Archive by Author | margaretgold

The Natural History Museum’s Digital Collections Programme

Crowdsourcing our data in 2017

The Digital Collections Programme at the Natural History Museum in London

The Digital Collections Programme has run two crowdsourcing projects on Notes from Nature in 2017. We wanted to say a massive thank-you to the 2,000+ volunteers who together have helped us to capture data from over 15,000 specimens this year. You have made a significant contribution to Science.

1) collage for blog

Crowdsourcing our data in 2017

We can digitally image individual microscope slides at a rate of up to 1000 slides per day, but we still need help with capturing the label information on each slide. Transcription is an essential part of our digitisation process.

By reading the labels and typing information such as the collection date and location into the relevant data fields, our digital volunteers make it possible for us to release this data freely and openly on the Museum’s Data Portal. This data is available worldwide for researchers to study and explore.

Over the past year we showcased our crowdsourcing projects at the Lyme Regis Fossil Festival, Science Uncovered 2017 and the global WeDigBio transcription event. We have also hosted 14 Visiteering Days, in which over 120 people took part. Anyone interested in taking part in our one-day Visiteering programme to support the Museum’s work can register online here.

The Killer Within: Wasps, but not as you know them

Fairy fly

Fairyflies average at only 0.5 to 1.0 mm long

Our first crowdsourcing project within the Digital Collections Programme consisted of 6,285 microscope slides containing tiny parasitoid wasps called chalcids (pronounced ‘kal-sids’), which lay their eggs inside other insects. Chalcids are the natural enemies of many insect pest species that damage our food crops, and are therefore used commercially as biological control agents.

Thanks to the help of over 1,300 digital volunteers for the Museum, the scientific information contained on these microscope slide labels have now been fully transcribed and are currently being processed for publication on the Data Portal.

From this data we learned that John S. Noyes, formerly of the Natural History Museum and developer of the Universal  Chalcidoidea Database, was our most active collector, that the majority of the specimens were collected in the 1980s and that the UK is the most prominently represented country in this collection.

Recently, we have been digitising the Museum’s parasitic louse slide collection – consisting of 70,667 slides at present. For each specimen, the whole slide has been imaged in to capture both the specimen and the labels.

From this collection we have isolated two subsets of louse specimens for two different crowdsourcing projects, each of which trialled a new platform for the transcription effort: lice from marsupial mammals – ‘Boopidae of Australasia’, hosted on DigiVol, and Lice of the Open Oceans, hosted on the Zooniverse.

 

Miniature Fossils Magnified: The smallest shells in the ocean

world oceans day

Foraminifera can help us learn how our ocean has changed over 500 million years

Our Miniature Fossils Magnified project features a collection of ~ 3,000 microscopic fossils, called foraminifera (or forams for short), embedded in slices of rock. The Museum has a strong tradition of foraminifera research dating back to the late 1800s, and the foraminifera collection – with approximately 250,000 slides – is one of the the most extensive in the world.

Foraminifera are microscopic single-celled organisms with shells (called tests), found in both modern and ancient marine environments. They either live on the sea bottom (benthic) or float in the upper water column (planktonic).

The 600+ digital volunteers have been helping to transcribe this label data so far and enabling research that can help us learn how our environment, climate and ocean have changed over 500 million years.

This project is almost complete, and with your help, we can start processing all of this data in the new year. As we process this data we look forward to sharing this data with you, and telling you of the scientific research that has thus been made possible.

If you have a few minutes to donate over the coming days, do join us on Notes from Nature to help finish off the Miniature Fossils Magnified Project. In the new year there will be new projects to join, and more outcomes to report.

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We’re preparing for WeDigBio – will you help us spread the word?

The Natural History Museum in London is pleased to be taking part in the upcoming WeDigBio global event again this year, from the 19th to the 22nd of October, and we hope that you’ll join us!

WeDigBio 2017 is all about digitising natural history collections to make them available to all to research and study, and participating Museums and Institutions around the world will be hosting live events  as well as inviting others to join us online.

The Natural History Museum will be hosting two Visiteer groups on the Thursday and Friday of WeDigBio to tackle Miniature Fossils Magnified. We’re going to aim to get this Expedition completed, so the more people you can invite to join us, the merrier!  You can follow our progress at @NHM_Digitise.

WeDigBio will be a great opportunity to meet other natural history enthusiasts around the world online, so be sure to follow the communications on @WeDigBio and #WeDigBio2017 to find out how to join the live video feeds during the day to connect with folks from Australia to Europe to North America.

