Rapid digitization of P Herbarium Switching to the fast track: Rapid digitization of the world's largest herbarium TDWG 2011- New Orleans Simon Chagnoux,

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Switching to the fast track: Rapid digitization of the

world's largest herbarium

TDWG 2011- New OrleansSimon Chagnoux, Henri Michiels

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The French Museum

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um An old institution

• Founded in 1635 (at that time the Royal garden of medicinal plants)

• In 1793, the French revolution turns the garden into the national Museum

• Now: 15 locations in France, 2000 people

20 Oct. 2011 TDWG - Orleans 3

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Renovating the Herbarium

An opportunity to digitize the entire collection

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The Paris Herbarium


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The Renovation Project (1)

• Two main drivers to this project :– the herbarium, designed for 6 million

specimens, was packed with 10 million sheets and fitted with old storage

– raising the storage density required to reinforce the floors


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The Renovation Project (2)

• The only way of doing this was to move away the entire collection and to put it back in the renovated place after works

• An opportunity for– New sorting, from geographic to phylogenetic

(APG3)– Reconditioning– Digitizing


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2006 – Start of the project

2009 – Start of the works

2010 (June) – Start of digitization

2011 (Nov) – Opening of the first rearranged spaces to researchers

2012 – End of the project

Renovation Calendar


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um Budget

• Overall project cost: 24,5 Million €– Building renovation 12 000 000– Movers 900 000– Attaching specimens 3 200 000– Reconditioning, digitization

and sorting 6 700 000– Supplies 1 600 000– Storage 100 000


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Herbarium

WarehouseIndustrial Partner

The renovation cycle

DigitizationReconditioningSorting

Floor by floor renovation


Before ....


... And after


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um Why digitize ?

• Because all the parts have to be manipulated in the course of the project

• Digitization gives us:– a virtual copy of specimens– the possibility to share and study specimens

without touching them

• More than an electronic copy of the collection catalog, we’ll have a collaborative tool for managing scientific knowledge inside, as well as outside the institution


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um 2D Digitization is cheap

• the cost of digitization is marginal compared to the full project

• full specimen processing (moving, sorting, reconditionning, new furniture)

• digitization and name processing

• digitization is appealing to funding

$1,5

$0,1


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um A new paradigm

• For 15 years we have been entering all information of some specimens, – 1 million entries in the database (rich information)– One fifth (200 000 images) was photographed

• Since summer 2010, we use a massive approach where digitization precedes data entry – 2 million records digitized in one year– limited information in the database (name and

geographic area)– The scientific information can be added without

manipulating the specimens themselves


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The workflow

Digitizing, reconditionning and sorting

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um An industrial process (1)

• We chose a contractor with an industrial know-how

• A dedicated place had to be set-up and equipped by the contractor

• Two teams of 20 workers in two shifts working from 6am to 9pm

• The process had to align on the schedule of the renovation works, floor by floor


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um An industrial process (2)

• Planned production rate: 17 000 sheets

per day over 24 months

ca. 15 seconds / sheet

• At this rate, a variation of ± 1 second per

specimen has an impact of ± 300 k€ over

the project cost


The Bussy-St-Georges site


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um Workflow overview

U P

D O W N

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D O W NU n p a c k in g a n d a d d in g b a r c o d e

D a ta e n tr y Im a g e c a p tu r e 3 0 0 D P I

R e c o n d i tio n n in g a n d S o r tin g

f rom Herbar ium T o Herbar ium


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um How to alleviate data entry

• We take advantage of the physical ordering of specimens

• We provide a name list to the contractor (APG 3 classification)

• The contractor enriches the list with the information generated during the process and provides us with a table containing consolidated information (image number, barcode numbers, classification,…)


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um 1 – Delivery (1)

A carting company transports the specimens to the facility where they arrive in clearly labeled boxes. Boxes receive a tracking barcode


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• The Museum provides two files:1. a “logistics” file

– number of boxes– family name and number– genus name and number– geographic area

2. a “taxonomy” file– List of available taxon names with family,

genus, species, authors, ID (taxon number)


