Journal archives for April 2019

April 05, 2019

Real-time Computer Vision predictions in Seek by iNaturalist version 2.0

On April 5, in conjunction with the release of the Our Planet series by Netflix, iNaturalist released a new version of Seek by iNaturalist. To heed David Attenborough’s call to action in Our Planet to protect biodiversity, we need to understand what’s here and what we might lose. Seek by iNaturalist unlocks curiosity about the natural world by giving speedy identifications with computer vision and challenging you to earn badges for finding species new-to-you.

How it works

When you open the Seek camera and point it at a living thing, the app immediately tells you what you’re looking at, even before you take a picture. This on-screen identification is tied to the tree of life, and guides you towards taking a more identifiable photo by getting more specific as you fill the frame and get the right angle or features. When the app narrows it down to species, it prompts you to take a picture, which earns you a badge and unlocks more information about the species. This “augmented reality” view of the world makes it easy to explore and interpret the natural world around you all while guiding you to take more identifiable photos.  Seek can’t always identify things to species (it’s still learning...), but it aims to provide the most precise correct name it can. Here’s some footage of it in action!

In Seek v1, which launched in March 2018 with support from HHMI Tangled Bank Studios, you needed to take a photo before you had a sense of whether or not it was even identifiable by Seek. This caused frustration when people repeatedly experienced the lack of a computer vision match. Now, since you can see predictions overlayed on the camera you get immediate feedback about what you see and the specificity with which Seek can identify it.

The species included in Seek are based entirely on photos and identifications made by the global iNaturalist community, so the Seek camera will work best in places where there is already an active community of iNaturalist users, and for species that are easily identified from photos. Seek also uses data submitted to iNaturalist to show suggestions for “species nearby,” but unlike iNaturalist, findings made with Seek will not be shared publicly, making it safe for children to use.

Seek is geared to encourage outdoor exploration of wild biodiversity (rather than pets, zoo animals, or garden plants). We hope kids, families, educators, and anyone into games will start exploring their natural surroundings with Seek, and we want this to inspire the next generation of biodiversity stewards by encouraging exploration and unlocking the names of species as a way to learn more about them. We want to make it easier for curious people who may not consider themselves naturalists to learn more about nature.

Innovations in computer vision came from research collaborations with Grant Van Horn, an Adjunct Scientist with iNaturalist. Van Horn’s dissertation research at CalTech, advised by Pietro Perona, made it possible to produce a refined dataset of iNaturalist observations, train the classification model, and export it for efficient inference on mobile devices. The computer vision model includes 15,798 species and 12,524 broader taxonomic groups (such as kingdom, phylum, class, order, family, and genus). The accuracy of predictions and breadth of species included will continue to improve as the iNaturalist community and dataset grows.

How to download it

Seek is freely available on both iOS and Android. Unlike the iNaturalist mobile apps which have separate code bases for iOS and Android, we used React Native for Seek, which is a relatively new technology that allowed us to build Seek for both Android and iOS with a single codebase. It’s still nascent — there’s not even a stable 1.0.0. release yet — but we liked the benefits:

  • Saves us time in development, since we’re only using one coding language.
  • Brings Seek to a wider, more varied audience, since we’re able to support 7,000+ devices on Android alone — this also allows for a more international audience, since Android tends to be more popular anywhere outside of North America, Australia, and western parts of Europe.

Seek is currently translated into 7 languages: English, Spanish, Hindi, Chinese, Portuguese, German, and French.

This major update to Seek was made possible with support from WWF and the Our Planet series on Netflix. Seek is created by iNaturalist, which is a joint initiative of the California Academy of Sciences and the National Geographic Society.

Posted on April 05, 2019 07:03 AM by tiwane tiwane | 69 comments

April 16, 2019

A Long-ago Butterfly in Thailand - Observation of the Week, 4/15/19

Our Observation of the Week is this Long-banded Silverline butterfly, seen in Thailand by @lesday!

If not for “a very nasty motorcycle accident” a few months ago, it’s possible the photo you see above would not have been posted on iNaturalist. But we’ll get there. Let’s go back more than five decades, when Les Day was a child in Britain and he collected “a small british moth, called the Brimstone, in a bucket at home.” With the help of his parents, “who often drove me out into the countryside, to look for insects,” Les eventually focused on butterflies, which “continued to be the main object of my curiosity.”

