@conference {799,
	title = {Biodiversity Information Standards (TDWG) 2013 Symposium Talk: Success (and challenges) in broadening participation and engagement in digitization},
	booktitle = {TDWG 2013 Annual Conference},
	year = {2013},
	month = {10/2013},
	publisher = {Biodiversity Information Standards (TDWG) Conference 2013},
	organization = {Biodiversity Information Standards (TDWG) Conference 2013},
	address = {Florence, Italy},
	keywords = {Biodiversity Information Standards, collaboration, digitization, Engagement, Human Resources, NIBA, Socio-Technical Issues, Sustainability},
	url = {https://mbgserv18.mobot.org/ocs/index.php/tdwg/2013/paper/view/379},
	author = {Deborah L. Paul}
}
@article {227,
	title = {Bringing Collections Out of the Dark},
	journal = {ZooKeys},
	volume = {209},
	year = {2012},
	month = {07/2012},
	type = {Editorial},
	chapter = {1},
	keywords = {Digitisation, digitization, Natural history collections, RI-261532, Specimens},
	doi = {doi: 10.3897/zookeys.209.3699},
	url = {http://www.pensoft.net/journals/zookeys/article/3699/bringing-collections-out-of-the-dark},
	author = {Vincent Smith and Vladimir Blagoderov}
}
@conference {1414,
	title = {A Computational- and Storage-Cloud for Integration of Biodiversity Collections},
	booktitle = {Proceedings of the 2013 IEEE 9th International Conference on e-Science},
	year = {2013},
	publisher = {IEEE},
	organization = {IEEE},
	address = {Beijing, China},
	abstract = {A core mission of the Integrated Digitized Biocollections (iDigBio) project is the building and deployment of a cloud computing environment customized to support the digitization workflow and integration of data from all U.S. nonfederal biocollections. iDigBio chose to use cloud computing technologies to deliver a cyberinfrastructure that is flexible, agile, resilient, and scalable to meet the needs of the biodiversity community. In this context, this paper describes the integration of open source cloud middleware, applications, and third party services using standard formats, protocols, and services. In addition, this paper demonstrates the value of the digitized information from collections in a broader scenario involving multiple disciplines.},
	keywords = {appliances, biocollections infrastructure, biodiversity, cloud computing, data access, data store, digitization, EF-1115210},
	doi = {10.1109/eScience.2013.48},
	url = {http://dx.doi.org/10.1109/eScience.2013.48},
	author = {Matsunaga, Andr{\'e}a and Thompson, Alex and Figueiredo, Renato J. and Germain-Aubrey, Charlotte C. and Collins, Matthew and Beaman, Reed S. and MacFadden, Bruce J. and Riccardi, Greg and Soltis, Pamela S. and Page, Lawrence M. and Fortes, Jos{\'e} A.B.}
}
@conference {523,
	title = {Digitization of Herbarium Specimens, a Collaborative Project},
	year = {2007},
	month = {March 29, 2007},
	publisher = {ALA - American Library Association},
	organization = {ALA - American Library Association},
	address = {Baltimore, Maryland},
	abstract = {Digital collections in museums, libraries, and other agencies are expanding rapidly. Digitization of books, maps, photographs, and other objects for both preservation and dissemination are changing the way libraries work. Librarians who have, historically, worked with collections in print formats are anxious to move toward digital content as the wave of the future. Rather than stand on the sidelines and watch as the digital movement passes by, librarians need to be proactive and create digital content using both collections within the libraries{\textquoteright} walls and proactively seek opportunities to work collaboratively with stakeholders outside of the libraries{\textquoteright} hallowed halls. The creation of the Grand Teton National Park Digital Herbarium is an example of a collaborative effort between librarians, botanists, and national park personnel. All three groups needed to work together to create a digital herbarium useful to botanists and other individuals interested in the flora of Grand Teton National Park. This paper describes the project and suggests how other institutions may emulate the collaborative effort where more than two disparate groups have a stake in the final outcome of the digital project.},
	keywords = {botany, collaboration, Digitisation, digitization, Herbarium specimen digitization, libraries},
	author = {Larry Schmidt}
}
@article {225,
	title = {Five task clusters that enable efficient and effective digitization of biological collections},
	journal = {ZooKeys},
	volume = {209},
	year = {2012},
	month = {07/2012},
	chapter = {19},
	abstract = {This paper describes and illustrates five major clusters of related tasks (herein referred to as task clusters) that are common to efficient and effective practices in the digitization of biological specimen data and media. Examples of these clusters come from the observation of diverse digitization processes. The staff of iDigBio (The U.S. National Science Foundation{\textquoteright}s National Resource for Advancing Digitization of Biodiversity Collections) visited active biological and paleontological collections digitization programs for the purpose of documenting and assessing current digitization practices and tools. These observations identified five task clusters that comprise the digitization process leading up to data publication: (1) predigitization curation and staging, (2) specimen image capture, (3) specimen image processing, (4) electronic data capture, and (5) georeferencing locality descriptions. While not all institutions are completing each of these task clusters for each specimen, these clusters describe a composite picture of digitization of
biological and paleontological specimens across the programs that were observed. We describe these clusters, three workflow patterns that dominate the implemention of these clusters, and offer a set of workflow recommendations for digitization programs.},
	keywords = {ADBC, biodiversity informatics, Biological specimen collections, curation, digitization, EF-1115210, iDigBio, Imaging, paleontological specimen collections, task cluster, workflow},
	doi = {doi: 10.3897/zookeys.209.3135},
	url = {http://www.pensoft.net/journals/zookeys/article/3135/five-task-clusters-that-enable-efficient-and-effective-digitization-of-biological-collections},
	author = {Gil Nelson and Deborah L Paul and Gregory Riccardi and Austin R. Mast}
}
@article {3520,
	title = {A Guide to Digitizing Insect Collections Using MANTIS and Following the Protocols of the Harvard MCZ Entomology Type Image Project},
	year = {2003},
	month = {08/2003},
	institution = {Harvard University},
	address = {Cambridge},
	abstract = {This guide is offered to help anyone wanting to database and / or digitally image their collections. It is written in very simple terms since this work should not require a computer expert.

