Aerial Footage of the Casperkill Creek

In support of the Environmental Studies focus on the Casparkill Watershed, we recorded a flight above the Casparkill Creek, from its source to its mouth in the Hudson River, a distance of about 10 miles. The course was covered by 6 separate flights, as shown below. We also flew a course over the Casparkill’s biggest tributary, the Fonteyn Kill.

Click on a red or green line segment to see a drone video of the corresponding section of the Casperkill Creek, flown north to south. (Click on the yellow line segment to see a drone video of the Fonteyn Kill.)

Casperkill section 1 Casperkill section 2 Casperkill section 3 Casperkill section 4 Casperkill section 5 Casperkill section 6 Fonteyn Kill
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3D Modeling a Thirteenth-Century Dove

The Eucharistic Dove, one of only a few left in existence, is found behind glass in the Frances Lehman Loeb Art Center, making it a difficult piece to investigate closely. Academic Computing Services students, Dylan MacDonald, Zechariah Lee, and Sufyan Abbasi, under the guidance of Amy Laughlin and Professor Andrew Tallon, were put to the task of producing a 3D model that preserves the texture of the Dove for closer inspection.

The model was produced using a technique called photogrammetry, which is the process of stitching together a 3D model based on a sequence of images. The technique combines novel application of computer vision with classical projection mapping that produces stunning results. The software used was Agisoft Photoscan, an industry standard photogrammetry software that allows users to stitch together an orbit of still photos into a 3D model, like so:

As a proof of concept, we began with trying to model a candlestick, donated to us by Professor Tallon, which had similar properties as the Eucharistic Dove in size and luster. Due to the reflective surface of the candlestick, we found that using a green screen was out of the question since the shades of green were reflecting off of the object and projected onto the model. After trying different techniques, we discovered that shooting with a white background in the Loeb photo studio proved to be the best way to eliminate any unwanted reflections in our model.

Once we took photos of all angles of the Dove (over 200 pictures total), we used Adobe Photoshop to mask out the backgrounds and loaded the images into Photoscan. There, a second masking process was done to tell the software the bounds of the object to be generated.

Once Photoscan was finished processing the files, we were left with a .obj file that formed the 3D model of the Dove, a .tif file that dictated the texture, (shown below) and a .mta file that maps the texture to the 3D model.

Next, we loaded the model into Blender, an open source 3D modeling software. Here, we made edits to the generated 3D model, such as filling in the bottom area of the Dove where photos were not available.

Finally, the model was ready to be published on SketchFab, an online publishing platform for 3D models, which allows users to manipulate the model in 3D space and view the model in virtual reality. 

From start to end, the process took about a semester for the initial research and testing, and half a semester for photographing the Dove and making edits to the model. Dylan and Zech worked on masking the Dove in Photoshop and Photoscan and generating the 3D model in Photoscan, and Sufyan worked with Blender to make the edits to the model.

Eucharistic Dove by Vassar College on Sketchfab

We hope that you enjoy the Dove as much as we enjoyed producing the model. If you have a project idea involving 3D modeling and need some help,  please contact Amy Laughlin in Academic Computing Services in CIS.

 

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High-Performance Computing at Vassar

What is HPC?
Have you ever tried to run some code or perform some data analysis on your personal computer, and it ended up taking several hours or even days to finish? Frequently, we interact with data sets or projects that are simply too taxing for a single computer (even a very powerful one) to complete. This happens very frequently in a variety of fields across disciplines. High-Performance Computing (or HPC as it is known) is a field in technology concerned with providing advanced computing resources to researchers in order to speed up their data processing or modeling projects. Typically, these computing resources take the form of what is known as a computing “cluster”, which is really just a fancy name for a large number of computers that are all connected together and process data in unison.

Who can benefit from HPC?
-Students
-Faculty
-Non-Faculty Researchers
-Administrative Staff

HPC at Vassar (on-campus)
Here at Vassar, we have a computing cluster named “Junior” that was built in 2010. Junior has been used by many faculty and students over the years to run countless analyses and simulations for coursework and research in the Sciences and Humanities. The big advantage of using a system like Junior is that it has what’s called a job scheduler program installed. In Junior’s case, the scheduler program is called SLURM. Slurm enables users to submit the code or analysis that they want to run, and then the system will automatically load the required packages and software to complete the job, and output it into a user-specified format. This means that a user can submit a job that might take the system several days to finish, and then go and work on something else while awaiting the results, confident that work is being performed by the automated processes on the computer the whole time.