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• This information is digested by the contractor’s Information System and used along the industrial process (labeling, sorting, quality assurance)


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um 2 – Folder processing

For each folder, the operator :1.replaces the jacket (color according to region)2.reads the species name and types the first letters on its computer3.selects the name in a list4.prints a label with barcode and identification information, and sticks it on the folder


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um 3 – Specimen Digitization (1)

• Datamatrix and barcode are stuck on each sheet– Datamatrix: for tracking purposes– Barcode: specific to Muséum and to int’l

herbarium standard

• The specimens are placed three by three on a tray


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um 3 - Specimen Digitization (2)

• The tray is placed on a conveyor belt

• The sheet is scanned

• The scan is checked (framing and focus)

• At the end of the chain, the barcode is read to check if all specimens are back in the folder


The Digitization Bench


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um 4 - Reconditioning

• After scanning, each sheet is inserted in a sulfurized paper liner

• The barcode of each specimen is read, allowing the system to check if all specimens are back in the right folder

• The folders are stored in a “cut box” before sorting


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um 5 - Sorting 1 (by genus)

• This sorting consists in storing specimens by family and genus names

• The operator puts the jackets in boxes and places them on shelves according to the family and genus numbers (the shelves are labelled in advance by the contractor)


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um 6 - Sorting 2 (by species)

• The operator takes a box, reads the barcode on each jacket

• The system displays the species name and assigns a number which is printed on a label

• The label is sticked on the folder, which is then stored on the shelf with the same number


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7 – Packing, transport and final storage


• The folders are put in boxes and sent to the Museum

• The contractor stores the folders in the Museum’s herbarium

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How to ensure quality in mass digitization?

60 000 images

produced each week

1% of the production

checked (ca. 600 images) Samples are

distributed among botanical staff

Checking:

•Focus

•Data quality

•Barcode number

•Barcode location

1

2

3

4

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Scanning Resolution and Image Format

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um Production of images

• The conveyor belt passes the specimens under a bidirectional scanner which produces 11x17” (A3), 300 dpi, 5000 x 3300 pixel images

• TIFF files are saved offline (one production day per disk of 1 TB)

• JPEG’s are made for online use


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Scanning resolution and image size

• One TIFF image is 50 MB

• One JPEG is 5 MB. This compression rate was chosen to have the same level of details as with TIFF (only colour is slightly changed)

• This choice is a technico-economic trade-off

• For 10 million images:– TIFF represents 500 TB

– JPEG represents 50 TB

– Data represents <100 GB


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um Why do we keep TIFF ?

• Partners seek lossless data (Reflora, Mellon)

• Standard for physical publishing

• Native scan output, which can be used for any future use or transformation


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um Handling TIFF data

• We cannot afford « live » storage of 500 TB

• … and even 1 Po with redundancy ! $$$• With a lot of energy consumption and heat

dissipation for rarely accessed images

• We are planning to start using tape storage next year, with HSM software

• For the time being, USB disks are stored in the collection warehouse


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um Exception for the types

• The types are not part of this industrial process

• They are manually digitized on-premises at 600 dpi (200 MB in compressed TIFF)

• This process was initiated by the Mellon foundation in 2004

• We now have about 100 000 type images


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What we’ve achievedand learned …

… after 12 months of collaboration between scientists and industrials (over an anticipated duration of 24 months)

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um Achievements

• 2,1 million specimens processed between June 2010 and August 2011

• Images and data are of good quality

• The new premises comply with today’s standards (space, safety, light, air-conditioning, …)


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um Fast but ... not fast enough


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Reasons for being behind schedule

• Logisticians have under-estimated the sorting work

• Only two digitization chains are operational, instead of three (due to lack of staff)


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Software and quality assurance

• There is more software needed for ensuring tracability and detecting failures than for data acquisition.

• Fast web publication of images allows a broader audience to perform quality control.