This guide is based on digitizing a type collection so it is more rigorous and careful than may be necessary for other collections, particularly the archive protocol. The user should take or leave whatever information they feel is necessary. However, if the guide is to be used for a type collection, it is recommended that the degree of rigor, if not the actual protocol, be matched.

Three different imaging setups are described, from a very inexpensive solution to the top of the range. These descriptions are not intended to prescribe the best or only setups, but to inform others about the setups we are using now as a result of over 5 years research--much of this with limited budgets. We developed these under the guidance of Dr. Piotr Naskrecki, with early and continued assistance by Dr. Gary Alpert and Dr. Brian Farrell.

In a similar way we describe a Filemaker Pro implementation called MANTIS. It is one of many database solutions for managing taxonomic information, but is recommended since it is easy to use, runs on both PC and Mac and is can be downloaded free from the web. It is also the creation of Piotr Naskrecki.},
	keywords = {digital imaging, digitization, Digitization Workflow, entomology, insects},
	url = {https://www.idigbio.org/sites/default/files/working-groups/INVI/Guide_to_digitizing.pdf},
	author = {Sarah Ashworth and Jennifer Fogarty}
}
@article {560,
	title = {iConference2013: Digitization of biocollections -- a grand challenge in scope, scale, and significance},
	year = {2013},
	abstract = {The world{\textquoteright}s natural history museums, herbaria, and other specialized collections documenting our planet{\textquoteright}s biodiversity, collectively known as {\textquoteleft}biocollections,{\textquotedblright} are estimated to contain between 2 million and 3 million specimens. These biocollections are truly global in scope, in terms of the taxa, regions, and periods of time represented by their holdings. Hundreds of years of expense and effort contributed to their collection, preservation, and study. These specimens hold clues that help us understand evolution, species distributions, the introduction of pests and diseases, the movement of invasive species, and may help us to predict the effects of extinction events and climate change. By creating and sharing a digital record of a specimen object, we can increase its discoverability and use in research, yet despite technological advances and supporting grant initiatives, digitization workflow bottlenecks continue to impede the flow of data needed for Big Science, and possibly for the future of humanity. Advancements in automation of optical character recognition, natural language processing, and interfaces to support these are necessary for a transformative breakthrough in high-throughput digitization of biocollections. },
	keywords = {Augmenting Optical Character Recognition, Biocollections, digitization, Discoverability, Scope},
	url = {http://prezi.com/ho8ipeilgqkk/digitization-of-biocollections-a-grand-challenge-in-scope-scale-and-significance/},
	author = {Amanda Neill}
}
@article {2477,
	title = {Imaging Workflows for the Digitization of Dry-preserved Vertebrate Specimens},
	year = {2016},
	keywords = {digitization, vertebrate, video, workflow},
	url = {https://vimeo.com/160615629}
}
@article {324,
	title = {Intro to iDigBio - PDF},
	year = {2012},
	abstract = {Integrated Digitized Biocollections (iDigBio) is the National Resource for Advancing Digitization of Biological Collections (ADBC) funded by the National Science Foundation. Through ADBC, data and images for millions of biological specimens are being made available in electronic format for the research community, government agencies, students, educators, and the general public.},
	keywords = {ADBC, digitization, documentation, Natural history collections},
	url = {https://www.idigbio.org/sites/default/files/sites/default/files/Intro_to_iDigBio.pdf},
	author = {iDigBio}
}
@article {571,
	title = {Organizing, Executing and Utilizing a Digitized Regional Herbarium},
	year = {2013},
	abstract = {The iDigBio Visiting Scholars Program provides early career
professionals an opportunity to explore a project and
produce deliverables advancing collections digitization
efforts. In her position as the 2012 Visiting Scholar, Anna
Monfils was able to address three proposed foci: 1)
advancing digitization efforts at the Central Michigan
University Herbarium (CMC), 2) conducting a workshop to
expand digitization efforts for regional collections in MI and
the Great Lakes, and 3) developing an Interactive web based
educational module integrating field, virtual and museum
experiences. Anna will discuss the unique challenges, marked
progress and lessons learned in the digitization of the CMC
regional collection. Highlights and deliverables from the Small
Collections Herbarium Workshop will be provided. Anna will
introduce an educational module utilizing digitized herbarium
records, place-based learning and TourGuide, an online tool
for creating interactive virtual tours. In addition to the
proposed foci, Anna will talk about {\textquotedblleft}value added{\textquotedblright} items that
have developed out of her iDigBio Visiting Scholar
opportunity including significant institutional investment in
the CMC collection, a collaborative proposal submitted to the
Hanes Foundation to digitize 11 regional collections in
Michigan, a partnership with iDigBio to assess student
learning in collections digitization, participation in a writing
workshop to produce a manuscript on the value of regional
collections and iDigBio sponsorship of a BOTANY 2013
Symposium on broadening participation in the botanical
sciences.