HPC at Vassar (off-campus/remote)
Here at Vassar, we have access to off-campus HPC resources as well:

  1. Through an agreement with the NSF-supported XSEDE system (The Extreme Science and Engineering Discovery Environment), Vassar researchers are able to apply for computing allocations on a variety of cluster environments that provide abundant libraries of packages, software, compilers, and user interfaces. The best part – It’s completely 100% free for Vassar! Your tax dollars are hard at work creating and maintaining this extensive network of HPC resources for use by all researchers.
  2. Vassar has an agreement with Amazon Web Services (or AWS) to provide for Virtual computing environments hosted in Amazon’s many data centers around the country. While we do pay by the hour for resources through AWS, the scalability and versatility afforded to us through this system are incredibly useful. Computing environments can be built and made accessible to the end-user very quickly and easily by administrators on campus. 
  3. We are exploring additional resources such as Google Cloud, Microsoft Azure, products from IBM, and partnerships with other colleges and universities with more robust computing infrastructure. We are also looking into avenues for the upgrade and/or replacement of Junior.

HPC Projects & Initiatives at Vassar
Many faculty at Vassar have been involved in using HPC in the course of their research and teaching. Courses and projects in BiologyChemistryCognitive Science, Computer Science, Mathematics, and Physics & Astronomy all make use of Junior and other HPC resources for course work and projects.

Just a few of the specific HPC projects underway or already completed include:

  • Chemistry Molecular research by Franco Caruso and Miriam Rossi which utilized Materials Studio in a cluster environment and has resulted in the publication of two successful journal submissions with a third in progress.
  • Biology research on viruses and bacteria using QIIME and other genetic analysis tools on both the local cluster and in AWS by David Esteban.
  • Deep learning research and course work using GPU-enhanced computational systems in the cloud by Joshua de Leeuw
  • Computational Quantum Chemistry research by Leah I. Bendavid on XSEDE.

Find out More!
If you’re interested in learning more about HPC, or getting in touch with other people at Vassar who are using HPC resources, please email Chris Gahn, the ACS Consultant for the Sciences.

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Early Spring Workshop Series 2017

ibook on macbook air, ipad and iphone

iBooks Author Workshop 

Friday Feb 3rd 2:00 pm Main Library Electronic Classroom 160

iBooks Author is a free program that allows anyone to create digital books with illustrations, audio, and interactive glossaries. iBooks can be shared or sold via Apple’s iBooks Store and viewed on any Apple device, or exported to other formats. Hands-on workshop led by Steve Taylor of Academic Computing Services. Open to the campus.

 

Final Cut Pro icon, desktop and camera

Final Cut Pro X

Wednesday Feb 8th 3:30 Library Electronic Classroom 160

Interested in learning editing video or recording a narrated presentation? Come to this hands-on workshop where you will learn to use Apple’s professional but easy to use video editing software. Led by Baynard Bailey and Amy Laughlin of Academic Computing Services. Open to the campus.

wordpress logo

Setting Up a WordPress Site 

Wednesday Feb 15th 3:30 Library Electronic Classroom 160

WordPress is an open source digital publishing platform that is great for building quick and easy websites for orgs, portfolios, research and more. Led by George Witteman of VC++. Open to the campus.

 

Linux Penguin

An Introduction to Linux: World’s Best OS!   

Wednesday Feb 22nd 3:30 Sci Vis Lab, Bridge Building

Linux is a free and open-source operating system used in all sorts of devices. Come and learn about the Bootloader, the Kernel, Daemons and the Shell!  Discover
why Linux runs most of the internet and how it is the one of the most reliable and secure OS’s available. Install it on your own machine! Led by special guest Stefan Crain of The Jahnel Group.

