Tag Archives: data visualization

Democratizing science .. neuroscience that is

What is going on with the neuroscience folks? First it was Montreal Neuro opening up its science  as featured in my January 22, 2016 posting,

The Montreal Neurological Institute (MNI) in Québec, Canada, known informally and widely as Montreal Neuro, has ‘opened’ its science research to the world. David Bruggeman tells the story in a Jan. 21, 2016 posting on his Pasco Phronesis blog (Note: Links have been removed),

The Montreal Neurological Institute (MNI) at McGill University announced that it will be the first academic research institute to become what it calls ‘Open Science.’  As Science is reporting, the MNI will make available all research results and research data at the time of publication.  Additionally it will not seek patents on any of the discoveries made on research at the Institute.

Will this catch on?  I have no idea if this particular combination of open access research data and results with no patents will spread to other university research institutes.  But I do believe that those elements will continue to spread.  More universities and federal agencies are pursuing open access options for research they support.  Elon Musk has opted to not pursue patent litigation for any of Tesla Motors’ patents, and has not pursued patents for SpaceX technology (though it has pursued litigation over patents in rocket technology). …

Whether or not they were inspired by the MNI, the scientists at the University of Washington (UW [state]) have found their own unique way of opening up science. From a March 15, 2018 UW news blog posting (also on EurekAlert) by James Urton, Note: Links have been removed,

Over the past few years, scientists have faced a problem: They often cannot reproduce the results of experiments done by themselves or their peers.

This “replication crisis” plagues fields from medicine to physics, and likely has many causes. But one is undoubtedly the difficulty of sharing the vast amounts of data collected and analyses performed in so-called “big data” studies. The volume and complexity of the information also can make these scientific endeavors unwieldy when it comes time for researchers to share their data and findings with peers and the public.

Researchers at the University of Washington have developed a set of tools to make one critical area of big data research — that of our central nervous system — easier to share. In a paper published online March 5 [2018] in Nature Communications, the UW team describes an open-access browser they developed to display, analyze and share neurological data collected through a type of magnetic resonance imaging study known as diffusion-weighted MRI.

“There has been a lot of talk among researchers about the replication crisis,” said lead author Jason Yeatman. “But we wanted a tool — ready, widely available and easy to use — that would actually help fight the replication crisis.”

Yeatman — who is an assistant professor in the UW Department of Speech & Hearing Sciences and the Institute for Learning & Brain Sciences (I-LABS) — is describing AFQ-Browser. This web browser-based tool, freely available online, is a platform for uploading, visualizing, analyzing and sharing diffusion MRI data in a format that is publicly accessible, improving transparency and data-sharing methods for neurological studies. In addition, since it runs in the web browser, AFQ-Browser is portable — requiring no additional software package or equipment beyond a computer and an internet connection.

“One major barrier to data transparency in neuroscience is that so much data collection, storage and analysis occurs on local computers with special software packages,” said senior author Ariel Rokem, a senior data scientist in the UW eScience Institute. “But using AFQ-Browser, we eliminate those requirements and make uploading, sharing and analyzing diffusion-weighted MRI data a simple, straightforward process.”

Diffusion-weighted MRI measures the movement of fluid in the brain and spinal cord, revealing the structure and function of white-matter tracts. These are the connections of the central nervous system, tissue that are made up primarily of axons that transmit long-range signals between neural circuits. Diffusion MRI research on brain connectivity has fundamentally changed the way neuroscientists understand human brain function: The state, organization and layout of white matter tracts are at the core of cognitive functions such as memory, learning and other capabilities. Data collected using diffusion-weighted MRI can be used to diagnose complex neurological conditions such as multiple sclerosis (MS) and amyotrophic lateral sclerosis (ALS). Researchers also use diffusion-weighted MRI data to study the neurological underpinnings of conditions such as dyslexia and learning disabilities.

“This is a widely-used technique in neuroscience research, and it is particularly amenable to the benefits that can be gleaned from big data, so it became a logical starting point for developing browser-based, open-access tools for the field,” said Yeatman.