The 3rd and final batch of Forams has launched

We’re thrilled to let you know that the Natural History Museum London launched the third and final batch of the Miniature Fossils Magnified expedition on Notes from Nature last week, although many of you have already discovered it, and the intrepid @PVerbeeck has already done one full sweep of the entire subject set!

At our annual European Researcher’s Night, which we dub Science Uncovered, we showcased the work of the Digital Collections Programme at one of the many tables showing off research that happens at the Museum, which you can see in this image to the left.

We had out our scanning equipment which we’ve been using to digitise our entire louse collection, which you can read about in more detail in this blog post on our Museum website.

As the theme for the night was Oceans, in keeping with our new blue whale display in the main hall and exhibition on wales, we also had a number of marine louse slides for folks to take a closer look at under the microscope.

We also invited folks to help us to process this newly digitised collection by typing in the collection date for each of the marine louse specimen records, using an interface that we developed especially for the night. They did a great job, and processed 129 classifications for us – a great result for a fun night out!

We may be asking for more help with this collection soon, so do keep your eyes peeled.

But in the meantime, a huge thank-you to all of you who are helping us to set our Foraminifera data free, the microscopic single-celled organisms that can tell us so much about the history of our oceans, going back 150 million years!

 

A brief summer break for the microscopic Foraminifera

A big thank-you to everyone who has helped us transcribe the first two batches of 2,071 foram slides. We are currently preparing the third and final batch, which will go live on Notes from Nature in September. Please share any suggestions with us on how we can improve the workflow and tutorials!

In the meantime, we thought you might like this piece on the Natural History Museum website about how much we can learn from these microscopic fossils:

Oceans under the microscope: mapping the future with fossils

http://www.nhm.ac.uk/discover/oceans-under-the-microscope.html

Coral fossils dating back to the Palaeozoic Era (about 541 to 252 million years ago). Different types of corals have thrived at different times in the past. Ancestors of living corals first appear in the fossil record about 245 million years ago, after a mass extinction at the end of the Permian Period (252 million years ago) wiped out all Palaeozoic corals.

What we’ve been learning thanks to your help and participation – a museum view.

This past month I seem to be in reporting mode, with a number of Conferences all lined up in a row. It’s been a great opportunity to meet many other scientists and researchers with Natural History collections and compare notes about our efforts to fully digitise those and get them online for anyone in the world to research or explore.

As we wait on the final few images in the Miniature Lives Magnified (MLM) expedition to be fully retired (don’t let that 100% complete fool you ), I thought it would be a nice moment to report back to you what we’ve been learning so far, thanks to your help!!

The slideshow below is the one that I presented to my SYNTHESYS consortium partners at a two-day meeting in the Natural History Museum to share all of our outcomes with each other. This is the source of my own funding up until this coming August, and all of us in the consortium have natural history collections that we have been digitising.

I always try not to put too many words on the slides themselves, so I’ve replicated my voice-over for you below, following the slides numerically.

(There is something going wrong with embedding that slideshow in the post here – so please open up the presentation in another tab, and read my notes below at the same time: https://www.slideshare.net/MobileMaggie/setting-collections-data-free-with-the-power-of-the-crowd-synthesys3 to open it.

