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.
- The title of my talk
- Where my work has fit into the total SYNTHESYS project (WP = Work Package, Obj = Objective)
- 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!
- We have a huge variety of types of specimens, that all have their own unique photography challenges
- And we’ve got some unique specimen label challenges as well!
- 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.
- 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…
- …getting a giggle from the audience…
- 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!
- 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).
- 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.
- And this is what your volunteer effort has helped us to accomplish so far. YAY!
- These are the two expeditions that the Natural History Museum London has on Notes from Nature, both in Magnified
- 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! 🙂
- This is what your pattern of contribution has been looking like for the three batches of the MLM expedition.
- 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 🙂
- 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!!
- 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).
- 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.
- Two of our partners in the SYNTHESYS consortium also have an expedition on Notes from Nature, which I helped them put together and launch.
- 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.
- 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
- and this one.
- 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.
- Going back up to the other project
- The Primulacae from Kew Gardens are still not completed yet, and are similarly slow going.
- Once again we think that the wide variety of labels is one of the factors
- as well as a more complicated workflow that is trying to capture all of the possibilities
- And then the most recent Natural History Museum London expedition is the Fossil slides.
- 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!
- Here is how the MFM project is going so far
- 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.
- 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!
- 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).
- 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.
- 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!
- 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.
- 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!
- 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.
- 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 :).
- 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!
- 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.
- 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)
- 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.
- 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.
- 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’.
- I then had a moment for our audience to ask any questions.
- These are spare photos that I had ready in case anyone had questions about our efforts to digitise all of our collections.
- 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!
- 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).
- 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 firstname.lastname@example.org.
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
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.
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.
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.’
I’m sure that many of you around the world are as big a fan as we are of David Attenborough here in England, and we hope that the new series of Planet Earth is reaching you where you are as well. (If not, we do encourage you to buy the DVD the second it comes out!)
If you watched the first episode, then you will have learned of the plight of the red crabs native to Christmas Island, and how they are being decimated by an invasive species of ant.
Well, we’re pleased to tell you that this marvelous creature in the image below is coming to the rescue!
Have you heard the one about the wasp that kills the bug that feeds the ants that kill the crabs that keep the forests healthy on Christmas Island?
If not, that’s because it hasn’t happened yet, but it is a tale worth telling.
In the coming weeks, Parks Australia will release a 2mm wasp on Christmas Island to control the island’s yellow crazy ant infestation. Crazy ants are a big threat to the island’s wildlife, including its famous red crabs.
Biological control – when we use one species to control another – is infamous for giving Australia its cane toad invasion. So, how do we know this one will work?
Read more about how A Tiny Wasp Could Save Christmas Island’s Spectacular Red Crabs from Crazy Ants.
Here on Notes from Nature, we have an entire collection of these marvelous microscopic parasitoid wasps – containing much valuable information for researchers around the world, with many more potential ‘biological control’ applications yet to be uncovered.
Help us set that information free, in our Magnified expedition: The Killer Within: Wasps, but not as you know them.
There has been a flurry of activity at Notes from Nature these past few days, as a number of new Expeditions join us in the Plants section, and new sections for Aquatics and Fossils are launched, all in time for the 3-day WeDig Bio event that launched today!
Starting in Australia….
It all kicked off at the Australian Museum, where the DigiVol team gathered a group of volunteers to spend the day transcribing some fascinating specimens – check out their projects here: https://www.wedigbio.org/content/digivol. You can help out with these projects at any time, or if that’s your corner of the world, why not join them on Saturday for a great chance to hang-out with others interested in Biodiversity Collections around the world?
….over to Europe – live in London at the time of writing ….
As the planet turned, we were handed the baton here in London at the Natural History Museum, where we have a team of Visiteers joining us in our Specimen Preparation Area in the Cocoon, helping us to transcribe our ‘Killer Within’ chalcid slides. These tiny wasps are parasitoids, meaning they lay their eggs inside other insects.
When chalcid eggs hatch, the emerging larvae eat the inside of their host. They then grow and pupate until mature enough to burst out as adults, finally killing the host. These tiny creatures play a very important role as biological control agents – they are the natural enemy of a wide range of insect pests that damage our food crops, thus reducing the need for chemicals and pesticides, and saving a significant amount of money as well. You can join us too!
Primulaceae from Royal Botanic Gardens Kew
The tropical Primulaceae form a species-rich but poorly known group. Research at Kew aims to further understand the taxonomy, evolution and diversification of the family to mirror our understanding of the temperate Primulaceae. When thinking of Primulaceae, most of us will picture the spring flowers primroses and cowslips.
These are not only charismatic wild flowers but are also important in horticulture. Traditionally, Primulaceae contained only temperate herbaceous groups and whilst known to be very closely related to Myrsinaceae, was kept separate, primarily on account of Myrsinaceae being woody and tropical. However, based on a suite of similar morphological characters and more recent DNA evidence, all species of Myrsinaceae have been placed in Primulaceae. Come take a look!
Amaranthaceae from the Botanischer Garten Berlin
And just a short trip down to the European continent, we are joined by the Botanischer Garten und Botanisches Museum Berlin, and their newly launched Amaranthaceae Expedition in the Herbarium.
These plants represent the most species-rich lineage within the flowering plant order of Caryophyllales, and are economically important to study because they include vegetables such as spinach (Spinacia oleracea) or forms of beet (Beta vulgaris) (beetroot, chard), and ‘pseudocereals’ such as lamb’s quarters (Chenopodium berlandieri), quinoa (Chenopodium quinoa) and kañiwa (Chenopodium pallidicaule).
