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Bioviz - UMBC Art

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Jeremy Swan

on 4 June 2015

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Transcript of Bioviz - UMBC Art

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Jeremy
Swan
W
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What do I do?
Printing
Videography
Art Curation
Audio Recording
Graphic Design
Computer Graphics
Software Development
Requirements Gathering
Photography
Editing
Script Writing
Sound Design
Segmentation
Social Media
CMS administration
Content Gardening
Website Development
Networking
QA Testing
Flier Distribution
Event Planning
Booth Design
Digitization
Digital Asset Management
Archiving
Digitization
Macro Photography
Portraiture
Direct vs Diffused
Photography
Event Photography
Bang Wong
Nature Methods
Points of View Column
Videography
Lighting
Tracking Shots
Smartphone vs DSLR
Segmentation
Shoot for Fun!
"Biovisualization Specialist"
Technical IRTA -
Intramural Research Training Award

Software Developer
- RN Solutions

Biovisualization Specialist
- Cyberdata Technologies
Graphic
Motion Graphics
508 compliance
captions
Licensing
Animation
- MRI and DTMRI
- CT and PET scan
Microscopy
Light
Electron Microscopy
Medical Imaging
- Ultrasonography
Visualization in the field of Computer Science
NIH-NSF Visualization Research Challenges Report
Graphic Design
Figures for Publications
When importing logos for your poster
- Choose EPS, SVG, maybe PDF
- If Raster, PNG supports transparency
- Be aware of white space and proportions
Raster Vs Vector
Raster Images:
Photos - a matrix of pixels that forms an image or represents data.
DPI:
dots per square inch
Formats:
tif, jpg, png, gif, psd, pdf
Apps:
Photoshop, Gimp, Graphic Converter

Vector graphics:
lines and shapes with infinite resolution
Scalable:
Bezier curves, points connected by lines, at varying angles to create curves, plus thickness. Shapes, gradients, symbols, etc.
Formats:
svg, eps, ai, pdf
Photos
Image data
Fonts/symbols




Logos
Web
Artifacts due to compression
Background is non-transparent (white)
JPG
JPG
Not enough margin
PNG
Artifacts due to compression
Transparency (Yay!)
Edges are crisp!
(too crisp?)
SVG
Limited depth of color
Jennifer Lippincott-Schwartz, PhD
3D Print Golgi Apparatus produced from TEM tomography and presented at the Golgi Conference in Pavia, Italy, where it now resides in the Camillo Golgi Science Museum.
1st Prize for Public Outreach - American Society for Cell Biology
We worked with the CBMP microscopist to
create 3D models from Electron Microscopy
Outreach to the public and scientific communities
Pros - Fast turnaround
- Instantly edit and upload
- Add value and context
- Edit photos and video
- Access Social Media
- Many 3rd party apps

Cons - Low quality
- Limited storage capacity
- Can't control focus or d.o.f.
- Tripods limited/flimsy
- Onboard audio is limited
- Risk of getting phone call
during video shoot
Pros - High Quality
- Full control over focus
- Control depth of field
- Interchangable Lenses
- Nearly Pro Video Quality
- Looks more Professional

Cons - Expensive
- Time consuming
- Lenses susceptable to dirt
- Battery life limited
- Chargers hard to find
- Large and bulky
- Complicated to operate
Amir Gandjbakhche
We explore various properties of light-matter interactions as sources of optical contrasts, such as polarization properties, endogenous or exogenous fluorescent labels, absorption (e.g., hemoglobin or chromophore concentration), and/or scattering.

We have used these contrast mechanisms for tomographic and spectroscopic methods to develop benchtop instrumentation for preclinical and clinical uses. We are identifying physiological sites where optical techniques might be clinically practical and offer new diagnostic knowledge and/or less morbidity than existing diagnostic methods.
Our objectives are to devise quantitative biophotonics methodologies and associated instrumentations in order to study
Tech Transfer and Marketing
Leonid Margolis, PhD
Acyclovir is an anti-retroviral drug commonly used in fighting the virus herpes simplex.

This animation was created to help Dr Margolis quickly explain basic concepts about Acyclovir in presentations.

The Acyclovir and amino polymerase models in this animation were based on crystal structures.

