Archive by Author | mwdenslow

Consortium of California Herbaria on NfN

California has the most diverse native flora of any state in the United States, containing more than 1/3 of all U.S. plant species. Over 7,400 plant species, subspecies, or varieties occur in this state, and 2,331 (32%) of these are endemic. The California Phenology Thematic Collections Network (CAP TCN) was established in August 2018—thanks to funding from the National Science Foundation—to better understand this diverse and beautiful flora and how it will be affected by anthropogenic change. This network of 22 California herbaria aims to fully digitize (image, transcribe, and georeference) nearly 1 million specimens over four years and capture reproductive data (i.e., phenology) from specimen images.

Many herbaria in this project have transcribed herbarium specimen data in the past in collaboration with the Consortium of California Herbaria; however, there are still many specimens for which there are no associated data. Moreover, the majority of herbaria in this project have never before imaged their specimens. The CAP TCN provides an exciting opportunity to discover specimens previously locked away in cabinets and make these data publically available for research, education, and other uses. Data and images are being produced daily and can be found on the project portal: cch2.org.

You can help make this possible by participating in our California Phenology Notes from Nature expeditions. Our first several expeditions will be label transcription projects like many other great projects on Notes from Nature. In later expeditions, we will introduce scoring reproductive structures on herbarium sheets. Determining the phenology (timing of reproductive events) of these plants is crucial for understanding biotic change in this biodiversity hotspot.

For more information and updates on the project, visit the CAP TCN website at capturingcaliforniasflowers.org, follow the project on Twitter (@CalPhenologyTCN), or contact the project manager, Katie Pearson at kdpearso@calpoly.edu.

The California Phenology Thematic Collections Network is composed of the following herbaria: CSU Chico (CHSC), CSU Los Angeles (CSLA), UC Davis (DAV), CSU Fresno (FSC), CSU Humboldt (HSC), UC Irvine (IRVC), UC Los Angeles (LA), CSU Long Beach (LOB), CSU Fullerton (MACF), California Polytechnic State University, San Luis Obispo (OBI), Rancho Santa Ana Botanic Garden (RSA), CSU San Bernardino (CSUSB), Colorado Desert District, California Dept. of Parks and Recreation (BSCA), Santa Barbara Botanic Garden (SBBG), San Diego Natural History Museum (SD), San Diego State University (SDSU), CSU Northridge (SFV), San Jose State University (SJSU), UC Berkeley (UC/JEPS), UC Santa Cruz (UCSC), UC Santa Barbara (UCSB), and UC Riverside (UCR). Acronyms follow Index Herbariorum.

Katelin Pearson, Project Manager, California Phenology Thematic Collections Network

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Arctic Oeneis 1 – Preliminary results

We are thrilled to report that first expedition of the Triplehorn Insect Collection with Notes from Nature was completed and it was a success! Ninety nine explorers joined us to transcribe data from 1,443 specimens in three species and 5 subspecies. The records are now in our online database and fully available to anyone interested.

Data from dry insect specimens are challenging to transcribe. Labels are small, often handwritten, and sometimes the collector’s handwriting is downright impossible to decipher. Collecting locality information is frequently abbreviated in cryptic ways, date formats may vary dramatically, and, to add insult to injury, labels frequently contain misspellings and typos. It is not uncommon to come across labels that contain only a number, say “3456”. The older the specimen the more acute the problems and the more complicated the task of transcription becomes.

Despite of these obstacles, the overall quality of the data transcribed by Notes from Nature volunteers was very good.

Here are a few cool facts about the first expedition of Arctic Oeneis. About 65% of the specimens were from Canada and 30% from the USA. The remaining 5% of the specimens were from other countries or had no label data.

There were 152 collecting localities, some very similar, but with different elevations or a different mile marker (example, localities along Dempster Highway.)

Locality farthest north: 69.1597°N Sheep Creek & Firth River, British Mts., YT, Canada (Oeneis alpina excubitor, OSUC 727955)

Locality farthest south: 33.9078°N Crescent Lake, Apache Co., AZ (Oeneis alberta, OSUC 722232, 722235, 722245, 722248, 722252)

Locality farthest west: 149.5303°W Anchorage, Anchorage Muni., AK, (Oeneis bore hanburyi, OSUC 735514)

Locality farthest east: Mont Albert tableland, 3500ft+, Gaspé Peninsula, QC, Canada (all 65 Oeneis bore gaspeensis)

We’re now kicking off our second expedition, featuring three species and 10 subspecies of Arctic Oeneis, and we would be delighted if you’d come along with us. We can’t wait to see what other interesting facts we’ll uncover.

As part of the Arctic Oeneis digitization project we have already photographed over 4,300 specimens with their respective labels. We expect to complete the photography part of the project this spring.

Thank you, volunteers! Now to the next expedition!

— Luciana Musetti, Curator, Triplehorn Insect Collection

We Have A New Field Book!

We are excited to announce our new Field Book! Here are some of the key improvements with the Field Book: 1) We now have specialized reporting of your effort over time. 2) We have compiled information about your “recent” and “favorite” classifications and transcriptions onto the Field Book; 3) We have revamped our badging system. This includes some new badges and shows you progress as you work towards your remaining badges. Some new badges include a “decade” badges you can earn for transcribing a number of records that were collected during a particular decade. We also have badges for working at specific times of day such as the Night Owl badge.