},
	keywords = {digitization, Education and Outreach, Herbarium, Visiting Scholar},
	url = {https://vimeo.com/idigbio/review/420496481/2d68acaafc},
	author = {Anna Monfils}
}
@conference {1824,
	title = {Reaching Consensus in Crowdsourced Transcription of Biocollections Information},
	booktitle = {2014 IEEE 10th International Conference on e-Science},
	year = {2014},
	month = {Oct/2014},
	publisher = {IEEE},
	organization = {IEEE},
	address = {Guaruj{\'a}, Brazil},
	abstract = {Crowdsourcing can be a cost-effective method for tackling the problem of digitizing historical bio collections data, and a number of crowd sourcing platforms have been developed to facilitate interaction with the public and to design simple "Human Intelligence Tasks". However, the problem of reaching consensus on the response of the crowd is still challenging for tasks for which a simple majority vote is inadequate. This paper (a) describes the challenges faced when trying to reach consensus on data transcribed by different workers, (b) offers consensus algorithms for textual data and a consensus-based controller to assign a dynamic number of workers per task, and (c) proposes further enhancements of future crowd sourcing tasks in order to minimize the need for complex consensus algorithms. Experiments using the proposed algorithms show up to a 45-fold increase in ability to reach consensus when compared to majority voting using exact string matching. In addition, the controller is able to decrease the crowd sourcing cost by 55\% when compared to a strategy that uses a fixed number of workers.},
	keywords = {Accuracy, Approximation algorithms, biocollections infrastructure, biodiversity, consensus algorithms, crowdsourcing, digitization, EF-1115210, Heuristic algorithms, Materials, Optical character recognition software, Reliability},
	doi = {10.1109/eScience.2014.30},
	url = {http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=\&arnumber=6972249},
	author = {Matsunaga, Andr{\'e}a and Mast, Austin and Fortes, Jos{\'e} A.B.}
}
@article {1321,
	title = {SPNHC 2014: Progress in Digitization: Automated mass-digitization line for individual insect specimens},
	year = {2014},
	abstract = {We present a novel solution for mass-digitization of individual insects. Each specimen will receive a unique ID, and the basic metadata including taxon name will be databased with the ID. A specially designed conveyer belt is being used in the imaging. On the imaging line, plastic pallets made with 3D-printers carry the specimens to the imaging unit. The insect is automatically imaged from above, and the labels attached to the pin are imaged from the side. The underside of labels will be visible through a mirror. At the moment, imaging line is applied to objects between 0.5 {\textendash} 30 mm in length, and the peak performance is around 500 specimens /day. 
This system is being used to process collections donated to the Finnish Museum of Natural History. Digitarium receives collections, and disassembles them, driving them through the automatic digitization line and placing them in units. After digitization, the specimens and produced data will be delivered in taxonomical order to FMNH. The original collection cabinets and drawers will not follow the specimens to the museum. From images, further metadata from the labels can be transcribed.   
},
	keywords = {automation, conveyor belt, digitarium, digitization, Finnish Museum of Natural History, insects, SPNHC 2014, SPNHC 2014: Progress in Digitization},
	url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/04_Digitarium_SPNHC2014_Cardiff_25062014.pdf},
	author = {Riitta Tegelberg and Janne Karppinen and Tero Mononen and Mira S{\"a}{\"a}skilahti and Hannu Saarenmaa}
}
@article {1318,
	title = {SPNHC 2014: Progress in Digitization: Creating a Swedish Digital Natural History Collection, e-BioColl.se},
	year = {2014},
	abstract = {Natural history collections constitute the major source of data for research in phylogenetics and systematics, and provide crucial information for analyses of long-term trends in ecology and environmental sciences. Recent mass-digitization efforts have opened up such collections abroad for transformative e-science approaches, but research dependent on Swedish objects is left behind. Out of an estimates 33 million Swedish specimens, almost 90\% are unavailable digitally, and it will take hundreds of years to eliminate this backlog at the current pace of digitization.
To address this problem and provide a proof-of-concept version of an e-science platform for Swedish natural history collections allowing complete digitization within 10 years we plan to develop and test standardized, re-usable, industrial-level digitization processes where innovation and automation will bring down the cost of obtaining specimen images and geospatial and taxonomic metadata from specimen labels. Robotic techniques employed to image insect collections, and automated text recognition and citizen-science based crowd sourcing for extracting information from specimen labels during the digitization of 1.4 million specimens in the Gothenburg herbarium will provide a full-scale feasibility test of tools and concepts. The digitized information will immediately support outstanding research in Sweden and elsewhere on this unique material, and boost international initiatives (e g GBIF, LifeWatch and IPBES).},
	keywords = {automation, Citizen Science, digitization, e-BioColl.se, e-science, optical character recognition, SPNHC 2014, SPNHC 2014: Progress in Digitization},
	url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/01_SPNHC_NRM_140626_KarinKarlsson.pdf},
	author = {Karin Karlsson and Ericson, Per and Fredrik Ronquist and Anders Telenius and Stefan Daume and Kevin Holston}
}
@article {1324,
	title = {SPNHC 2014: Progress in Digitization: Designing a Workflow to Help with Error Detection in a Paleontology Digitization Project},
	year = {2014},
	abstract = {The Field Museum is implementing a three-year IMLS grant using summer interns to digitize approximately 15,000 Silurian fossil lots. Workflow for this project has each intern working on six drawers of fossils at a time; the fossils are all from the same geologic period and taxonomic group (as they are arranged in the collection). Interns cycle their fossils through three workstations: a label photography station, a fossil photography station, and a KE EMu data entry station. The average time per specimen to complete this cycle is 9.5 minutes with times ranging between 4 to 18 minutes. After cycling their cart through each workstation I edit, upload, and link the images to the catalogue records. In the first year 7,785 image were generated and linked to catalogue records. 