A number of species are popular garden ornamental plants, (such as Alternanthera, Amaranthus, Celosia, and Iresine), others are considered weeds (such as redroot pigweed (Amaranthus retroflexus) and alligatorweed (Alternanthera philoxeroides)), and many others cause pollen allergies.
Up Next: North America
Where will you visit? What projects will you join?
Now it’s your turn!
Your help transcribing these specimen labels will allow many more scientists around the world to study the mechanisms of their evolution and investigate biological diversity around the world.
It is essential to link information about organisms and specimens in the collections, to secure this data sustainably and to make it widely accessible and usable. You are helping us to make these collections accessible around the world, and this important information on biodiversity available to everyone.
Many of the Expeditions on Notes from Nature are taking part in the upcoming WeDig Bio event from the 20th to the 23rd of October. It’s all about digitising natural history collections around the world, and we’ll be hosting live events at our home institutions, as well as inviting others to join us online.
It will be a great opportunity to meet other natural history enthusiasts face-to-face (check out the event listing to find one near you), or engage with other volunteers online who will be helping us to transcribe specimen information to set the data free!
For members of the Notes from Nature community there will be plenty of your favourite projects to choose from, plus a number of new ones that are launching just for the occasion.
Miniature Lives Magnified from the Natural History Museum
The collection that the Natural History Museum is profiling as part of WeDigBio focuses on a group of wasps called chalcids (pronounced ‘kal-sids’). These tiny wasps are parasitoids, meaning they lay their eggs inside other insects. When chalcid eggs hatch, the emerging larvae eat the inside of their host. They then grow and pupate until mature enough to burst out as adults, finally killing the host.
These tiny creatures play a very important role as biological control agents – they are the natural enemy of a wide range of insect pests that damage our food crops, thus reducing the need for chemicals and pesticides, and saving a significant amount of money as well.
We have imaged 100,000 microscope slides of these tiny insects, barely visible to the naked eye. Now we need your help to transcribe information from the specimen labels so that the data can be used for scientific research.
This ‘Miniature Lives Magnified‘ project is part of our mission to mobilise the world’s natural history collections, and digitise the 80 million specimens we hold in our collection. at the Natural History Museum. We want to make the information the specimens contain about the natural world more openly available to scientists and the public – and you can help make this happen!
Other Notes from Nature projects taking part:
On Friday the 30th of September, from 16.00 – 22.00, the Natural History Museum in South Kensington London will be hosting our annual festival of science as part of European Researchers’ Night. The theme is Uncovering the hidden worlds of nature – from the depths of the oceans to planets beyond our own – and the Miniature Lives Magnified team at the museum will be showing off our Chalcids!
“Beyond our sight: using the latest technology, scientists can reveal the natural world in more detail than ever before. From bacteria to bioacoustics, learn how microscopic details are helping us understand our future challenges.”
The event is free to attend, and is a wonderful chance to discover rare items from the Museum’s collections, meet hundreds of experts, and take part in interactive science stations, debates and behind-the-scenes tours. You can find out more about the event on the Museum Website.
The team will have a range of slides from our Collection that are being used in our The Killer Within Expedition, which focuses on a group of wasps called chalcids (pronounced ‘cal-sids’). These tiny wasps are parasitoids, meaning they lay their eggs inside other insects. When chalcid eggs hatch the emerging larvae eat the inside of their host. They then grow and pupate until mature enough to burst out as adults, finally killing the host.
Almost invisible to the naked eye the insects in this project inhabit a little known world we rarely notice, but their lifestyles have a huge impact on nature and our human lives. Whilst some insects are vital for pollinating our crops or providing food to higher levels of the food chain, the insects in this project are terrors, either as pests causing destruction to our crop plants through their feeding, or as parasitoids killing these pest species by hatching out of their bodies.
By helping us to transcribe some of the 6286 microscope slides we have in the collection, you are making data and information available to scientists worldwide that can help address some of the key environmental issues we are facing right now, such as sustainable agriculture, the impacts of climate change, and how diseases affect wildlife and humans.
All data transcribed by the expedition will be made freely available for anyone to use on the Museum’s open Data Portal (http://data.nhm.ac.uk).
Come meet the Notes from Nature team at Science Uncovered in the Birds Gallery (Green Zone) of the Natural History Museum:
We always appreciate all the hard work spent transcribing records on Notes from Nature, and we want to celebrate your accomplishments. As you gain expertise on Notes from Nature, you earn badges that are added to your “Transcriber’s Life” page (if you have a Zooniverse account — its so easy to get one, and totally worth the 20 seconds it takes to have it).
When we launched Notes from Nature, we had badges for SERNEC and Calbug. Since some you might not know all the badges available, and since, right now, we only show three on each “collection page”, I wanted to walk you through them all, especially because we just added some new ones! In particular, we added one new badge for SERNEC and CalBug, and three new badges for our Macrofungi project.
Now you can earn a “mature tree badge” for 1000 records transcribed.
Here are the three original Calbug badges (egg, catepillar, and butterfly), earned when you transcribe 1,25, and 100 records.
Now you can also get the “butterfly swarm badge” when you transcribe 500 records.
And introducing the new Macrofungi badges (spore, mycelium, and mushroom) for transcribing 1,25,and 100 records! Sweet!
We hope you want to earn all 13. I guess we do like and need those badges, and we hope you do too.