The AFQ-Browser — the AFQ stands for Automated Fiber-tract Quantification — can receive diffusion-weighted MRI data and perform tract analysis for each individual subject. The analyses occur via a remote server, again eliminating technical and financial barriers for researchers. The AFQ-Browser also contains interactive tools to display data for multiple subjects — allowing a researcher to easily visualize how white matter tracts might be similar or different among subjects, identify trends in the data and generate hypotheses for future experiments. Researchers also can insert additional code to analyze the data, as well as save, upload and share data instantly with fellow researchers.

“We wanted this tool to be as generalizable as possible, regardless of research goals,” said Rokem. “In addition, the format is easy for scientists from a variety of backgrounds to use and understand — so that neuroscientists, statisticians and other researchers can collaborate, view data and share methods toward greater reproducibility.”

The idea for the AFQ-Browser came out of a UW course on data visualization, and the researchers worked with several graduate students to develop and perfect the browser. They tested it on existing diffusion-weighted MRI datasets, including research subjects with ALS and MS. In the future, they hope that the AFQ-Browser can be improved to do automated analyses — and possibly even diagnoses — based on diffusion-weighted MRI data.

“AFQ-Browser is really just the start of what could be a number of tools for sharing neuroscience data and experiments,” said Yeatman. “Our goal here is greater reproducibility and transparency, and a more robust scientific process.”

Here are a couple of images the researchers have used to illustrate their work,

AFQ-Browser.Jason Yeatman/Ariel Rokem Courtesy: University of Washington

Depiction of the left hemisphere of the human brain. Colored regions are selected white matter regions that could be measured using diffusion-weighted MRI: Corticospinal tract (orange), arcuate fasciculus (blue) and cingulum (green).Jason Yeatman/Ariel Rokem

You can find an embedded version of the AFQ-Browser here: http://www.washington.edu/news/2018/03/15/democratizing-science-researchers-make-neuroscience-experiments-easier-to-share-reproduce/ (scroll down about 50 – 55% of the way).

As for the paper, here’s a link and a citation,

A browser-based tool for visualization and analysis of diffusion MRI data by Jason D. Yeatman, Adam Richie-Halford, Josh K. Smith, Anisha Keshavan, & Ariel Rokem. Nature Communicationsvolume 9, Article number: 940 (2018) doi:10.1038/s41467-018-03297-7 Published online: 05 March 2018

Fittingly, this paper is open access.

Art/sci projects (+ related events) in Vancouver

There are a couple of art/science (or sciart projects) available for viewing in Vancouver, Canada which I’m listing in what is roughly in date order with a few out-of-order additions at the end including a January 18, 2018 movie screening.

Art/sci exhibitions

From the Curiosity Collider calendar of art + sci events around town,

Work in Progress: The Making of A Science Illustrator

When: 24 Nov 2017 – 24 Jan 2018 [emphasis mine]

Where: Creative Coworkers, 343 Railway St, Vancouver, BC V6A 1A4, Canada (map)

Description:  Science illustrator Jen Burgess graduated from California State University Monterey Bay’s renowned science illustration program in 2015, and since then the varied body of work she created has been idle in flat files. When the opportunity arose to share this work in person and find it some new homes, she could not resist.

The work is primarily natural history subject matter, in a variety of media including graphite, pen and ink, coloured pencil, watercolour, gouache, acrylic, and digital. To reflect the location of the show, the theme of the show is “Work in Progress,” so adjacent to many of the pieces Jen will display some sketches, work in progress scans, photos, and/or write ups, so you can get a glimpse into the process of creating each piece. In addition, there will be work from Jen’s June 2016 self-imposed residency in Haida Gwaii, from the show entitled “On a Tangent Tear” which was on display at Emily Carr House in Victoria in September 2016. Most original works and some prints will be available for sale. Please join Jen Burgess and the team at Creative Coworkers on Friday November 24th to have a drink after work or after dinner and see some artwork before heading out to your late evening plans. There will be a cash bar and some light snacks provided. Admission is free but donations will be gratefully accepted if you would like to help Jen cover the costs of framing. Please RSVP! The show will be up from November 24 through January 24, so if you cannot make it, please stop by and see the work on your own time. There may be plans afoot for a closing reception as well, perhaps with a silent auction. Stay tuned!