During the process of connecting images to the catalogue there are three opportunities to check for errors. First, KE EMu generates an error log of images that fail to link during the batch input.  The error rate is less than 2.2\%. Common errors include simple format errors in the batch upload, specimens not entered into the catalogue, and typos in the specimen{\textquoteright}s catalogue number.  Second, because specimens in each batch are from the same geologic period and taxonomic group it is easy to spot any inconsistencies or missing data when reviewing the records in a table format. Finally each record should have two images linked to it. Any missing images are easy to add.
},
	keywords = {digitization, error checking, Field Museum, fossils, interns, Silurian, SPNHC 2014, workflow},
	url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/07_1130_MayerPS.pdf},
	author = {Paul S. Mayer and L. Connolly and N. Karpus and A. P. Layng}
}
@article {1326,
	title = {SPNHC 2014: Progress in Digitization: Exploitation of digital collection data at the Museum f{\"u}r Naturkunde Berlin},
	year = {2014},
	abstract = {Item information of many collections in the Museum f{\"u}r Naturkunde Berlin (MfN Berlin) - as in many other museums - is often stored locally by each curator in different formats such as Excel spreadsheets. These files are often accessible exclusively by collection staff members. Within the project {\textquotedblleft}Exploitation of digital collection data{\textquotedblright} funded by the Deutsche Forschungsgemeinschaft (DFG) the data from the MfN Berlin mammal collection were transferred from Excel spreadsheets to an SQL server using scripts developed by a database specialist at the MfN Berlin. The data were subsequently standardised, for example in terms of their taxonomic and geographical information. The revised data were then transferred from the SQL server into Specify - a museum database software application. Further aims of this project are the development and implementation of common transfer tools to achieve data migration to open-access databases such as BioCASE and GBIF as well as information retrieval like the current distribution of the specimen from databases like the IUCN redlist. This will allow external information retrievals of collection data and thus will open new avenues for scientific exploration of the collections. We have successfully applied our data transfer pipeline to the mammal collection of the MfN Berlin which is the 4th largest worldwide of its kind. These methods and tools can be used for the data migration of other collections of the MfN Berlin with its approximately 30 million collection objects, and also by other museums.},
	keywords = {database management, digitization, Museum f{\"u}r Naturkunde Berlin, Specify, SPNHC 2014, SPNHC 2014: Progress in Digitization, standardization},
	url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/09_Jancke_et_al_SPNHC2014_draft_SJ200614.pdf},
	author = {Saskia Jancke and Dirk Striebing and Frieder Mayer}
}
@article {1319,
	title = {SPNHC 2014: Progress in Digitization: From massive digitisation of Paris Herbarium to a nation-wide program},
	year = {2014},
	abstract = {The Mus{\'e}um national d{\textquoteright}Histoire naturelle of Paris (MNHN) completed a massive digitisation program of the herbarium specimens (P, PC). Nearly 6 million images went online between 2008 and 2012. The resulting database records contain only a minimum set of attributes (scientific name, catalog number and continent of origin). As many more information is most often available from the photographed labels, optical character recognition and a crowdsourcing site have since been used to enrich the database without physical access to the specimen.
Building on the experience gained from these projects, a national program {\textquotedblleft}e-ReColNat{\textquotedblright} was launched to extend the digitisation to the remaining herbariums and most zoological and paleontological types. The result will be available online for annotation and label retranscription to a broad audience mixing the general public and the scientific experts.
},
	keywords = {crowdsourcing, digitization, e-ReColNat, Herbarium, Mus{\'e}um national d{\textquoteright}Histoire naturelle of Paris, optical character recognition, SPNHC 2014, SPNHC 2014: Progress in Digitization},
	url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/02_SPNHC2014_chagnoux.pdf},
	author = {Simon Chagnoux and Marc Pignal}
}
@article {1336,
	title = {SPNHC 2014: Progress in Digitization: From Museum Specimen Database to Ecological Statement},
	year = {2014},
	abstract = {	The goal of the Thematic Collections Networks, Tri-trophic Digitization Project (TCN-TTD) is to database and image, in part, plant-associated Hemiptera ({\textquotedblleft}true bugs{\textquotedblright}), parasitoid insects associated with Hemiptera, and the plants on which Hemiptera feed, totaling approximately 2.5 million specimens from 18 insect and 14 plant institutional collections. Integrating these data with other extant datasets, particularly from diverse sources (databases, institutions) with diverse historical workflows and standards such as these, provide a unique opportunity to generate and test various biogeographical and ecological hypotheses. Here we present our progress to date on the digitization efforts and demonstrate the usefulness and some of the inherent challenges of these data with a relatively small dataset of treehoppers and their associated oak species derived from our efforts. We also demonstrate some simple tools to examine database data for quality problems.},
	keywords = {collector bias, data analyses, data quality, digitization, ecological statement, museum specimen database, pseudoreplication, SPNHC 2014, SPNHC 2014: Progress in Digitization},
	url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/19_Johnson_Rabler_Bartlett_SPNHC_2014.pdf},
	author = {Christine A. Johnson and Richard K. Rabeler and Charles Bartlett}
}
@article {1331,
	title = {SPNHC 2014: Progress in Digitization: Georeferencing Fish Collections from the FishNet Network},
	year = {2014},
	abstract = {FishNet2 (www.fishnet2.net) is a global network of fish collection databases that gives researchers access to  data on roughly 4 million fish species lots,  representing over 30 million specimens. Before this project began, only about two-thirds of the records in Fishnet2 were georeferenced. The goals of this collaborative project were to georeference all localities without geographic coordinates and repatriate the results to data providers. The Collaborative Georeferencing Client  (CoGe)of the GEOLocate Platform was used to georeference and verify the roughly 250,000 localities in FishNet2 lacking coordinates at the start of the project. Each of the twelve collaborating institutions hired a full-time georeferencing technician to verify and correct the CoGe generated geographic coordinates for localities assigned to his or her institution. Since January 2013, when the georeferencing phase of the project began, more than 244,000 localities of have been processed (214,000 corrected), and over 1 million specimens records have been processed (935,000 corrected). Records that could not be georeferenced were skipped and reasons for not correcting the coordinates were recorded. Every corrected record includes geographic coordinates in decimal degrees, an uncertainty radius, and most of the records have a user generated error polygon to define the uncertainty in the determinations.},
	keywords = {Collaborative Georeferencing Client (CoGe), digitization, FishNet, GEOLocate, georeference, SPNHC 2014, SPNHC 2014: Progress in Digitization},