  1. The title of my talk
  2. Where my work has fit into the total SYNTHESYS project (WP = Work Package, Obj = Objective)
  3. The context of my work here at the Natural History Museum London, it’s a pretty big collection, so a very ambitious project to digitise it all!
  4. We have a huge variety of types of specimens, that all have their own unique photography challenges
  5. And we’ve got some unique specimen label challenges as well!
  6. Not the least of which is, reading handwritten labels – and this is the main reason that we can’t use Optical Character Recognition software to let computers digitise it for us.
  7. Because of the scale of the challenge, we’ve been asking people’s help by donating some of their ‘down-time’ to transcribe these labels – that’s YOU! 🙂 Did you know that you were using your cognitive surplus? 😉  The reason I like this example of how many hours people have spent watching Gangnam Style on YouTube, is that time could have built Wikipedia a time and a half over again. This relates pretty closely to what we’re trying to do – we want to make the data in our collections available for anyone in the world online, and our even longer term goal is to link that to research, curators, scientists, etc…
  8. …getting a giggle from the audience…
  9. We started by scanning all of the things in our collection that are small and flat – because they are the easiest to start with – and that’s why you are seeing so many microscope slides from us!
  10. This is our Open Data Portal, where everything that you help us process will be published. I’m really looking forward to sending you a link to the final data there by the end of the summer (fingers crossed).
  11. As we get better at the scanning work, we’re starting to be able to handle large volumes. This is my colleague Louise, who is currently scanning our Louse collection, both imaging the microscope slides AND making lovely enlarged images of the specimen itself. We’re hoping that this might become an expedition, and it will be FAR more enjoyable to be able to see the specimens up close like that.
  12. And this is what your volunteer effort has helped us to accomplish so far. YAY!
  13. These are the two expeditions that the Natural History Museum London has on Notes from Nature, both in Magnified
  14. Introducing Notes from Nature to the SYNTHESYS audience, with thanks to NfN for their support in being able to use this great platform, and to be working closely with the NfN community – that’s YOU! 🙂
  15. This is what your pattern of contribution has been looking like for the three batches of the MLM expedition.
  16. Those big spikes are the days that we’ve had a group of volunteers in the Museum with us for the whole day on the expedition – it’s been wonderful to be able to give them face-to-face training and support, and once they get the hang of it, some of them have been stellar super-transcribers. This slide is our record holder day 🙂
  17. This is an event format that we call “Visiteering” because it is both volunteer work with us for the day, but also visiting the museum and meeting the curator. If you’re ever in London (yes, I’ve got your name on my list GH!!) please do tell me so that you can join one of these days!!
  18. Some of you are really super 🙂  – super-transcribers that have made a HUGE contribution as an individual – but the whole picture of lots of little contributions also absolutely adds up to something very valuable. (This is the data from our first batch of Chalcid slides).
  19. The first data that we got from the first batch showed us what we already new to a degree – telling the difference between the scientific name of the Chalcid specimen itself, and the host insect it had parasitised, and the host plant on which that was found – is pretty tough!! The errors we were finding were mostly related to that. But your transcription work isn’t lost in those cases – where it looks like a piece of data is in the wrong field, we’ll simply move it over to a catch-all notes section so that it is still fully searchable.
  20. Two of our partners in the SYNTHESYS consortium also have an expedition on Notes from Nature, which I helped them put together and launch.
  21. The Amaranthacae were still not done yet at that time, and they have been more slow going. They are completely transcribed now though – HUGE thanks! We look forward to sharing information with you about what that partner (The Botanisher Garten in Berlin) learns from the collection.
  22. We think (thanks to your comments in Talk and Chat), that this has been more difficult partially because there is such a wide range of label styles, such as this one
  23. and this one.
  24. And we (I) made the mistake of trying to capture all of the possibilities – which resulted in a pretty long workflow, that can be confusing.
  25. Going back up to the other project
  26. The Primulacae from Kew Gardens are still not completed yet, and are similarly slow going.
  27. Once again we think that the wide variety of labels is one of the factors
  28. as well as a more complicated workflow that is trying to capture all of the possibilities
  29. And then the most recent Natural History Museum London expedition is the Fossil slides.
  30. This is the display table that I had out at the Lyme Regis Fossil Festival where we launched that project. The pyramid is made out of the same sandstone that the real pyramids are built out of, and they contain Nummulites, a Formanifera fossil that is shown in the specimen beside it. On the smooth side of the pyramid you can see what these fossils look like as a ‘slice’ – which is how they appear on the Miniature Fossils Magnified (MFM) microscope slides!
  31. Here is how the MFM project is going so far