 

Photographing artwork lines

How to Photograph your Artwork

Friday March 3rd 2:00 Taylor Hall 328

Need to put together your senior portfolio? Want to submit work to galleries or other
exhibition calls for entry? Come to this workshop and learn how to photograph 2D and 3D artwork. Led by Amy Laughlin of Academic Computing Services. Open to the campus. Contact: amlaughlin@vassar.edu

 

illustrator environment pencil imac

Poster Making

Wednesday March 8th 3:30 Library Electronic Classroom 160

Need a poster for an academic conference? Want to print a giant poster for your event? Come to this hands-on workshop, learn basic design and how to use Adobe Illustrator to lay out a poster. Learn about campus printing resources. Open to the campus

 

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Computing Workshops Fall 2016

WordPress 101wordpress logo

Wednesday Oct 26 3:30 GIS Lab 
WordPress is an open source digital publishing platform t
hat is great for building quick and easy websites for orgs, portfolios, research and more. Led by George Witteman of VC++ and Academic Computing Services.

High Performance Computing & Amazon Web Services AWS Logo

Friday Nov 4 2:00 Sci Vis Lab

Come and learn about the “why” and “how” of high performance computing and the resources available at Vassar. Specific topics will include an overview of the field of HPC, and an introduction to Amazon Web Services. Led by Academic Computing Services’ Chris Gahn.

Intro to HTML and CSS html css picture

 

Wednesday Nov 9 3:30 -Web Design 101 – I Sci Vis Lab, Bridge Building

Sometimes Tumblr, Squarespace or WordPress just won’t do it! George Witteman of VC++ will walk you through the beginning steps of hand coding a website.

 

Game Design 101
pong-mobile-tablet-game-980x276

Wednesday Nov 16 3:30 Sci Vis Lab, Bridge Building

Ever want to get a taste of making a video game? Thinking of an alternative to another boring paper? Learn the basics of game design by hacking pong! Tom Lum of Indiebrew will lead a hands-on workshop on simple game programming using Love2D.

3d idea to print

3D Printing Open House

 Wednesday Nov 30 3:30  Library Electronic Classroom 160

Curious about 3D Printing? Come to our open house where we’ll discuss and visit campus resources for 3D Printing. Hosted by Amy Laughlin of Academic Computing Services.

Sound Editing with Audacityaudacity logo

 

Wednesday Dec 7 3:30  Library Electronic Classroom 160

Interested in podcasting? Perhaps have an interview you need to edit? Come to this workshop and learn tips on making good recordings and the basics of editing sound files with Audacity. Led by Baynard Bailey of Academic Computing Services.

 

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Make Better Videos with Your Phone or Computer (Free!) – Vimeo Video School

Impressed by Vimeo’s Video School

by Baynard Bailey

I am a long time fan of Vimeo and I’ve used it to share video for a bunch of Vassar projects over the years. (FTR those who don’t know, Vimeo is “a video-sharing community for original creative work and the people who create it”.) I was excited to see that Vimeo has launched a series of videos under the heading of “Vimeo Video School“. The series is really well done, practical, and even entertaining. I have watched and sent out links to a lot of instructional videos over the years and I have to say, this series is as good or better than anything I’ve ever seen (in the genre). Here’s an example from the series “Mastering Mobile Video“:

In addition to the Mobile Video Series (which by the way totally vindicates my ire when I see people shooting their video in portrait mode) they also have these series of lessons:

Video School Lessons

Introducing Windows Movie Maker
For PC people who are new to video editing, this free series is a friendly introduction to Windows Video Maker.

iMovie for Mac
Mac-friendly folk: edit videos without the stress. Easily master iMovie essentials in this free Video School series

Final Cut Pro X
Kick your video editing up a notch (or three) with our premium series focusing on the ins and outs of Final Cut Pro X for Mac. BAM.

Adobe Premier
Brush up on the basics and learn the finer points of Adobe Premiere in this free Video School series.

This is a fun series and makes good use of technology we have in hand or on campus.

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ACS Collaborates with ART 386 students and faculty on “first-of-its-kind exhibition.”

Amitabha Buddha, Central Tibet, 19th century; pigment on cloth; 38 1/2 x 25 1/2 in.; The Rubin Museum of Art, New York, F1997.6.3.

Amitabha Buddha, Central Tibet, 19th century; pigment on cloth; 38 1/2 x 25 1/2 in.; The Rubin Museum of Art, New York, F1997.6.3.

ART 386,  Embodying Compassion in Buddhist Art: A Curatorial Training Seminar was taught by Karen Lucic during Fall semester, 2014. The purpose of the class was to give students the opportunity to research and curate an exhibition at the Frances Lehman Loeb Art Center. During the summer of 2014, Professor Lucic contacted me to discuss creating a website for her students to use as a repository for their research and eventually this site would become a companion site to the final exhibition in April, 2015. Over the course of the Fall semester, students wrote and compiled content for the site and they worked closely with ACS to design and populate the site.