	url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/14_RIOS-spnhc2014.pdf},
	author = {Nelson E. Rios and Henry L. Bart and Michael H. Doosey}
}
@article {1332,
	title = {SPNHC 2014: Progress in Digitization: iDigBio{\textquoteright}s Biospex System for Engaging the Public in Digitization},
	year = {2014},
	abstract = {New web resources provide scientists opportunities to engage the public in ways and at scales not previously possible. Many ecological and environmental citizen science projects focus on generating present-day occurrence data on populations, species, and communities to address urgent societal challenges, such as the extinction crisis and biotic responses to climate change. Biodiversity research collections provide the opportunity to produce the important historical and present-day baseline data on distributions with which to compare the new observations and project future change. However, the majority of information about the specimens in these collections has yet to be digitized. Public engagement might provide an important strategy to accelerate digitization. Out of a 2012 workshop emerged the idea of an iDigBio public participation in digitization management system, which would permit the creation of record sets of incomplete specimen data and/or images from the iDigBio Cloud, management of their digitization using collaborating citizen science tools, monitoring of digitization progress, advertisement of the projects on the go-to sites for members of the public interested in citizen science, and return of the new data to the data providers and those involved in the digitization. We will introduce this emerging system, called Biospex for Biodiversity Specimen Expeditions. We will provide an overview of the management system and its interoperability with biodiversity specimen data management systems and citizen science tools via Darwin Core Archive and Ecological Markup Language files.},
	keywords = {Biospex, Citizen Science, digitization, digitization management, iDigBio, SPNHC 2014, SPNHC 2014: Progress in Digitization},
	url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/15_Ellwood_SPNHC_2014.pdf},
	author = {Elizabeth R. Ellwood and Austin R. Mast and Robert Bruhn and Jeremy Spinks and Greg Riccardi}
}
@article {1322,
	title = {SPNHC 2014: Progress in Digitization: Image segmentation in high throughput digitisation workflows},
	year = {2014},
	abstract = {Advances in imaging technologies have made the acquisition of high throughput, multi-specimen images a trivial task. However, the subsequent movement of specimens (e.g. due to curatorial or research activity) breaks the synchronisation between the physical collection and its digital representation, degrading the value of multi-specimen images over time. Furthermore, the data record of a single specimen cannot be unambiguously linked to its digital image with this approach. In order to realise the full potential of multi-specimen imaging technology, software is required to automate or semi-automate the segmentation of images into individual specimens and support subsequent annotation. We demonstrate a potential approach for two types of specimens: microscopic slides and pinned insects. This approach will form part of the large scale digitisation programme being developed at the NHM which has the ambitious goal of digitising 20 million specimens in the next five years.},
	keywords = {automation, digitization, insects, microscope slides, Natural History Museum, SPNHC 2014, SPNHC 2014: Progress in Digitization, synchronization},
	url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/05_BlagoderovEtAl_ImageSegmentation_sm.pdf},
	author = {Vladimir Blagoderov and Laurence Livermore and Ben Price and St{\'e}fan van der Walt and Pieter Holtzhausen and Vince Smith}
}
@article {1329,
	title = {SPNHC 2014: Progress in Digitization: Incorporating OCR into a digitisation and curation workflow},
	year = {2014},
	abstract = {The digitisation of natural history collections is a priority for many institutes for reasons including opening access to users around the world, incorporation of specimen data in research, disaster planning, etc. However, digitisation of natural history specimens is expensive and labour intensive. For this reason, digitisation of specimens has moved towards minimal data capture and imaging as part of large scale processes. The workflow can be summarised in the following steps: 1) minimal curation; 2) attach barcode as a unique identifier; 3) minimal data entry; 4) image specimen; 5) additional data entry. There has been some investigation by institutes into the use of Optical Character Recognition (OCR) within the digitsation and curation workflow. The Royal Botanic Garden Edinburgh (RBGE) now routinely processes all specimen images through OCR software. The OCR process is integrated into the overall digitisation and curation workflow and has been used to speed up the process of adding data to over 100,000 specimens. The following additional steps have been incorporated into the workflow at RBGE: 4a) assess condition of specimen; 4b) process image through OCR software; 5a) additional curation. The incorporation of OCR into digitisation workflows is being explored by the Synthesys project funded by the European Union within Framework 7, and by iDigBio funded by the United States Government within the National Science Foundation programme. The work being carried out at the Royal Botanic Garden Edinburgh to integrate OCR into the digitisation and curation workflow is discussed as part of the work of Synthesys and iDigBio.},
	keywords = {digitization, optical character recognition, SPNHC 2014, SPNHC 2014: Progress in Digitization, workflow},
	url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/12_Haston_et_al_Incorporating_OCR.pdf},
	author = {Elspeth Haston and Robyn Drinkwater and Robert Cubey}
}
@article {1325,
	title = {SPNHC 2014: Progress in Digitization: Making molehills out of mountains: Crowdsourcing digital access to natural history collections},
	year = {2014},
	abstract = {The development of cheap mass imaging techniques has made transcription the bottleneck in digitising natural history collections. Internet crowdsourcing has been successfully used across different scientific communities and has the potential to become an effective method for transcribing our natural history data. We review current crowdsourcing platforms and communities, analyse their efficacy and discuss their potential role in improving digital access to natural history collections worldwide.},
	keywords = {access, crowdsourcing, digitization, Natural History Museum, SPNHC 2014, SPNHC 2014: Progress in Digitization, Transcription},
	url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/08_SPNHC\%20Crowdsourcing\%20Talk\%20\%28New\%29.pdf},
	author = {Laurence Livermore and Vince Smith and John Tweddle}
}
@article {1320,
	title = {SPNHC 2014: Progress in Digitization: Putting the contents of the Geological Museum on the web},
	year = {2014},
	abstract = {The Museum of Practical Geology (Jermyn Street, 1851-1935) displayed most of the British Geological Survey{\textquoteright}s specimen collection. With the move to the Geological Museum and then to Nottingham (Keyworth, 1985 onwards) most items were consigned to drawers. The internet has provided the means to re-exhibit these collections. BGS has been at the forefront of collections digitization since the 1970s. By 2000, the collections had digital catalogues of varying completeness, and in October 2000 the borehole and rock catalogues went on line. By 2006, all the main collections had online text and GIS searches.