The Curiosity Collider calendar also listed this event (from the Beaty Biodiversity Museum Exhibition page),

Life In Colour

Drawings by Angela Gooliaff, colouring by you
September 16, 2017 – February 18, 2018

Colour your way through nature on a giant mural that showcases ecosystems from BC and around the world.

Presented by Hemlock Printers, artist Angela Gooliaff explores keystone species in both the terrestrial and aquatic ecosystems, employing feminine symbology of peace and wisdom, and story through a giant interactive colouring book mural. “I have connected my investigation of keystone species with the adult colouring book movement as an interruption to the current story of the natural world,” says Gooliaff.

By presenting a web of life for visitors to interact with, it will be visually apparent just how biodiverse our ecosystems are and how drastic an impact the removal of one species from the environment could be. Gooliaff concludes that by “giving the audience control to own their story through colour, perhaps will get them thinking about their own story and placement within the natural world.”

Science get together

Vancouver’s H. R. MacMillan Space Centre is hosting a January 25, 2018 event in their Cosmic Night series in January 2018, from the Cosmic Nights: Beyond Our Universe event page,

Is there anything beyond the universe? What came before the Big Bang? These are questions that don’t have answers, but we have theories! This installment of Cosmic Nights we delve into theories of the Multiverse!

Cosmic Nights is a themed party featuring a custom planetarium show, music, drinks, science demonstrations, games, and a special guest lecturer – all surrounding an exciting theme. Experience the Space Centre after hours in a 19+ environment!

Cosmic Nights returns on Thursday, January 25 [2018] with Cosmic Nights: Beyond our Universe. Jump into multiple universes, the Big Bang and other ideas that are bending our cosmic minds. Select your preferred Planetarium Star Theatre show time and then come early or stay late to experience all this event has to offer!

6:30pm – 10:00pm – Drinks | Music | Games | Demonstrations I Lecture I Planetarium

7:30 or 9:00pm – Planetarium Star Theatre show: Cosmology Questions
How did it all begin? What is the Big Bang Theory and what does this theory suggest about an end to our universe? Are there universes in addition to the one we live in? How do scientists even attempt to answer these mind-blowing questions? We’ll talk about some of the biggest questions about the universe and leave you with even more ideas to explore.

8pm and 9pm – “The Multiverse” lecture by Dr. Douglas Scott
Can there be more than one universe?  Why is the Universe that we live in the way that it is?  Does our existence imply that the universe has to have certain properties? Can we imagine universes that are quite different? What does the word “multiverse” even mean? These and other questions will be tackled in this special talk (and others quite like it, all across the multiverse!).

Bio: Douglas Scott is a Professor of Physics & Astronomy at the University of British Columbia, who was trained in Edinburgh, Cambridge and Berkeley.  He specialises in cosmology- the study of the universe on the largest scales and has co-authored more than 500 papers on a wide range of both concrete and speculative astrophysical topics.

7pm-9pm – Groundstation Canada Theatre  – Cocktail Crash Course: String Theory and Quantum Gravity 
A fun, interactive science demo on string theory and quantum gravity – enough fun facts to impress at a cocktail party. Trivia prizes are also up for grabs!

TICKETS: $20 early bird tickets until January 11th, $25 after.
Tickets available online through Eventbrite. Or, save the service fee by purchasing in person at the Space Centre or by calling 604.738.7827 ext. 240.

Beer from Red Truck Beer Company, wine frrom Hester Creek Estate Winery. Games by Starlit Citadel.

19+ event. All attendees will be required to provide photo ID upon entry.

You can go here to buy tickets.

