To celebrate Citizen Science Day 2019, which is this coming Saturday 13th April, a different member of the Zooniverse team will be posting each day this week to share with you some of our all-time favourite Zooniverse projects. Watch this space!

In this week’s edition of our Who’s who in the Zoo series meet one of our Chicago based developers, Will Granger

– Helen

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Name: Will Granger

Location: Adler Planetarium, Chicago, IL, USA

 

 

 

Tell us about your role within the team:

I’ve been with the Zooniverse team since Spring 2016 when I started as a Web Developer. Since then, I’ve expanded my roles a bit helping out with mobile development, when needed. Currently, my main project is working on a touch table application for Galaxy Zoo which should be at the Adler Planetarium Summer 2019.

 

What did you do in your life before the Zooniverse?

I’ve led many lives before joining the Zooniverse; however, my main occupation was teaching. I taught in various K – 12 schools in Alabama with non-profits and as a substitute teacher. I also spent a couple years overseas with the Peace Corps teaching at a university in Ukraine. Intermittently, I also spent some time opening a music venue in Alabama and touring in various bands.

 

What does your typical working day involve?

My typical working day involves keeping my eye on several code bases while also trying to develop the touch table application. Usually, I’ll spend part of the day doing maintenance on custom projects and the main Zooniverse page before checking on any mobile updates that need review. After that, I’ll continue building out the touch table, adding new features weekly.

 

How would you describe the Zooniverse in one sentence?

The Zooniverse is always expanding.

 

Tell us about the first Zooniverse project you were involved with

The first Zooniverse project I worked on was Astronomy Rewind. My task was to create a sort of astronomical calculator to take coordinates of celestial objects (RA, DEC, etc.) and put those into the World Wide Telescope API to see how images and charts from astronomical journals would appear in space. This was my first task as a web developer, and I was constantly under the impression that every change I made would break the Zooniverse. In the end, my work succeeded and I looked back with satisfaction that I was able to convert once-intimidating Astrometry calculations into code.

 

Of all the discoveries made possible by the Zooniverse, which for you has been the most notable?

It’s difficult to choose one, but I’d say the discovery of a new exoplanet system during Stargazing Live in 2017 was the most exciting for me. Our team spent the prior month or so preparing for a spike of people visiting the site, and it was rewarding to see our work pay off, especially as the volunteer who made the discovery was interview on the BBC program.

 

What’s been your most memorable Zooniverse experience?

The first Zooniverse Team Meeting I attended was memorable. Our team is more or less separated between Chicago, Minneapolis, and Oxford, and we have the opportunity to meet together once a year. It was nice to meet everyone in person I had been working with since I started at the Zooniverse, especially since we were able to spend time after work hours getting to know each other in Chicago.

 

What are your top three citizen science projects? 

Anti-Slavery Manuscripts: This project is important to me because it was one of the first projects I took a lead on, and we did several new things with the Zooniverse, such as saving classifications in progress to return to later.

Galaxy Zoo: The longest running project on the Zooniverse deserves a mention, and I’m glad to be a part of the transition of this project to a touch table.

Snapshot Serengeti: Any camera trap project deserves a mention here, but it’s exciting to see what animal(s) will show up on an image.

 

What advice would you give to a researcher considering creating a Zooniverse project?

Taking a look at several active projects is a good first step. It’s good to have some ideas on how to setup a project if you’re more familiar with the breadth of projects available on the Zooniverse. Next, I’d play around with the project builder, even create a few test projects to make sure you know how those tools can be used. Once your familiar with that, I think a team should be in a good place to start implementing a project.

 

How can someone who’s never contributed to a citizen science project get started?

I’d recommend downloading the Zooniverse app and finding a swipe workflow to work on. These projects are easy to get into an would open the door to other projects we have on the Zooniverse. iNaturalist is also another citizen-science project worth checking out with an app available for download.

 

Where do you hope citizen science and the Zooniverse will be in 10 years time?

I hope we are able to grow in ways beyond our online presence. We have already started doing this with the mobile app and touch table, but I’m curious how this will continue developing in the future as technology advances. I would also like to see the Zooniverse partner with more institutions. We have projects with some Chicago-area museums, but it would be great to see the Zoooniverse in museums around the globe.

 

Is there anything in the Zooniverse pipeline that you’re particularly excited about?

I’m excited to see how the Zooniverse will partner with new telescopes being sent to space. In the next several years, there will be many advancements in data collection for such telescopes, and I think the Zooniverse can help researchers in their data collection.