• Continuous control is mandatory


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um People

• Working under constant time pressure during two years is really difficult in an academic context

• The contractor must be considered as a service provider and not just the team next-door (not obvious in an academic context)


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um Working with a contractor

ROI

speed

robustness

quality

exhaustivity

specifity

• Culture clash

• Many parameters were not known at the beginning of the project (processes, numbers, ...)

• Quality control is a key point to make sure that scientific excellence governs the industrial throughput (to be defined upfront)

• Write everything and always refer to the contract20 Oct. 2011 TDWG - Orleans 47

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um Digitizing other objects

• Digitizing herbarium is « easy »: – same dimensions for all objects– Easy manipulation and scanning– The plant itself is not touched – only the

paper

• Digitizing 3D objects is a lot more complex and generally requires to manipulate the specimen itself


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Is it over ?

Digitization is just a very first step…

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um Virtual herbarium

• The amount of information available on-line will lower the number of physical visits to the Herbarium

• … but visitors leave post-it note on the sheets How to replace this ?– Annotation systems– « virtual visit » website


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um Spot the differences …

AFM

FABACEAE

Abrus aureus R. Vig.

?


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um Differences are

• Occurrence– occurrenceID | catalogNumber | occurrenceDetails | occurrenceRemarks | recordNumber | recordedBy | individualID |

individualCount | sex | lifeStage | reproductiveCondition | behavior | establishmentMeans | occurrenceStatus | preparations | disposition | otherCatalogNumbers | previousIdentifications | associatedMedia | associatedReferences | associatedOccurrences | associatedSequences | associatedTaxa

• Event– eventID | samplingProtocol | samplingEffort | eventDate | eventTime | startDayOfYear | endDayOfYear | year | month | day |

verbatimEventDate | habitat | fieldNumber | fieldNotes | eventRemarks • Location

– locationID | higherGeographyID | higherGeography | continent | waterBody | islandGroup | island | country | countryCode | stateProvince | county | municipality | locality | verbatimLocality | verbatimElevation | minimumElevationInMeters | maximumElevationInMeters | verbatimDepth | minimumDepthInMeters | maximumDepthInMeters | minimumDistanceAboveSurfaceInMeters | maximumDistanceAboveSurfaceInMeters | locationAccordingTo | locationRemarks | verbatimCoordinates | verbatimLatitude | verbatimLongitude | verbatimCoordinateSystem | verbatimSRS | decimalLatitude | decimalLongitude | geodeticDatum | coordinateUncertaintyInMeters | coordinatePrecision | pointRadiusSpatialFit | footprintWKT | footprintSRS | footprintSpatialFit | georeferencedBy | georeferenceProtocol | georeferenceSources | georeferenceVerificationStatus | georeferenceRemarks

• Identification– identificationID | identifiedBy | dateIdentified | identificationReferences | identificationRemarks | identificationQualifier | typeStatus

• Taxon– taxonID | scientificNameID | acceptedNameUsageID | parentNameUsageID | originalNameUsageID | nameAccordingToID |

namePublishedInID | taxonConceptID | scientificName | acceptedNameUsage | parentNameUsage | originalNameUsage | nameAccordingTo | namePublishedIn | higherClassification | kingdom | phylum | class | order | family | genus | subgenus | specificEpithet | infraspecificEpithet | taxonRank | verbatimTaxonRank | scientificNameAuthorship | vernacularName | nomenclaturalCode | taxonomicStatus | nomenclaturalStatus | taxonRemark


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um OCR / NLP ?


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um Projects to fill the gap

• Remote Taxonomists– Yack web tool

• Citizen Science / CrowdSourcing– « les collecteurs » project

• Repatriation project– Reflora (Brasil)


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um Thank you !

A project managed by:

•Direction of Collections– Michel Guiraud mguiraud (at) mnhn (.) fr– Pascale Joannot joannot (at) mnhn (.) fr

•DSI (Information Systems)– Henri Michiels michiels (at) mnhn (.) fr– Simon Chagnoux chagnoux (at) mnhn (.) fr


Documents

Rapid digitization of P Herbarium Switching to the fast track: Rapid digitization of the world's largest herbarium TDWG 2011- New Orleans Simon Chagnoux,