During the past five years, BGS has made high resolution digital images of various collections available, including building stones and 4000 early twentieth century glass plates of the Kidston palaeobotanical collection. 125,000 7216 x 5412 pixel images of UK Continental Shelf cores1 were made available online in 2012, a project requiring a conveyor belt and extensive use of barcodes. 100,000 rock thin sections2 were added in 2013. The most innovative project to date has been a collaboration between BGS, the National Museum Cardiff, the Sedgwick Museum Cambridge, the Oxford Museum of Natural History and the Geological Curators{\textquoteright} Group (representing other national, university and local museums) to create an online database3 of British macrofossil types.  The web portal provides data about each specimen, searchable on taxonomic, stratigraphic and spatial criteria. High resolution photographs, stereo anaglyphs and many 3d digital models are available. We are keen to share our experiences, particularly of 3d digital models.

1 https://www.bgs.ac.uk/data/offshoreWells/wells.cfc?method=searchWells
2 http://www.largeimages.bgs.ac.uk/iip/britrocks.html?id=250000/258489
3 http://www.3d-fossils.ac.uk/ 
},
	keywords = {3D models, automation, British Geological Survey, conveyor belt, digitization, fossils, SPNHC 2014, SPNHC 2014: Progress in Digitization},
	url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/03_SPNHC_Digitization_Howe_P3_V2.pdf},
	author = {Mike Howe and Bob McIntosh and Simon Harris and Michela Contessi and Graham Tulloch}
}
@article {1335,
	title = {SPNHC 2014: Progress in Digitization: Seaweed Collections Online: Mobilising data from national and regional museums},
	year = {2014},
	abstract = {The seashores and shallow seas around Britain support an important component of UK biodiversity with over 650 species of red, green and brown seaweeds which represent c. 7\% of the described seaweed flora of the world. However, over 55\% are Data Deficient according to IUCN criteria, there is increasing evidence that large brown habitat-forming seaweeds (kelps and fucoids) are disappearing and invasive seaweed species are increasing. Consequently there is an urgent and increasing need for good quality, verifiable data on past and present species occurrence to inform research into these issues. Museum collections provide crucial evidence points for mapping changing patterns in species distribution around the 
UK. For this project we aimed to capture seaweed collections data from UK national and regional museums, focussing on our target list of seaweed species which we prioritised by their relevance to environmental change and conservation research. The project also enabled us to develop a network of persons responsible for seaweed collections at the participating institutions. These collections data are disseminated online via the project website. We used a Scratchpad for this purpose (http://scratchpads.eu) which provided tools for delivering specimen data and associated information in a customisable website: http://seaweeds.myspecies.info/. Fifteen institutions participated in the project over the course of one year and over 8000 records were received, 4334 of which were newly generated as part of the project. This project was funded by the Esm{\'e}e Fairbairn Collections Fund.
},
	keywords = {Britain, Data Deficient, digitization, Scratchpad, seaweed, species distributions, SPNHC 2014, SPNHC 2014: Progress in Digitization},
	url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/18_Wilbraham_SeaweedsOnline_SPNHC.pdf},
	author = {Jo Wilbraham and Juliet Brodie}
}
@article {1333,
	title = {SPNHC 2014: Progress in Digitization: Supporting Data Flows in the New England Vascular Plant Network with FilteredPush Technologies},
	year = {2014},
	abstract = {FilteredPush is supporting digitization in two Thematic Collections Networks (TCNs), the Southwest Arthropods Collections Network (SCAN) and the New England Vascular Plant project (NEVP).  In NEVP, minimal data records, including current taxonomic identification, state and town of collection, and date collected are created during imaging at high-throughput digitization stations at digitization sites.  Current identification is obtained at the folder level in a pre-capture step and associated with the specimens upon imaging.  FilteredPush transports data from the digitization sites by wrapping DarwinCore terms in Open Annotation ontology documents, including metadata about the when, where, and who of digitization, typing as New Occurrence records, and minimal AudubonCore for the images.  These annotations are ingested into the NEVP Symbiota portal.  The annotations are then available for ingest into the databases of record through new occurrence ingest tools in the Specify 6 collections management system.   Additional data will be transcribed, in Symbiota, from the specimen images, and, supporting the science goals of the project, flowering and fruiting state will be coded for some taxa.  These assertions will be wrapped in annotations, typed to reflect domain business operations, and transported to the relevant collections for ingest.  Records harvested from network participants into datastores within FilteredPush will be subject to quality control from an Akka workflow that tests the taxon name, georeference, and date collected values of each record. Quality control issues (including proposed corrections) are reported in response to queries by researchers and transported through annotations to both Symbiota and the databases of record.},
	keywords = {DarwinCore, digitization, FilteredPush, quality control, Specify, SPNHC 2014, Symbiota},
	url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/16_Morris_gwyth_ei_hidlo_NEVP_mini.pdf},
	author = {Paul J. Morris and James Hanken and Maureen Kelly and David B. Lowery and Bertram Lud{\"a}scher and James A. Macklin and Chuck McCallum and Robert A. Morris and Tianhong Song and Patrick Sweeney}
}
@article {1330,
	title = {SPNHC 2014: Progress in Digitization: The virtually browseable collection: connecting GIS to whole drawer imaging},
	year = {2014},
	abstract = {Accessibility is one of the most problematic aspects of offsite storage for collections. This project approaches that issue by creating virtual access to a large collection stored 8 miles from the main institution. To create virtual access, we used two elements that already exist for our collection. A GIS map of all cabinets in the repository and a Specify 6 database of records, which relates the specimens in those cabinets to their spatial locations. We combined database and spatial data using ArcGIS Online, because it has cross-platform compatibility. We related a third aspect, drawer and specimen images that are linked to the specimen records and can be viewed alongside the data and spatial records.