 

When not at work, where are we most likely to find you?

I’m often at a show somewhere in Chicago. It’s great to live in such a large city where bands on tour make it a point to play a show. It’s always great to head out and see artists from bucket-list bands to friends coming through.

 

Do you have any party tricks or hidden talents?

I used to speak Russian fluently from living in Ukraine, but my skills are now a bit rusty. Writing people’s names in Cyrillic is always a crowd-pleaser.

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In this week’s edition of our Who’s who in the Zoo series meet Becky Rother, who is visual design lead here at the Zooniverse.

– Helen

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Name: Becky Rother

Location: Adler Planetarium, Chicago, IL

 

 

 

Tell us about your role within the team: 

I’ve been the Zooniverse designer for a little over a year. In this role, I design custom projects like Scribes of the Cairo Geniza in addition to general Zooniverse.org and public-facing design needs. I also help organize public Zooniverse events here at the Adler Planetarium.

 

What did you do in your life before the Zooniverse?

I actually have a degree in Journalism, and have worked in various roles from newspaper page designer to mobile app designer.

 

What does your typical working day involve?

Being on the US team, there’s usually some catch up to be done from our UK colleagues involving reviewing an implemented design or answering questions on our Slack channel. Besides that, every day is different! I may design a giant banner one day, then the next work on wireframes for a new project we’re just getting started.

 

How would you describe the Zooniverse in one sentence?

Zooniverse is an exceptional group of people working together to positively effect science and the humanities.

 

Tell us about the first Zooniverse project you were involved with

The first custom project I worked on was the Anti-Slavery Manuscripts, a collaborative transcription project in partnership with the Boston Public Library. It’s a really special project for a number of reasons, and a great introduction to the Zooniverse community.

 

What are your top three citizen science projects?

I’m obsessed with our camera trap projects – Chicago Wildlife Watch in particular. It’s SO COOL to get to see actual animals in their native habitats. I also really enjoy Gravity Spy – as a non-astronomer, it’s neat to be able to help scientists study gravitational waves. Lastly, I may be biased but I really enjoy Anti-Slavery Manuscripts. Reading these first-hand accounts from people actually involved in the abolitionist movement during the Civil War really brings history to life.

 

When not at work, where are we most likely to find you?

Chicago has so many great music venues, so I love taking advantage of that and going to indie rock shows. I also love travel and will take any opportunity to explore somewhere new.

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Below is a guest post from Dr Philip Fowler, who leads our award-winning bug-squishing project BashTheBug. This project aims to improve the diagnosis and treatment of tuberculosis, which remains one of the leading causes of death worldwide.

This project has a huge amount of data to get through, so Phil is working hard to make sure this is being done in the most efficient way possible. Read on to find out more. 

– Helen

 

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Focussing effort where it is needed: picking out the Bugs that are harder to Bash

 

BashTheBug has been running for a little over a year now and in that time 11,303 volunteers have classified 834,032 images of the bacterium that causes tuberculosis growing on 14 antibiotics at different strengths. These images correspond to a bit less than 4,000 different samples of M. tuberculosis since each image is shown, by default, to different 15 volunteers to generate a consensus.

The goal of the larger CRyPTIC project that BashTheBug belongs to is to match all this data with the genomes of each and every sample and thereby produce the most comprehensive and accurate catalogue of what genetic variants confer resistance to specific antibiotics. This is important because there is a shift towards using genomic methods to diagnose which antibiotics would be best to treat individual patient infections because genomics can be faster, cheaper and probably more accurate as well.

 

Too many new images?

The CRyPTIC project has produced a new dataset of 4,286 samples. These have been collected from people with tuberculosis from all over the world.

This dataset alone would need 900,060 classifications if we were to simply require each antibiotic lane to be seen by 15 different volunteers and, unless a lot more people joined the project, would take at least a year. Our problem is the project is producing around 1,000 samples a month, which would require 210,000 classifications a month, which our volunteers at present could not keep up with!

Ultimately the CRyPTIC project will collect at least 30,000 samples over the next few years, so we are only at the beginning!

 

Some images are easy…

What might help is we’ve found that some of the images of bacterial growth are easy to classify. For example, all 15 volunteers identify well number 2 as the first well in which there is growth.

If the volunteers find this easy, a computer might also, so we wrote some computer software (called AMyGDA) that tries to measure the growth in each of the wells on the 96-well plate. It does a good job on these simple cases, but is confused by cases where this is little growth, or there are artefacts on the image, like air bubbles, contamination or shadows.

