Difference between revisions of "Digitalisierung am BGBM"

Revision as of 15:38, 10 April 2013

Scanner hardware

Pentacon Scan 5000 (body) cameras with max. resolution 8192 x 12000 (depending on lens), trilineare CCD-lines, colour depth 3 x 12 Bit (2 workstations)

• Lens: Schneider Kreuznach APO COMPONON HM 4,0/60 (provides maximum resolution)
• Camera mounting system: with integrated transmitted light source. Transmitted light base with four 13 W daylight fluorescents 5400 K, illuminated area 43 x 35 cm (16.9 x 13.8 in.). Illuminance 3300 cd/m2., Column height: 1 m (40 in.) , metal plate with magnets
• Camera 1) Lighting equipment: Fa. Kaiser Fototechnik, 2 lamps: 4 x 36 w each, daylight fluorescent lamp 5400 K, CRI = 90-100, light emitting area approx. 50 x 21 cm (19.7 x 8.3 in.)
• Camera 2) Lighting equipment: Fa. Kaiser Fototechnik, 2 lamps: 2 x 55 w each, daylight fluorescent lamp 5400 K, CRI = 90-100, light emitting area approx. 64 x 21 cm (25.2 x 8.3 in.)

Pentacon Scan 6000 camera (body) with max. resolution 10600 x 10600 (depending on lens), trilineare CCD-lines, colour depth 3 x 12 Bit

• Lens: Schneider Kreuznach APO COMPONON HM 4,0/60 (provides maximum resolution)
• Camera mounting system: with integrated transmitted light source. Transmitted light base with four 13 W daylight fluorescents 5400 K, illuminated area 43 x 35 cm (16.9 x 13.8 in.). Illuminance 3300 cd/m2., Column height: 1, 50 m , metal plate with magnets
• Lighting equipment: Fa. Kaiser Fototechnik, 2 lamps: 2 x 55 w each, daylight fluorescent lamp 5400 K, CRI = 90-100, light emitting area approx. 64 x 21 cm (25.2 x 8.3 in.)

ProServe ScannTech 602i-3 with max. scanformat 60 cm x 42 cm, 300dpi, colour depth 3 x 12 Bit

• Lens: Schneider Kreuznach APO COMPONON HM 4,0/60 (provides maximum resolution)
• Camera mounting system: with integrated transmitted light source. Transmitted light base with four 13 W daylight fluorescents 5400 K, illuminated area 43 x 35 cm (16.9 x 13.8 in.). Illuminance 3300 cd/m2., Column height: 1, 50 m , metal plate with magnets
• Lighting equipment: Fa. Kaiser Fototechnik, 2 lamps: 2 x 55 w each, daylight fluorescent lamp 5400 K, CRI = 90-100, light emitting area approx. 64 x 21 cm (25.2 x 8.3 in.)
• Portable single-device-solution, 20 seconds per scan (including data storage on hard disk or network drive), foot control possible, both herbarium sheet and book scans possible, remote maintenance via Internet, robust technology, no wear parts, tolerant of temperature and light influences

Digitization workstation - computer hardware and software

• Intel Core2Duo 6300
• 4 GB RAM
• 1000 GB hard disk
• 1512 MB Graphic Card
• MS Windows XP
• Adobe Photoshop CS4
• MS Access 2003
• Silverfast AI

Digitizing server infrastructure

Database server

• Dual Intel Xeon processor
• 8 GB RAM
• SATA hard disks
• MS Windows Server 2003
• MS SQL Server 2005

Image server (publishing the tif files for the WWW

• VMWare based Intel XEOn Core 2
• 98 GB RAM
• 30 TB hard disk
• MS Windows Server 2008 R2
• Neptune Labs FSI Server
• Neptune Labs FSI Cache Server

Storage server for images

• Dual Intel Xeon processor
• 8 GB RAM
• Three external raid 6 systems with a capacity of 30 TB over SCSI and ISCSI
• MS Windows Server 2003
• MS Access 2003
• ThumbsPlus

Web publishing server

• HP Server LPR 2000
• 1 GB RAM
• Three 36 GB SCSI hard disks as raid 5
• MS Windows 2000 Adv. Server
• IIS 5
• Adobe ColdFusion MX
• Neptune Labs FSIViewer

Backbone

• 4 GBit in-house backbone
• 1 GBit server connection to the backbone
• 1 GBit connection to the internet

Digitizing workflow

• Specimen data inserted via MS Access client in our MS SQL database
• Herbarium sheet is scanned via Silverfast in Photoshop
• Adjusting contrast and brightness
• Image saved as an uncompressed tiff file with ~ 250 MB, using the object barcode as filename
• Nightly cron job converts the tiff file to

• fpx file; ~ 70 MB
• jpg file; ~ 2-3 MB
• jpg thumb file; 20 KB

• ThumbsPlus scans for updates in the fpx file directory tree and insert the image metadata in our database where it is connected via the filename (barcode) with the specimen data also containing the barcode
• The specimen data is published with a Adobe ColdFusion MX driven website
• Serving the tiff images with the Neptune Labs FSI Server by using the Neptune Labs FSIViewer as an flash interface for image handling See flash film...
• By using the Neptune Labs FSI Cache Server every request to an image area is cached and will be served from this cache when it is requested again

Digitizing workflow Microscopy

• Specimen data inserted via MS Access client in our MS SQL database
• Microscopic preparation is put unto the microscope stage (cross table) of the ZeissImager, the target cell and the appropriate object lens are chosen.
• Contrast and brightness are adjusted,
• The viewed cell is aligned and cut to size with the help of the cross table (75x50/240°),
• The viewed cell is digitized using AxioVision Imaging software 4.8,
• A scale bar is added to the image,
• The image is saved as an uncompressed zvi and jpeg and/or tiff file with up to 11 MB, using the scientific name as the beginning of the file name.
• For diatom Z-stack imaging up to 45 jpg pictures in 5 minutes à 11 MB, are taken and converted into a video.

Further reading

Berendsohn, W. G., Einsiedel, B., Merkel, U. Nowak-Krawietz, H., Röpert, D. & Will, I. 2005: Digital imaging at the Herbarium Berolinense. In: Häuser, C. L., Steiner, A., Holstein, J. & Scoble, M. J. (ed.): Digital Imaging of Biological Type Specimens - A Manual of Current Best Practice. Stuttgart.