Our final result is an online resource that allows the user to virtually examine the collection, query a database file and view the drawer content, individual specimens, and label images when they exist. This product is useful for researchers, teachers and the general public. The latter group is important from an educational stand point but also because many of the collections were amassed using public funds. It fulfills an additional role in that it is a time stamp marker for each drawer. What was located in that drawer, what was its condition? Over time additional images of drawers will be taken providing an archival record of their content and condition.
},
	keywords = {accessibility, digitization, education, GIS map, Specify, SPNHC 2014, SPNHC 2014: Progress in Digitization, whole drawer imaging},
	url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/13_Molineux-SPNHC2014-The\%20virtually\%20browseable\%20collection.pdf},
	author = {Ann Molineux and Robert W. Burroughs and Faye Geigerman}
}
@article {1334,
	title = {SPNHC 2014: Progress in Digitization: Using Complementarity to Improve Plant Specimen Digitization},
	year = {2014},
	abstract = {Unlike most zoological specimens, botanical collections distinguish themselves by having duplicates, that is, multiple specimens generated from the same collecting event. These are either from the same plant or from a close population and are distributed among multiple herbaria.  Over the last two decades, as digitization has become a significant part of doing business in systematics collections, it{\textquoteright}s become clear that a great deal of {\textquotedblleft}duplication{\textquotedblright} of effort has followed  {\textquotedblleft}duplication{\textquotedblright} of plant collections.  Aggregators of specimen data, such as GBIF and iDigBio, recognize this phenomenon, as do individual herbaria.  In 2005, a GBIF Workshop in Crete, led by the late Larry Speers, addressed this topic and Rusty Russell was tasked with investigating the issues surrounding {\textquotedblleft}duplication{\textquotedblright}.  More recently, a joint effort is underway at RBG-Kew, RBG-Edinburgh and the Smithsonian Institution to develop tools to harness the potential that plant duplicates offer toward making digitization a more efficient enterprise.  Past and present activities to address this issue will be described.},
	keywords = {botanical specimens, digitization, duplication, efficiency, exsiccatae, herbaria, SPNHC 2014, SPNHC 2014: Progress in Digitization},
	url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/17_Russell-SPNHC\%202014-Complementarity.pdf},
	author = {Rusty Russell and Elspeth Haston and Nicola Nicolson}
}
@article {1328,
	title = {SPNHC 2014: Progress in Digitization: Using optical character recognition (OCR) output in digitization},
	year = {2014},
	abstract = {Before iDigBio, that{\textquoteright}s Integrated Digitized Biocollections, others began the work of figuring out how to use OCR output with machine learning (ML) and natural language processing (NLP) to improve the efficiency and speed with which data from museum specimen label images can be captured and validated. The Augmenting Optical Character Recognition (aOCR WG) Working Group at iDigBio is pleased to be building on that foundation. Improvements have been realized in parsing algorithms and visualization of data. Recently, researchers at The Royal Botanic Garden Edinburgh (RBGE) successfully used word clouds from OCR output to reveal useful data, otherwise dark, until a specimen label was digitized completely (Haston, et al TDWG 2013). Their work indicates this method results in greater transcriber job satisfaction. Inspired by this work, the OCR Integration Track Team at the iDigBio Citscribe Hackathon showed how indexing, scoring, and visualizing OCR output reveals otherwise hidden search terms, uncovers errors, and can improve the data transcriber and data validator experience. Using open-source software, we presented these ideas to those with transcription tools up-and-running including Notes From Nature, Biodiversity Heritage Library (BHL), ALA Biodiversity Volunteer Portal, Smithsonian Digital Volunteers, and the Lichen, Bryophytes and Climate Change Volunteer Portal using Symbiota software. The aOCR WG is working collaboratively with the Joint Research Activity (JRA) Synthesys3 Project to share expertise for automated data collection for digital images. Got text in your images? How might OCR output work for you? Come talk to our aOCR WG to find out and to share your expertise.},
	keywords = {confidence scores, data visualization, digitization, Machine Learning, Natural Language Processing, optical character recognition, SPNHC 2014, SPNHC 2014: Progress in Digitization},
	url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/Paul_UsingOCRoutput.pptx},
	author = {Deborah L Paul and Andrea Matsunaga and Miao Chen and Jason Best and Sylvia Orli and Elspeth M Haston}
}
@article {1323,
	title = {SPNHC 2014: Progress in Digitization: Workflows in the cooperative IMLS Silurian Digitization project},
	year = {2014},
	abstract = {Milwaukee Public Museum (MPM) is implementing a three-year IMLS grant in conjunction with The Field Museum to digitize our Midwest Silurian collections and create a shared online database.  The first workflow was between the institutions.  The joint nature of the project required information exchange between museums.  To coordinate a shared online database an effort was made to use shared vocabulary and Internal Record Numbers (IRN) for lithostratigraphy, chronostratigraphy and taxonomy data. Internal Records were generated at The Field Museum and shared with MPM.  After the first large data export smaller updates have been made.  MPM maintains a shared Google Drive spreadsheet with corrections and new data to be updated at The Field.  Sharing data creates an error check point.  
