scholarly journals A Novel Automated Mass Digitisation Workflow for Natural History Microscope Slides

2019 ◽  
Vol 7 ◽  
Author(s):  
E Louise Allan ◽  
Laurence Livermore ◽  
Benjamin Price ◽  
Olha Shchedrina ◽  
Vincent Smith
Keyword(s):  
Natural History ◽  
Human Error ◽  
Microscope Slide ◽  
Unique Identifier ◽  
History Museum ◽  
Comparative Efficiency ◽  
Collection Management System ◽  
Scientific Collections ◽  
Automated Processes ◽  
Microscope Slides

The Natural History Museum, London (NHM) has embarked on an ambitious programme to digitise its collections. One aim of the programme has been to improve the workflows and infrastructure needed to support high-throughput digitisation and create comprehensive digital inventories of large scientific collections. This paper presents the workflow developed to digitise the entire Phthiraptera (parasitic lice) microscope slide collection (70,663 slides). Here we describe a novel process of semi-automated mass digitisation using both temporary and permanent barcode labels applied before and during slide imaging. By using a series of barcodes encoding information associated with each slide (i.e. unique identifier, location in the collection and taxonomic name), we can run a series of automated processes, including file renaming, image processing and bulk import into the NHM’s collection management system. We provide data on the comparative efficiency of these processes, illustrating how simple activities, like automated file renaming, reduces image post-processing time, minimises human error and can be applied across multiple collection types.

scholarly journals High-Throughput Digitisation of Natural History Specimens

2019 ◽  
Vol 3 ◽  
Author(s):  
Elizabeth Louise Allan ◽  
Steen Dupont ◽  
Helen Hardy ◽  
Laurence Livermore ◽  
Benjamin Price ◽  
...  
Keyword(s):  
Natural History ◽  
High Throughput ◽  
Human Error ◽  
Data Matrix ◽  
Post Processing ◽  
Unique Identifier ◽  
Digital Collections ◽  
Specimen Handling ◽  
History Museum ◽  
Microscope Slides

The Natural History Museum, London (NHM) has embarked on an ambitious Digital Collections Programme to digitise its collections. One aim of the programme has been to improve the workflows and infrastructure needed to support high-throughput digitisation and create comprehensive digital inventories of large scientific collections. Pilot projects have been carried out for a variety of collection types, from which high-throughput imaging workflows have been developed and refined. These workflows have focused on pinned insect specimens (Blagoderov et al. 2012, Paterson et al. 2016, Blagoderov et al. 2017, Price et al. 2018), microscope slides (whole slide and specimen imaging; Allan et al. 2018, Allan et al. 2019) and herbarium sheets. The rate and time taken to digitise specimens is influenced by a number of factors that include, among others, the level of preparation and post-processing required, imaging approach, the type of specimens as well as the complexity and condition of the collection. As part of this presentation we will include information on the rate, cost and time to digitise various NHM collections, illustrating how our processes have improved digitisation efficiency and allowed us to maintain quality. The programme has run a variety of digitisation projects, gathering data about rates of digitisation (preparation, imaging, transcription etc.) and developing improvements. Collection types such as microscope slides and herbarium sheets lend themselves to higher imaging rates, while other collections such as pinned insects, which require greater amounts of specimen handling to remove labels, tend to have lower imaging rates (Fig. 1). In order to increase efficiency, we have developed approaches that minimise specimen handling. For example, workflows for pinned insects such as the Angled Label Image Capture and Extraction (ALICE) do not require the removal of specimen labels from the pin as the system can capture angled images of the labels, thus increasing the imaging rate three-fold (Fig. 1). Another approach taken is to semi-automate mass digitisation using a combination of temporary and permanent Data Matrix barcode labels (Allan et al. 2019). By using multiple barcodes at the imaging stage to encode information associated with each specimen (i.e. unique identifier, location in the collection, taxonomic name, type status etc.; Fig. 2), we can run a series of automated processes, including file renaming, image processing and bulk import into the Museum’s collection management system. Through adaptation of our workflows with this new approach we have increased the efficiency of digitisation processes, illustrating how simple activities, like automated file renaming, reduces image post-processing time, minimises human error and can be applied across multiple collection types.

scholarly journals History of the publishing activity of the State Natural History Museum of the NAS of Ukraine

2019 ◽  
pp. 157-160
Author(s):  
O. Klymyshyn
Keyword(s):  
Natural History ◽  
The State ◽  
Natural History Museum ◽  
Museum Collections ◽  
History Museum ◽  
Book Series ◽  
Publishing Activity ◽  
History Of ◽  
Scientific Collections