  32. There are a number of things I’ve been learning from your feedback in the Talk forums, and from the data you’ve been generating for us – such as Drop Down menus making the workflows much easier, and lowering the risk of error.
  33. And this is the latest project that I’ve helped a SYNTHESYS partner to launch – the Exploring Tropical Sweden expedition that was built directly onto the Zooniverse platform instead of Notes from Nature, because we were offering both an english and a swedish-language workflow for the local audience of Swedish Museum of Natural History fans. Luckily they needed less information from their labels, so the workflow is very easy!
  34. This project got a huge boost when it first launched, thanks to the communications from the Museum in Stockholm, and the Zooniverse community of testers for new projects built on Panoptes (the open project builder that we used to launch this).
  35. The Museum in Stockholm held an in-house Citizen Science day where they invited the public to take part in helping to transcribe their Brachiopod labels, and they really enjoyed speaking to volunteers like yourselves.
  36. Their Talk forums have been very active, and you can see a few peaks when a person really dove in and did lots of transcribing, and also had lots of interesting questions!
  37. So coming back to the context of the SYNTHESYS project, as this presentation is being given to my consortium partners (21 institutions from all over Europe, who all have natural history collections). In particular I wanted them to know that the value of the effort you’ve been making on our behalves is not just about the volume of transcriptions – there are all sort of other ‘non-quantifiable’ benefits of institutions doing projects like this together with the public.
  38. I shared an example of one of you lovely people who went diving into a thorough research of the web to discover the exact location of Wema Island (with apologies again from me for mis-reporting the country, after an in-house volunteer also did a deep search for this) – I know from the Talk forums that many of you have been enjoying finding out more and are really great detectives for these collections!
  39. I shared the example of our favourite ‘nature blogger’ in the Talk forums 🙂 sharing so many lovely observations of the plants and flowers in her immediate environment, and how she is encouraging others to share their observations as well.
  40. And I shared some of my own examples of a computer-room session I ran at my daughter’s primary school here in England, with a group of 10 and 11 year olds doing the Tiger Beetles. Through this project they learned the names of the provinces of Canada, which we wrote on the whiteboard along with their abbreviations. They learned what ‘altitude’ meant. We talked about why collectors write down all of this information on labels, and why it is important. They had great questions for me, such as ‘Are there any Tiger Beetles in England?’ – so we did some internet searching together. And these quotes are what they told me at the end :).
  41. There are sometimes some lovely little surprises in these collections. For example, some of the Brachiopod fossils in the Swedish Museum of Natural History collection were collected by the then King of Sweden!
  42. And although this example is from someone who works with collections in Ontario, and is not related to one of these projects, it does show that sometimes there is some quite poignant history captured in these collections as well.
  43. From our point of view at the Natural History Museum in London, providing more awareness of our collections behind the scenes is an important part of our public outreach. (That is our Chalcids curator Natalie showing our Visiteers her specimen work space, and some of the pinned Chalcids in her collection)
  44. This is the Data Portal where all of your hard work will be published, and made available for anyone in the world to research. As a Museum we hold these specimens in trust for the public. They don’t belong to us. And that is why it is so important that they are truly available to anyone – which includes folks without research & accommodation budgets to come and spend time physically studying our collections, as well as those who are just generally curious.
  45. We’ve been showcasing this data, via our Data Portal and the Application Programming Interface (API) through which you can access that data, to the developer community as well. This is a ‘Hack Day’ event that I ran with 200+ developers, where we invited them to explore our collections data and do interesting things with it.
  46. This is the team that won our Natural History Open Data Challenge‘, by creating a wonderful interface into our Bioaccoustica data, that allows you to listen to them ‘spatially’.
  47. I then had a moment for our audience to ask any questions.
  48. These are spare photos that I had ready in case anyone had questions about our efforts to digitise all of our collections.
  49. Here you see a contraption that one of my colleagues invented to hold an ancient folio of bound herbarium sheets open for photographing, in a way that won’t tear the pages or break the spine. He built it using LEGO Mechanics, with the cut-off fingers of surgical gloves on their tips to protect the pages!
  50. This is what the first photo looks like, using this method (on the left), and then with software we’re able to straighten that image out a bit better (on the right).
  51. And this is our set-up for photographing the pinned-insects, that not only need to be captured from more than one angle to study them properly, but also to capture the labels that are pinned underneath the insect itself.