The second workflow for the digitization project is within MPM. The collection is organized stratigraphically.  The specimens all have a locality number but most do not have a unique specimen number.  Workflow starts with data entry into KE EMu using specimen labels.   Specimens without numbers are assigned the KE EMu Internal Record Number as specimen number.  The photography station is divided into two parts, fossil photography and photo processing. The fossils are processed by drawers and include a photo of the drawer and photos of each fossil in the drawer. A batch process is used to convert the raw image to .dng, .tif and .jpeg formats. The .jpeg images are then associated with the KE EMu catalogue data and the .dng and .tif images are saved in MPM{\textquoteright}s image repository.
},
	keywords = {digitization, Field Museum, fossils, Milwaukee Public Museum, Silurian, SPNHC 2014, SPNHC 2014: Progress in Digitization, taxonomy, workflow},
	url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/06_Workflows\%20in\%20the\%20cooperative\%20IMLS\%20Silurian\%20Digitization\%20project_B.pdf},
	author = {Patricia Coorough Burke and A. Caywood and M. James and E. Malueg and D. Miller}
}
@article {1327,
	title = {SPNHC 2014: Progress in Digitization: ZooSphere - A tool for automated spheric image capturing and interactive 3D visualization},
	year = {2014},
	abstract = {Entomological collections, particularly the type specimens therein, are the fundament of the taxonomic research on insects. Since the beginning of collecting activities in the 18th century, some million type specimens (e.g. holotypes, lectotypes, paratypes.) are stored in museums worldwide. There are various threats to these collections: Valuable type specimens are damaged or even destroyed by museum beetles (e.g. Anthrenus verbasci) or moths (e.g. Teneola biselliella). Also changes and fluctuations in light exposure, temperature and high humidity may have negative effects on the objects. Especially the types are even more in danger by shipping them from the museums to specialists for their taxonomic work. 
To give full scientific access on the type specimens without shipping the valuable material across the globe, we developed a tool (ZooSphere) for automated image capture from about 400 positions around one specimen. A high resolution image with extremely high depth of focus is produced by using stacking technology in each position. The images will be freely available in the world wide web and will be displayed by a web-based tool developed for rotating and zooming the digital object in browsers. The same technology will be used for an interactive 3D presentation of the objects. 
The next steps are 1) joining the ZooSphere images with microCT images from internal specimen structures and 2) creating 3D models of the specimens by applying photogrammetric methods on the ZooSphere images.
},
	keywords = {3D, automation, digitization, Imaging, insects, Museum f{\"u}r Naturkunde Berlin, SPNHC 2014, SPNHC 2014: Progress in Digitization, ZooSphere},
	url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/10_kroupa\%20et\%20al\%20zoosphere.pdf},
	author = {Alexander S. Kroupa and Martin Pluta and Bernhard Schurian and Falko Gl{\"o}ckler}
}
@article {2291,
	title = {Workforce-efficient consensus in crowdsourced transcription of biocollections information},
	journal = {Future Generation Computer Systems},
	year = {2015},
	abstract = {Abstract Crowdsourcing can be a cost-effective method for tackling the problem of digitizing historical biocollections data, and a number of crowdsourcing platforms have been developed to facilitate interaction with the public and to design simple {\^a}{\texteuro}{\oe}Human Intelligence Tasks{\^a}{\texteuro}. However, the problem of reaching consensus on the response of the crowd is still challenging for tasks for which a simple majority vote is inadequate. This paper (a) describes the challenges faced when trying to reach consensus on data transcribed by different workers, (b) offers consensus algorithms for textual data, (c) implements a consensus-based controller to assign a dynamic number of workers per task and per field of a task, (d) proposes the use of clustering to further eliminate redundant work and (e) proposes enhancements of future crowdsourcing task assignments in order to minimize the need for complex consensus algorithms. Experiments using the proposed algorithms show multifold increase in the ability to reach consensus when compared to majority voting using exact string matching. In addition, the workforce controller is able to decrease the crowdsourcing cost per task and per task field by 37\% and 50\%, respectively, when compared to a strategy that uses a fixed number of workers. The accuracy of clustering is also good and it has the potential to increase the quality of tasks that can be clustered.},
	keywords = {biocollections infrastructure, biodiversity, consensus algorithms, crowdsourcing, digitization, EF-1115210},
	doi = {http://dx.doi.org/10.1016/j.future.2015.07.004},
	url = {http://www.sciencedirect.com/science/article/pii/S0167739X15002277},
	author = {Matsunaga, Andr{\'e}a and Mast, Austin and Fortes, Jos{\'e} A. B.}
}
@article {226,
	title = {ZooKeys 209 (2012) Special Issue,  No specimen left behind: mass digitization of natural history collections},
	year = {2012},
	abstract = {See Editorial: Bringing Collections Out of the Dark},
	keywords = {Digitisation, digitization, Mobilization, Natural history collections, Specimens},
	url = {http://www.pensoft.net/journals/zookeys/issue/209/},
	author = {Vladimir Blagoderov and Vincent Smith}
}