The publishing activity of the museum for the whole period of its existence is analyzed, starting from the first published in the museum by V. Didushitsky in 1880 and up to 2018 inclusive. Approximately this work is about 3.5 thousand publications, among which 84 monographs; 35 issues of the scientific miscellany "Proceedings of the State Natural History Museum"; 5 issues of the book series "Scientific Collections of the State Natural History Museum"; more than 50 catalogs of museum collections, thematic miscellanies, qualifiers, dictionaries and guides; about 2.2 thousand scientific articles; about 1 thousand materials and abstracts of reports of scientific conferences, as well as dozens of popular scientific articles, brochures and booklets.

scholarly journals A contribution to knowledge on the terrestrial malacofauna of the Kastellorizo (Megisti) island group (SE Greece)

2019 ◽  
Vol 26 (1) ◽  
Author(s):  
Moisis Mylonas ◽  
Katerina Vardinoyannis ◽  
Nikos Poulakakis
Keyword(s):  
Natural History ◽  
Late Pleistocene ◽  
Natural History Museum ◽  
Snail Species ◽  
History Museum ◽  
Source Areas ◽  
Island Group ◽  
Scientific Collections

Abstract Background The Kastellorizo island group (in the Dodecanese, Greece) is situated in the southeast corner of the Aegean Archipelago. It consists of twenty islets, of which the three largest (Kastellorizo, Ro and Strongyli) and seven smaller ones belong to Greece. Knowledge of the malacofauna on the islands is relatively poor. Only eight species were known prior to the present study, all from the islet of Kastellorizo. Results Here, using the scientific collections at the Natural History Museum of Crete collected mainly by the authors and also by several researchers since 1976, we reappraise the malacofauna of the island group. Thirty-one species were found in total (23 from Kastellorizo, 19 from Ro, 15 from Strongyli, 10 from Agios Georgios, 14 from Agrielia, 6 from Psomi and 10 from Psoradia). Conclusions The fact that there are no endemic snail species in the islands can be accounted for by their proximity to the Turkish coast, their common paleogeography with Turkey until the Late Pleistocene and Holocene, and the influence of humans. All but two species, Mastus etuberculatus and Vitrea riedeliana, are known from the adjacent Turkish coasts. Together with the subfossil species found on the smaller islets, the predominance of different species on each islet suggests a continuous substitution from the source areas of Turkey and the Aegean.

scholarly journals Imaging natural history museum collections from the bottom up: 3D print technology facilitates imaging of fluid-stored arthropods with flatbed scanners

ZooKeys ◽  
2018 ◽  
Vol 795 ◽  
pp. 49-65 ◽  
Author(s):  
Patina K. Mendez ◽  
Sangyeon Lee ◽  
Chris E. Venter
Keyword(s):  
Image Quality ◽  
Natural History ◽  
Imaging Techniques ◽  
Natural History Museum ◽  
Laboratory Equipment ◽  
History Museum ◽  
3D Print ◽  
Natural History Collection ◽  
3D Printed ◽  
Microscope Slides

Availability of 3D-printed laboratory equipment holds promise to improve arthropod digitization efforts. A 3D-printed specimen scanning box was designed to image fluid-based arthropod collections using a consumer-grade flatbed scanner. The design was customized to accommodate double-width microscope slides and printed in both Polylactic Acid (PLA) and nylon (Polyamide). The workflow with two or three technicians imaged Trichoptera lots in batches of six scanning boxes. Individual images were cropped from batch imagess using an R script. PLA and nylon both performed similarly with no noticeable breakdown of the plastic; however, dyed nylon leeched color into the ethanol. The total time for handling, imaging, and cropping was ~8 minutes per vial, including returning material to vials and replacing ethanol. Image quality at 2400 dpi was the best and revealed several diagnostic structures valuable for partial identifications with higher utility if structures of the genitalia were captured; however, lower resolution scans may be adequate for natural history collection imaging. Image quality from this technique is similar to other natural history museum imaging techniques; yet, the scanning approach may have wider applications to morphometrics because of lack of distortion. The approach can also be applied to image vouchering for biomonitoring and other ecological studies.

E.E. Green’s collection of scale insects (Hemiptera: Sternorrhyncha: Coccomorpha) in The Natural History Museum, London, U.K.