Curiosity Colllider Café

The Curiosity Collider folks themselves are holding a January 31, 2018 Collider Café with the theme: Art. Science. Fusion. (from a January 9, 2018 announcement received via email),

Save the date – our next Collider Cafe will be on Wednesday, January 31 [2018]. Speakers include:

  • Visualizing Medicine (Paige Blumer, medical illustration)
  • Art = Science in Love (Martin Krzywinski, data visualization)
  • Geo-synth Music Video (Mika McKinnon, science communication)
  • Sciart Zine (Raymond Nakamura & Katrina Wong, creative collaboration)

I found more details,

Date(s) – 31/01/2018
8:00 pm – 9:30 pm

Café Deux Soleils
[2096 Commercial Drive, Vancouver]

Curiosity Collider calls

I believe this is the first time the organization has announced calls for submissions. There are two (from the January 9, 2018 announcement received via email),

Call for Submissions

Do you exist in both the worlds of art and science? Does your artistic practice rely on science? Does your scientific practice rely on art? We are launching two calls for submissions:

Want to receive future calls for submissions? Update your email subscription options so you don’t miss out!

More from Curiosity Collider

This January 9, 2018 announcement was very full,


Mathematicians get illustrative

Frank A. Farris, an associate Professor of Mathematics at Santa Clara University (US), writes about the latest in mathematicians and data visualization in an April 4, 2017 essay on The Conversation (Note: Links have been removed),

Today, digital tools like 3-D printing, animation and virtual reality are more affordable than ever, allowing mathematicians to investigate and illustrate their work at the same time. Instead of drawing a complicated surface on a chalkboard, we can now hand students a physical model to feel or invite them to fly over it in virtual reality.

Last year, a workshop called “Illustrating Mathematics” at the Institute for Computational and Experimental Research in Mathematics (ICERM) brought together an eclectic group of mathematicians and digital art practitioners to celebrate what seems to be a golden age of mathematical visualization. Of course, visualization has been central to mathematics since Pythagoras, but this seems to be the first time it had a workshop of its own.

Visualization plays a growing role in mathematical research. According to John Sullivan at the Technical University of Berlin, mathematical thinking styles can be roughly categorized into three groups: “the philosopher,” who thinks purely in abstract concepts; “the analyst,” who thinks in formulas; and “the geometer,” who thinks in pictures.

Mathematical research is stimulated by collaboration between all three types of thinkers. Many practitioners believe teaching should be calibrated to connect with different thinking styles.

Borromean Rings, the logo of the International Mathematical Union. John Sullivan

Sullivan’s own work has benefited from images. He studies geometric knot theory, which involves finding “best” configurations. For example, consider his Borromean rings, which won the logo contest of the International Mathematical Union several years ago. The rings are linked together, but if one of them is cut, the others fall apart, which makes it a nice symbol of unity.

Apparently this new ability to think mathematics visually has influenced mathematicians in some unexpected ways,

Take mathematician Fabienne Serrière, who raised US$124,306 through Kickstarter in 2015 to buy an industrial knitting machine. Her dream was to make custom-knit scarves that demonstrate cellular automata, mathematical models of cells on a grid. To realize her algorithmic design instructions, Serrière hacked the code that controls the machine. She now works full-time on custom textiles from a Seattle studio.

In this sculpture by Edmund Harriss, the drill traces are programmed to go perpendicular to the growth rings of the tree. This makes the finished sculpture a depiction of a concept mathematicians know as ‘paths of steepest descent.’ Edmund Harriss, Author provided

Edmund Harriss of the University of Arkansas hacked an architectural drilling machine, which he now uses to make mathematical sculptures from wood. The control process involves some deep ideas from differential geometry. Since his ideas are basically about controlling a robot arm, they have wide application beyond art. According to his website, Harriss is “driven by a passion to communicate the beauty and utility of mathematical thinking.”

Mathematical algorithms power the products made by Nervous System, a studio in Massachusetts that was founded in 2007 by Jessica Rosenkrantz, a biologist and architect, and Jess Louis-Rosenberg, a mathematician. Many of their designs, for things like custom jewelry and lampshades, look like naturally occurring structures from biology or geology.

Farris’ essay is a fascinating look at mathematics and data visualization.