Fast forward to 2007, when he emigrated Thailand’s Ko Samui island in 2007, and Les continued to concentrate on butterflies, including the male Long-banded Silverline butterfly that is the subject of this post. “It is not uncommon on Koh Samui, but usually it is found with wings closed,” he says. “The opportunity to photo the upper side of the species, particularly the more flamboyant male, does not come that often.” Members of the family Lycaenidae, or gossamer-winged butterflies, the underside of its wings are not too shabby either - a real stunner. It is thought that the eye spots near the antenna-like projections of its hindwings act as a “false head”, causing predators such as birds to attack the insect there rather than its actual noggin.

After finding most of the butterflies that resided on Ko Samui, Les “needed something else to occupy me during my daily walks in the hills away from the tourist areas.” After doing some research he realized that the Hemiptera of Thailand were not well known so he decided to shift his focus from butterflies to bugs - specifically Cercopoidea (froghoppers), which “seemed very interesting and in much need of study.”

Which leads us to iNaturalist and that motorcycle crash.

“I started using INaturalist a couple of years ago on the advice of a friend, but I only posted a few moth photos then,” says Les (above). And I will let him tell the story from here.

It took a very nasty motorcycle accident on the Thai peninsular mainland a couple of months ago for me to re-evaluate the importance of my photos. I had already been advised by researcher friends at various museums and universities around the world that many of my hemipteran photos were species new to Thailand and furthermore, there were quite a few totally undescribed species as well. Whilst stuck at home, unable to go out in the field, I realised that these photos would be lost if anything more serious should happen to me, as they were kept on my hard-drive and on my personal website, both of which would be lost after a year or so. I needed to find somewhere where they would remain available to researchers and the general public and iNaturalist came to mind, so, since I have been holed up at home recovering, I have been placing nearly all my photos on iNaturalist. I have been fortunate that some new identifications have been forthcoming from informed identifiers for which I am very grateful.

I have nearly finished posting my old photos, just about 1500 butterfly species and subspecies left from around S.E.Asia. Once finished, it will be easy to update daily findings when I am finally able to go out into the field again.

- by Tony Iwane.

- The larvae of Long-banded Silverlines are associated with ants, as seen in this video. Check out its reaction when an ant gets too close to its posterior!

- The photo of Les is was taken by Johnny Patterson, for this article.

Posted on April 16, 2019 04:36 AM by tiwane tiwane | 9 comments | Leave a comment

April 21, 2019

A Mass Emergence of Cottonmouths - Observation of the Week, 4/21/19

Our Observation of the Week is this large group of Cottonmouths, seen in the United States by @wildlandblogger!

A few weeks go, while on a hike in a central part of North America, looking for birds and plants Jared Gorrell had gotten a bit lost but was able to use his phone’s GPS to navigate back to his car. However, something caught his eye. “I noticed a pond along the way and decided to look around it and see if I could find some birds, insects or plants that would be new for me,” he recalls.

I didn’t realize the pond had dirt cliffs around it, and as I walked downslope I nearly stumbled over the edge of one of these, and then I looked down into that pile of cottonmouths. I backed up and sat down, and then proceeded to put my hand down six inches from a juvenile cottonmouth. After moving it out of the way with a long stick and then going uphill to have a slight panic attack over the close call, I came back down to take pictures and count.

You definitely don’t want to get bitten by a cottonmouth, which is a viper endemic to the United States. While fatalities are rare, this species’ cytotoxic venom can cause severe tissue damage and pain. Although it has a fierce reputation, this snake (like most others) is not aggressive (PDF) and will choose to either escape or engage in threat displays when encountering a human. One of those displays involves showing off the bright white interior of its mouth, giving the species its common name (although it’s also known as a water moccasin, as well). These semi-aquatic snakes eat a wide variety of prey and are often found near water sources, although usually not in such large numbers.

“What you see in the photo is a pile of sunning cottonmouths that have recently emerged from a den site, presumably someplace on a nearby hill,” says Jared.

In this temperate area, snakes form groups like this in sunny spots to warm up more quickly, after leaving a cool underground refuge where they spent the previous winter. Unfortunately, many of these “mass emergences” have been targeted by locals afraid of venomous snakes, so this “ball of cottonmouths” is a rare sighting nowadays, and I’ve intentionally kept the location private for that reason...since poaching and/or harassment are serious issues for reptiles like these cottonmouths, I generally obscure or privatize my herp locations.

Jared, who tells me “at three years old I spoke vaguely with an Australian accent because I watched Steve Irwin, the Crocodile Hunter, so often,” will soon be graduating from Southern Illinois University - Carbondale with a degree in plant biology specializing in ecology, and this summer plans on “working with the Critical Trends Assessment Program in Illinois surveying plants and insects at various field sites across the state.”