Zootaxa ◽  
2017 ◽  
Vol 4318 (2) ◽  
pp. 201
Author(s):  
D.J. WILLIAMS
Keyword(s):  
Sri Lanka ◽  
Natural History ◽  
Developmental Stages ◽  
British Museum ◽  
Scale Insect ◽  
Natural History Museum ◽  
Scale Insects ◽  
History Museum ◽  
Authentic Material ◽  
Microscope Slides

In 1940, E.E. Green’s collection of scale insects, consisting of 6505 microscope slides and 2172 boxes of dry material, was donated to the The Natural History Museum, London, U.K. (then the British Museum (Natural History)). Green was a tea and coffee planter in Sri Lanka, and later became Government Agricultural Entomologist there before retiring to England in 1913. He continued to work on scale insects and became one of the foremost scale insect specialists at the time. His collection includes most of the species he described as new, but is also important because it contains authentic material sent to Green by other contemporary workers on scale insects.                         The collection is listed as it was when originally donated, firstly giving the names of species that Green recognised at the time, followed by the number of microscope slides, followed by numbers of developmental stages in the material; lastly is provided the current name of each species. The list is divided into the 31 extant families represented in Green’s collection. 

scholarly journals iCollections methodology: workflow, results and lessons learned

2017 ◽  
Vol 5 ◽  
Author(s):  
Vladimir Blagoderov ◽  
Malcolm Penn ◽  
Mike Sadka ◽  
Adrian Hine ◽  
Stephen Brooks ◽  
...  
Keyword(s):  
Natural History ◽  
Digital Image ◽  
Lessons Learned ◽  
Natural History Museum ◽  
Economic Aspects ◽  
British Isles ◽  
Pilot Projects ◽  
History Museum ◽  
Scientific Collections ◽  
Collection Date

The Natural History Museum, London (NHMUK) has embarked on an ambitious programme to digitise its collections. The first phase of this programme was to undertake a series of pilot projects to develop the workflows and infrastructure needed to support mass digitisation of very large scientific collections. This paper presents the results of one of the pilot projects – iCollections. This project digitised all the lepidopteran specimens usually considered as butterflies, 181,545 specimens representing 89 species from the British Isles and Ireland. The data digitised includes, species name, georeferenced location, collector and collection date - the what, where, who and when of specimen data. In addition, a digital image of each specimen was taken. A previous paper explained the way the data were obtained and the background to the collections that made up the project. The present paper describes the technical, logistical, and economic aspects of managing the project.

A description of Macrobiotus horningi sp. nov. and redescriptions of M. maculatus comb. nov. Iharos, 1973 and M. rawsoni Horning et al., 1978 (Tardigrada: Eutardigrada: Macrobiotidae: hufelandi group)

Zootaxa ◽  
2017 ◽  
Vol 4363 (1) ◽  
pp. 79 ◽  
Author(s):  
ŁUKASZ KACZMAREK ◽  
ŁUKASZ MICHALCZYK
Keyword(s):  
New Species ◽  
New Zealand ◽  
Natural History ◽  
Oral Cavity ◽  
Morphometric Traits ◽  
Morphometric Characters ◽  
History Museum ◽  
Hungarian Natural History Museum ◽  
Microscope Slides ◽  
One New Species

We examined microscope slides from Horning and Iharos tardigrade collections from Museum of New Zealand Te Papa Tongarewa in Wellington and Hungarian Natural History Museum in Budapest with species of the Macrobiotus hufelandi group. Based on this material we describe one new species, Macrobiotus horningi sp. nov., and re-describe two others, M. maculatus comb. nov. Iharos, 1973 and M. rawsoni Horning et al., 1978. With the oral cavity armature of the patagonicus type and chorion of the hufelandi type, Macrobiotus horningi sp. nov. is most similar to: M. personatus Biserov, 1990, M. sandrae Bertolani & Rebecchi, 1993, M. serratus Bertolani et al., 1996, M. sottilei Pilato et al., 2012, M. terminalis Bertolani & Rebecchi, 1993 and M. vladimiri Bertolani et al., 2011, but it differs from them in morphological and morphometric traits. With eggs of the maculatus type, M. maculatus comb. nov. is most similar to: M. biserovi Bertolani et al., 1996, M. denticulatus Dastych, 2002, M. macrocalix Bertolani & Rebecchi, 1993 and M. ramoli Dastych, 2005, but differs from them in morphological and morphometric characters. 

scholarly journals Redescription of the holotype of Finlaya lepchana Barraud, 1923 (Diptera: Culicidae: Aedini)

Zootaxa ◽  
2008 ◽  
Vol 1767 (1) ◽  
pp. 64
Author(s):  
JOHN F. REINERT
Keyword(s):  
Natural History ◽  
Male Genitalia ◽  
Original Description ◽  
White Paper ◽  
Microscope Slide ◽  
History Museum ◽  
Cover Slip ◽  
Plastic Stage ◽  
Paper Label ◽  
Holotype Male

