoretical maximum
–
1
SatScan: 7000 slides per day (5-8 people)
label
load
2
image
unload
label
load
image
label
load
image
unload
label
load
label
load
image
unload
label
label
load
image
unload
3
4
–
Other: 700 - 1000 slides per person per day

26. Future Plans
•
Specimen Imaging
–
Type material

27. Acknowledgments
Peter
Johanna
Lyndsey
Sara
Flavia
Elisa

28. Questions?