In addition to new features, this is also part of our process to transition to an updated Zooniverse platform over the coming months. For this reason you may notice some differences in they way badge counts are calculated at launch time. This is mostly between group badges (e.g., Herbarium) and level badges (numbers of classifications). Nevertheless, we very excited about the new badges available and those still to come in this new framework going forward.

Take a look at the new Field Book and let us know what you think. We’ll also start a thread on Talk where you can report any issue you see or ask question.

— The Notes from Nature Team

What a great week and a special thanks

Last week was just fantastic. We saw some great activity on Notes from Nature and reached 1,000,000 transcriptions again! Thanks to all that contributed and continue to contribute!

Our millionth transcription was done by user acorlett54! The image was a beautiful specimen of Valerianella ozarkana (Benjamin Franklin bush) from Washington County, Arkansas, U.S.A. A special thanks to acorlett54 again for helping us reach this wonderful milestone.

— The Notes from Nature Team

Thanks a million (again)!

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Artwork by Hannah Mathews (@hcmatthews on NfN Talk)

 

Well, you’ve done it again. Notes from Nature 2.0 just reached 1 MILLION, so let’s celebrate. It took about 994 days, which is around 1,000 classifications/transcriptions a day. We’ve had so many wonderful milestones along the way such as online and onsite events, transcription challenges and lots of lots of engaging research questions. Not to mention the many wonderful interactions with our amazing volunteers. We could never have imagined the community that would coalesced around this project. It would literally be nothing without all of you!

You can even review the over 175 expeditions that we have completed since starting Notes from Nature 2.0. We transitioned from Notes from Nature 1.0 with about 1,011,400 transcriptions, so this puts us well over 2 million for the entire project!

As always the site has lots of content to engage with and always plenty of herbarium specimens to transcribe. We have been particularly excited about our Labs, which currently feature 3 different phenology projects.

With gratitude,

The Notes from Nature Team

Who will it be?!

As some have already noticed we are very close to a very big milestone! We are about 2,000 classification away from reaching 1 MILLION on Notes from Nature 2.0. Yes, we have reached 1 million before, but we are even more thrilled this time around.

There is so much great activity on Notes from Nature and we continue to plan for an exciting future. We have 20+ expeditions with a wide variety of content at the site right now. There are a number of school projects going on as well as specific research question being addressed. On top of all that we engage with potential new collaborators on a daily basis!

With all that said, the question on our minds right now is who will make the 1 million classification? Please consider spending a few extra minutes on the site the next few days to help us celebrate all of the wonderful effort.  And maybe you will be the one to take that 1 millionth classification!

— The Notes from Nature Team

Training the Machines I

Artificial intelligence. Machine learning. I’m sure you’ve heard these buzzwords; they’re all the rage in technology lately. As it turns out, they are all the rage in biodiversity informatics too. The newest Notes from Nature expedition for plant specimens from the genus Prunus – which includes many plants you’re familiar with like cherries, almonds, and peaches – is part of a larger project on machine learning led by scientists at the Florida Museum of Natural History. Over the past year, we have scored thousands of images of digitized herbarium specimens from the genera Prunus and Acer for different character states – the presence of fruits, flowers, and unfolded leaves. We used these manually scored images to train and test a machine learning algorithm to see how well it is able to identify these characters on its own.

To get a better idea of whether or not our machine learning algorithm performs better than a human given the task of scoring these images, we recruited volunteers to score images of Prunus and Acer herbarium specimens using our criteria. On average, the volunteers were able to properly identify flowers, fruits, and unfolded leaves more than 95% of the time. That is pretty good! This led us to wonder if scoring by citizen scientists could create a training set comparable to the training set we made by spending hours poring over thousands of specimen images.

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A flowering Prunus virginiana specimen from the University of Wisconsin Madison herbarium.

If this effort proves to be a success, crowdsourcing could be a great way to coordinate efforts to expand the possibilities of machine learning to new groups of plants! This could expand datasets about plant phenology – the study of the timing of life cycle changes in plants – at a more rapid pace than is possible right now. The phenology of plants is known to be closely linked to environmental conditions that plants experience. As the Earth’s climate changes in new ways, the impact of these changes may affect species of plants differently, depending on the areas where they are found and the different characteristics of the species. In order to fully understand the changes plant phenology is undergoing due to current climate change, though, we need a stronger understanding of plant phenology in the past. Herbarium specimens inherently carry phenological information, but it is not easily accessible in a usable format for researchers. Help us learn more about plant phenology and machine learning methods by participating in this Prunus phenology expedition!

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If you are unsure what criteria we are using to determine scoring for flowers, fruits, or unfolded leaves, click on the “need some help with this task?” (outlined here in red) link to view the volunteer handbook.

For Notes From Nature volunteers who have participated in plant phenology expeditions in the past, it is important to note that our criteria for scoring the presence of flowers, fruits, or unfolded leaves may differ from previous expeditions. We encourage all volunteers for this expedition to view the help materials for these scorings by clicking the “need more help with this task?” link on the scoring page. This will undoubtedly help you make more accurate decisions! Also, you may come across some specimens where it is very hard to tell whether a specific trait is present or absent. Don’t stress, and just make your best possible guess! Happy scoring!

Laura Brenskelle (naturalista), University of Florida

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