Barraud (1923a) provided the original description of Finlaya lepchana and based it on the holotype male and two other males from India, Tindharia, Darjeeling Hills, which were reared from larvae collected from bamboo stumps in October 1922.  The description is brief and lacks many morphological details.  Therefore, the holotype male, deposited in the Natural History Museum (NHM), London, United Kingdom, is redescribed below.  The specimen is mounted on a minuten pin extending more or less vertically through the thorax between the mesal margins of the upper proepisterna and exiting the scutum anterior to the prescutellar area.  The lower part of the minuten pin is inserted in a rectangular, yellow, plastic stage which is attached near its margin to an insect pin.  Four labels are attached to the insect pin and include the following information:  Finlaya lepchana Barr., % TYPE (handwritten in black ink except TYPE is typed on a red, paper, triangular label); terminalia ON SLIDE (hand printed in black ink on a white, paper, rectangular label); India: Tindaria, Darjiling Hills, IX.1922, bamboos, Capt. P.J. Barraud, B.M. 1923-207 (partially handwritten and remainder typed in black ink on a white, paper, rectangular label); HOLO- TYPE (printed in black ink on a small, circular, white, paper label with red border).  The male genitalia, previously mounted on a microscope slide, have two labels as follow:  AЁDES (FINLAYA) LEPCHANA Barr., INDIA, TINDHARIA, DARJEELING Dist., x.1922, from Bamboos, Coll. P. J. BARRAUD, B.M. 1923-207 (hand printed in black ink on a rectangular, brown paper label attached to the left side of the slide); HOLO- TYPE (label printed on a small, circular, white paper label with red border attached to the left side of the slide).  The genitalia are mounted beneath a square cover slip and five psocids are embedded in the mounting medium on the margin of the cover slip.  The spelling of “Tindaria” and “Darjiling” on the adult label differs from that reported by Barraud (1923a).

scholarly journals iCollections methodology: workflow, results and lessons learned

2017 ◽  
Vol 5 ◽  
Author(s):  
Vladimir Blagoderov ◽  
Malcolm Penn ◽  
Mike Sadka ◽  
Adrian Hine ◽  
Stephen Brooks ◽  
...  
Keyword(s):  
Natural History ◽  
Digital Image ◽  
Lessons Learned ◽  
Natural History Museum ◽  
Economic Aspects ◽  
British Isles ◽  
Pilot Projects ◽  
History Museum ◽  
Scientific Collections ◽  
Collection Date

The Natural History Museum, London (NHMUK) has embarked on an ambitious programme to digitise its collections. The first phase of this programme was to undertake a series of pilot projects to develop the workflows and infrastructure needed to support mass digitisation of very large scientific collections. This paper presents the results of one of the pilot projects – iCollections. This project digitised all the lepidopteran specimens usually considered as butterflies, 181,545 specimens representing 89 species from the British Isles and Ireland. The data digitised includes, species name, georeferenced location, collector and collection date - the what, where, who and when of specimen data. In addition, a digital image of each specimen was taken. A previous paper explained the way the data were obtained and the background to the collections that made up the project. The present paper describes the technical, logistical, and economic aspects of managing the project.

Edward Heron-Allen FRS (1861–1943): a review of his scientific career, with an annotated bibliography of his foraminiferal publications

2004 ◽  
Vol 31 (1) ◽  
pp. 6-29 ◽  
Author(s):  
Richard L. Hodgkinson ◽  
John E. Whittaker
Keyword(s):  
Natural History ◽  
Royal Society ◽  
Annotated Bibliography ◽  
Natural History Museum ◽  
Scientific Career ◽  
History Museum ◽  
First Time

ABSTRACT: In spite of his many other interests, Edward Heron-Allen also worked for nearly 50 years as a scientist on minute shelled protists, called foraminifera, much of it in an unpaid, unofficial capacity at The Natural History Museum, London, and notably in collaboration with Arthur Earland. During this career he published more than 70 papers and obtained several fellowships, culminating in 1919 in his election to the Royal Society. Subsequently, he bequeathed his foraminiferal collections and fine library to the Museum, and both are housed today in a room named in his honour. In this paper, for the first time, an assessment of his scientific accomplishments is given, together with a full annotated bibliography of his publications held in the Heron-Allen Library. This is part of a project to produce a bibliography of his complete publications, recently initiated by the Heron-Allen Society.

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