And that’s a wrap 🙂 Do let me know if you have any questions!! You can contact me at any time at m.gold@nhm.ac.uk.

If you’re interested in finding out more about our digisitsation work at the Natural History Museum in London, you can read our own blog here: https://blog.nhm.ac.uk/tag/digital-collections-programme/, and you can find out more about the Digital Collections Programme itself here: http://www.nhm.ac.uk/our-science/our-work/digital-museum/digital-collections-programme.html

It’s clearly #FossilFriday at NfN, as the Trilobites are joined by Foraminifera!

A big thanks to everyone who helped us to classify our first test batch of  slides featuring rock slices with microscopic fossils in  Miniature Fossils Magnified. 

We are thrilled to be joining the Trilobites over in the Fossil section by bringing you a second batch of  Foraminifera in the Magnified section of Notes from Nature.

A few words from our Senior Curator of Micropalaeontology, Giles Miller, about the Larger Benthic Forams in this collection:

One of my curatorial predecessors Randolf Kirkpatrick (1863-1950) thought that larger benthic foraminifera (LBFs) were so important that he published a theory that they were vital to the formation of all rocks on earth. Our collection of LBFs has received relatively little attention over the 20 years I have been at the Museum, but recently it has been the most viewed part of the microfossil collection.

Some images of larger benthic foraminifera (LBF) taken by Antonino Briguglio, a recent SYNTHESYS-funded visitor to our collections. The images represent specimens roughly the size of a small fingerprint.

Traditionally LBFs have been difficult to study but new techniques, particularly CT scanning, are changing this perception. This post “The importance of being the largest microfossils” tells the story of Kirkpatrick and explains how the collection is currently being used for studies in stratigraphy, oil exploration, past climates and biodiversity hot spots.

Larger benthic foraminifera (LBF)

Larger benthic foraminifera are classified as microfossils because they were produced by a single celled organism, but they can reach a size of several centimetres. Their study is difficult because it usually relies on destructive techniques such as thin sectioning to make precise identifications.

My first line manager at the Museum Richard Hodgkinson was an expert at producing these thin sections. He described the technique of cutting the specimens exactly through the centre as an art rather than science.

Sadly there are very few people in the world skilled enough to make these sections, but thankfully the Museum collection is packed with LBF thin sections available for study.

Thank-you for helping to make this possible, by making all of the data in this collection available to research, along with the images of the specimens themselves.

Get Started Here

 

Miniature Fossils Magnified

Help scientists learn secrets of ancient seas

Today we drove down from the Natural History Museum in London to the jurassic coast of Dorset for the Lyme Regis Fossil Festival – where we are launching our latest crowdsourcing project – Miniature Fossils Magnified – just in time for #FossilFriday!!

The slides feature fossils of single-celled organisms called foraminifera, or forams for short, embedded in slices of rock.

Foraminifera are found in both modern and ancient marine environments and preserve well thanks to shells called tests.

The foraminifera specimens in the Miniature Fossils Magnified project lived in shallow tropical seas from 500 million years ago to the present day.

More than 2,000 microscope slides have been digitally imaged so far. Now the Museum needs as many people as possible to help transcribe the information on the specimen labels – such as the species name, location of where the sample material came from and its geological age – so that the data can be used for scientific research.

The project was set up by Dr Stephen Stukins and Dr Giles Miller, senior curators of micropalaeontology, and Science Community Coordinator Margaret Gold.

Dr Stukins says,

These fossilised organisms were very sensitive to their environment, so with this data we can better understand past conditions in the oceans and climate change through time.

‘All of this knowledge can be applied to what is happening now and in the future, giving us a better understanding of how our climate and oceans are changing.

Ocean organisms with a tale to tell

Foraminifera are among the most abundant shelled organisms in our oceans. A cubic centimetre of sediment may hold hundreds of living individuals, and many more shells.

Some forams spend their lives floating in the ocean. When they die, they sink to the seafloor and gradually become buried in sediment. Others – benthic foraminifera – live on or near the seafloor. The Miniature Fossils Magnified project features a collection of large benthic foraminifera.

Their sizes range from a few tens of microns in diameter – like a small grain of sand – to several centimetres across.

The material was collected during the mid-twentieth century as part of oil exploration in the Middle East. The scientists involved in dating rocks described many new foraminifera species and the slides were later given to the Museum due to their scientific value.

The data on the slide labels are invaluable. Analysing them can help us to understand how our climate and sea levels have changed, and also tell us the geological history of the area in which they were found.

A record of ancient environments

Foraminifera shells are often divided into chambers and can be quite elaborate, although simple open tube or hollow sphere forms exist.

Because of the abundance and variety of foraminifera, their fossils are extremely important for dating rocks.

They also provide a record of the environment where they’re found. Sea level and temperature changes affect the diversity and population sizes of foraminifera species, as well as the growth of individuals, impacting their size. Studying fossil foraminifera can therefore help scientists to understand past conditions.

Scientists can also study fossils from known periods of change to observe how foraminifera responded to particular climate and ocean conditions. If we then see similar changes to foraminfera living on tropical reefs in the future, this can help scientists to deduce how quickly the changes are happening and predict what may happen.

People-powered science

Dr Miller says,

‘The Museum collection of larger benthic foraminifera is one of the most significant in the world but is little used because much of it remains undigitised.

‘By helping to digitise this collection, you will keep it relevant for scientific studies long into the future.’

 

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