And during his free time, Jared’s out and about looking for plants, birds, reptiles and amphibians, and has “recently developed an interest in dipnetting for fish and netting for dragonflies and butterflies.” He uses iNat to “log all of my sightings, compete with friends, and share my observations with those around me. iNaturalist has inspired my interest in dragonflies, butterflies and fish, especially fish since they’re so under-reported on this website. I definitely take a lot more pictures now too!”

- by Tony Iwane

- Bird and Moon has a great comic about the myths and facts surrounding cottonmouth snakes.

- Here’s thorough advice on how to survive a snakebite in the wilderness. (Disclosure: I previously worked with Jordan Benjamin, founder of The Asclepius Snakebite Foundation)

- Water snakes of the genus Nerodia are often mistaken for cottonmouths. The University of Florida has a nice resource showing you how to differentiate them.

Posted on April 21, 2019 11:23 PM by tiwane tiwane | 18 comments | Leave a comment

April 23, 2019

Tips and tricks for welcoming & helping new users

The short version: You can use these links to filter for observations made by users who created their accounts in the last day or last week. Uncheck “verifiable” in filters to see even more observations that could use additional guidance. Bookmark these links to verifiable observations in the identify tool needing identification from new users in the last day or week. For dealing with common observation issues, you can copy/paste from these frequently used responses.

From the iNaturalist Stats page

We’re in the April bump! April tends to have several factors driving people to iNaturalist:
-Northern Hemisphere spring
-Earth Day/month activities, press, and promotion (e.g. there was a big media promotion in the UK last week)
-City Nature Challenge happening in 160+ cities around the world April 26-29

With all the new users, it helps to have more experienced members of the community as welcoming guides to help people correct common observation and identification mistakes and improve the likelihood that their future observations will be identifiable by the community. No one can do this task alone, but if we each take a few minutes to help a few people, then together we help steer new people in the right direction.

You can add additional query parameters such as &user_after=1d to a url to only see observations from users who created their accounts in the last day.
E.g. Observations from users who joined:
In the last 2 days (&user_after=2d)
In the last 1 week (&user_after=1w)
More than 1 month ago (&user_before=1m) (if you don’t have the patience to work with brand new users at the moment!)

Want to filter just for observations made from a mobile app? Add &oauth_application_id=2 for Android and &oauth_application_id=3 for iOS.
E.g. iOS observations from users who joined in the last 2 days
Android observations from users who joined in the last week

There are even more tips from @bouteloua posted in the Forum on dealing with low quality and inappropriate content on iNaturalist.

If welcoming new users isn’t your thing and you’d rather just focus strictly on identifications, that’s great too! We know there are hundreds of you who are extremely dedicated identifiers with thousands of identifications and 70K+ people have chipped in. iNaturalist works because of many people doing good things to help each other, so thanks for everything and anything that you’re doing to help.

-by Carrie Seltzer

Posted on April 23, 2019 01:05 PM by carrieseltzer carrieseltzer | 16 comments | Leave a comment

April 25, 2019

City Nature Challenge 2019 begins in 150+ cities around the world!

Guest post by City Nature Challenge co-organizers Lila Higgins (@lhiggins) from the Natural History Museum of Los Angeles County and Alison Young (@kestrel) from the California Academy of Sciences

It’s early morning in Los Angeles and San Francisco, where the City Nature Challenge began in 2016, but it’s midnight in Christchurch, New Zealand where the first city begins the challenge this year on Friday, April 26. From now until 11:59 pm in Maui, Hawaii on Monday, April 29, people will be out in almost 160 cities documenting their local biodiversity.

Observations must be made between April 26 and 29, but can still be uploaded and identified until 9 am local time on Monday, May 6. The final tally from each project will be recorded at that time with the complete results announced later on Monday, May 6 after the tally is made in Maui. During the challenge and beyond, you can watch the dynamic leaderboard on the City Nature Challenge umbrella project to see how the cities rank and easily click through to individual city projects.

If you want to read more about the origin and past results of the City Nature Challenge, check out:
-Last year’s blog post
-The official City Nature Challenge website
-City Nature Challenge projects from 2016, 2017, and 2018.

If your city is part of the challenge this year - good luck and have a great time! Even if your city is not participating in this year’s challenge, we hope you have a chance to get outside and document your own local nature as part of this global event celebrating biodiversity in and around urban areas. The more we know about biodiversity in cities, the better we can plan for cities of the future that work for humans and wildlife. And if you’re interested in organizing the City Nature Challenge in your city in 2020, please sign up here.

Posted on April 25, 2019 12:01 PM by carrieseltzer carrieseltzer | 1 comment | Leave a comment