The animator collaborated with a fellow to learn how the molecules should move.
Intercommunication between scientists
Rhesus Macaque
Steve Suomi, PhD
This animation was created for use in mirror
neuron experiments, which employed electroencephalography (eeg) and incorporated
the use of eye tracking, to determine where the
test subjects were looking and for how long.
"Our research involves broad-based investigations of primate biological and behavioral development through comparative longitudinal studies of rhesus monkeys and other primates."
Computer graphics in research
Computer graphics as visual stimulus
High degree of "control" in experiments
Programable for artificial intelligence
Experiments more repeatable
Nanoscale animation
created for the Office
of the Director as
promotional material
Nanotechnology Week
Public outreach and education
Get the person to relax! Feed ego
Use a stand-in to perfect lighting
and camera settings beforehand
Tell Bad Jokes
Remove badges, pagers, clean up!
Shoot more photos than you think
Use a copy stand or a tripod
White balance!
Use a lens which doesn't distort
Cut hole for lens in black construction paper to reduce reflections
Light from the sides
Shoot next to a window (diffused sunlight only!)
Use a remote or set timer, to reduce vibration
Tips:
Tips:
DIY-VIZ
- Use natural light when possible
- Dusk, Dawn and Diffused sunlight
- OR 3-point lighting (for people)
- Facing Window when inside
- Bounce light to create "fill light"
- Don't mix light sources (color temps)
- "Sunny 16" rule for full sun
- No photos in front of projectors!
James Jeffrey
A portrait with three-point lighting: a 300 watt key light, a 150 watt back light, and fill light from a bounce board
Color Temperature
3 Point lighting
Sunlight
- Free
- All cameras work with it

Tungsten
- Hot
- Orange/Yellow

Fluorescent
- Cool
- Blue
LEDs
- Cool
- Flexible light temperature range
- Prices coming down
Lighting types:
Onboard Flash
- Macro photography
- Fast motion
- Fill light, augment other light
- Experiment! Shoot both
- Vary ISO settings and exposure
Don't use onboard flash unless absolutely necessary.
Tips:
- Tripod and photos for time lapse
- intervolometer on DSLR cameras
- Time Lapse Apps on smartphones
- Combine shift in focus with movement
Regular tracking shot
Tracking shot with shift in focus
Panning shots with fluid head tripod
and time lapse photos
Skateboard Wheels
Designer
Nicki
Swan
BIO-VIZ
An overview
of providing biological visualization support.
Medical Illustration
3D Graphics and Animation
Amateur Musician
Combat Lifesaver
Medical Support Unit
Heavy Wheel Vehicle Mechanic
Nursing Program
Technology Liaison
Bridging the generation gap
Thinking outside the box
Bloody tumors
Patient photos
Unexplainable
People Smiling
Having Fun!
Newsletters
Catalyst
NIH Record
Social media
Video
JoVE
Practice until it's not fun, then keep it up!
Learn to see
light and shadow
as an artist
and Teleconferencing
CONTRAST
CONTRAST
Insight Segmentation and Registration Toolkit (ITK)
Visualization Tool Kit (VTK)
3D Printing
Source of free, 3D printable models
and data processing pipelines
Medical Imaging
Isosurface
Molecular
Processing Pipelines
Trainable weka segmentation
FEI Amira
Bitplane Imaris
Meshlab
Model Processing
Janet Iwasa
Special Thanks: Darrell Hurt, Meghan Coakley, Erin Fincher, and the entire 3D Print Team, plus Nicki Swan, Tim Mrozek, Chandan Sastry and Vasudha Kowtha
HDRI
high dynamic range imaging
Trey Ratcliff
Stuck in Customs
Tim Mrozek
Tutorial on 3dprint youtube channel
Adrian Bowyer

Conferences
ieee vizweek
SIGGRAPH
Web3D
VizBi
BioCommunications Association
Guild of Natural and Scientific Illustrators
American Med. Illustrators
People
- Gael McGill
- Drew Berry
- Graham Johnson
- Art Olson
(Iwasa and Goodsell)
Interactive Technology
- Unity3D
- x3d
- Unreal Engine
- Blender Game Engine
Lovely Wife
Digital Asset Management!
John Rouse - Consulting and Damn Good Friend
Government vs Free Market
Working in the
Altruistic (hopefully)
Growth limited
Amazing resources (often)
Job security
Local
Wide range of clients
Commercially driven
Start-up challenges
Risky
There is a bottom line
Character Animation Train
- Biology Train?
Visual Effects Train!
Be the
BEST!
or at least try to be.
Habitually doing many jobs at once;
before the army
attending UMBC
Tim Mrozek
Bryan Twomey
Richard McAllen
Anna Schmidt
Andre Mercier
Erin Fincher
Sam Farabaugh
Recruited from UMBC
Connect!
Don't Burn Bridges
Or trying to anyway.
HELP!
Fellows, PostDocs, students
Researchers, scientific staff
Doctors and hospital staff
Leadership, administrators
Communications staff/outreach
Cut through bureaucracy
Create advocacy network
Develop skills
Build team
Collect resources
License software
Produce content
Wayne Rasband
Model
Processing

Molecular Visualization
http://learn.genetics.utah.edu/
UTAH - Games
David Goodsell
PDB.ORG
Molecule of the Month

- Eric Martz
- Keith R Porter
Historical
Advice?
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