We can identify the “easier” images based on how much growth there is, and whether the computer software agrees with the single reading we have of each plate done by a laboratory scientist. On our new dataset of 4,286 samples, this approach identifies 84% of the antibiotic lanes as easy to classify.

If we only send the remaining 16% of images to the volunteers, that reduces the number of classifications we need to complete this dataset down to 144,000 with a monthly growth rate of 34,000 which is much more achievable!

 

…and some are hard.

But this means you will all be seeing images that are harder to interpret and classify and therefore should be more of a challenge.

This is an example of an image that is harder to classify.

In our existing dataset, these images have typically elicited a range of answers. Some volunteers might say they cannot classify the image, whilst others would identify a range of wells as being the first with no growth. We can, of course, still form a consensus (I’d say well 5), but the variation is itself telling us something about how and why the image is hard to classify, which is potentially useful (for example, for training a machine learning classifier).

 

A few things to think about

Because the images should be, on average, more challenging now, you will have to make more frequent judgment calls about whether that blob in well 5 is an artefact or whether it “looks like” growth, and if you think it is, whether or not it is big enough to be relevant. Personally, I’d say for something to be growth it has to look like the growth in the positive control wells. If it is a lot smaller (like a dot) then I personally tend to ignore it. Don’t spend too long on individual images – rely on the collective power of the volunteers to allow us to extract a consensus from all your answers!

 

Focussing your efforts

In summary

– there are a lot of new images available to classify on our Zooniverse project page and
– they should be, on average, a lot more interesting and challenging

 

To get more frequent project updates,

– check for banners on the Zooniverse project page
– follow BashTheBug on Twitter, Instagram and Facebook
– check out our blog

 

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Philip W Fowler
6 August 2018

In this week’s edition of Who’s who in the Zoo, meet Science Scribbler‘s Michele Darrow.

– Helen

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Project: Science Scribbler

Researcher: Michele Darrow, Development Scientist

Location: TTP Labtech & Diamond Light Source

 

What are your main research interests?

I’m interested in various imaging techniques and how best to process the data collected from them to answer both biological questions and to develop algorithms to automate the process in the future.

 

Who else is in your project team? What are their roles?

Our team spans biologists, imaging technique experts and software engineers.

 

Tell us more about the data used in your project

Right now, Science Scribbler is working to process a dataset related to Huntington’s Disease. Many of the circular objects marked by volunteers as part of the project are organelles. These are smaller compartments inside of each cell, and each type of compartment has a different job. In Huntington’s Disease, some of the compartments are dysfunctional, but details about how the disease leads to this dysfunction aren’t really known. By comparing a diseased cell to a non-diseased cell we’re hoping to learn about organelle changes due to the disease.

 

How do Zooniverse volunteers contribute to your research? 

Zooniverse volunteers are amazing! Without them, this project would be moving at a glacial speed!

For this project, volunteers are asked to place marks in the centers of objects and outline the objects. This information will first tell us where all of the organelles are so we can begin to answer our biological question. And second, using this dataset as a standard, we hope to create a computer algorithm that will use just the center points to find the outlines of the objects, making the task easier and faster in the future.

 

 

What discoveries, and other outputs, has your project led to so far?

We have retired 50% of the images in this first dataset. Because we’re far enough along, Mark, one of the software developers on the project, has begun to process the data. You can see the code that he is working on and his descriptions of what it does here.(https://github.com/DiamondLightSource/zooniverse/blob/master/notebooks/science_scribbler.ipynb)

 

 

What’s in store for your project in the future?

The problem of segmentation – marking out parts of a dataset in order to analyze is – is a common problem across many imaging techniques and disciplines. One of the benefits of working on these problems at Diamond Light Source is that there are always people and projects that need improved segmentation. Our next project on Science Scribbler will focus on a new imaging technique and a new segmentation problem. This switch in focus will give the original project some time to process the data, come up with potential computer algorithms to improve the process and think about the next steps. And it will give a new project and new researchers a chance to interact with the Zooniverse to jumpstart their research!

 

What are your favourite other citizen research projects and why?

I love Wildwatch Kenya! I find it super chill and it’s always fun when you find an animal in the picture!

 

 

And finally, when not at work, where are we most likely to find you?

Long walks with my husband and dogs (Jinx and Charm) and reading good books (right now, re-reading the Harry Potter series).