From ART 386 Syllabus:

Each student will be responsible for the digital content and interpretation of 2-3 works in the exhibition. The instructor will assign the objects to each student, based on her/his experience and preparation. These student contributions will be posted on the exhibition application and/or website. (60% of grade.)

Students will work in teams to produce additional resources for the exhibition: gallery guide, interactive maps, guide to web resources, etc. Students in the team will also give feedback on other team members’ work before submission (20% of grade.)

From ART 386 Assignment Sheet:

The purpose of this assignment is to create digital educational content for the exhibition. Always remember who your audience is: visitors to the exhibition, or online users, who might not know much—or anything—about the topic. What you write, and your choice of materials should be based on your assessment of what will enhance their experience and understanding of the exhibition. Texts should be concise and to the point. Other materials should be short but engaging.

For each work you have been assigned:

1) Write an interpretative text (no more than 100 words) for app/website

2) Select one comparative image (must be open access and high resolution); include full caption of comparative image

3) Write a text (no more than 100 words) explaining the comparison

4) Select an audio file, if possible, that enhances the work (no more than two minutes). Examples: chanting, singing, mantra recitation, etc.

5) Select a video file, if possible, that enhances understanding of the work (no more than 2 minutes). Examples: practitioners circumambulating, prostrating, spinning prayer wheels, making sand mandalas, offering incense, etc.

6) If there are no appropriate audio or video files, choose another comparative image.

7) Compile a list of unfamiliar terms from your texts, with definitions

8) Map your work, at least by country. With some works (Putuoshan, Nachi, etc.), it may be possible to be more precise about locations.

9) Record your written contributions.

While students were working to create the content for the site, ACS student employee Bryce Daniel worked on building a wireframe for the WordPress site. Professor Lucic also collaborated with Duke University students to design an App for the exhibition. The App hosted audio files recored and edited by ACS Consultant, Baynard Bailey. These recordings, narrated by both students and Professor Lucic, include short commentaries describing individual pieces in the exhibit, as well as a pronunciation guide for a glossary of terms.

The Embodying Compassion WordPress site is a comprehensive online exhibit reference guide, containing audio, video, images, interactive hotspot maps, and extensive research, curated by ART 386 students. This project proved to be a excellent example of how students, faculty, and ACS consultants collaborate to produce educational materials for the classroom and public audience.

 

Links:

Embodying Compassion Website

The Frances Lehman Loeb Art  Center: Embodying Compassion is a first-of-its-kind exhibition celebrating one of the most important figures in Buddhist art, April 23-June 28, 2015

Get the App

 

 

 

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The Bamboo® Graphic Input Tablet

Do you ever need to draw or write free-hand on your computer, but doing it with a mouse is too awkward and you don’t want to buy an iPad or any other tablet computer? You may be happy with a graphic input tablet, like the Bamboo® Connect Pen, which Vassar faculty members can borrow from ACS.

710x440_Connect_01

A graphic input tablet is a device on which you can draw with a stylus— it doesn’t have its own display, but you see the results of your drawing on your computer screen. It’s essentially like using a mouse, but one that you can control as well as you can control a pen.

While using any software that allows you to draw free-hand— Photoshop, Powerpoint, and many others— you can draw diagrams or write equations. The Bamboo Connect tablet is made by Wacom, which is known for its large tablets that are favored by graphic designers. The Bamboo Connect is just 11″ x 7″, with a 5.8″ x 3.6″ drawing area.

Here’s a demonstration and review:

If you’d like to try it out, contact your ACS liaison.

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GIS Tools for Teaching and Research

by Baynard Bailey

Anthropology Professor April Beisaw is a very active user of GIS (Geographic Information Systems) and other technologies in her research and in her classroom. ACS recently produced a video featuring Professor Beisaw employing mobile mapping devices in the field (devices she was able to purchase via the Frances D. Fergusson Technology Exploration Fund). Using the GPS mobile mapping device makes it easy to collect data that can then be imported/loaded into GIS to make nice maps. The video features April Beisaw using mobile mapping devices for field research.

Professor Beisaw continues to be a dynamic user and an advocate for using various GIS (Geographic Information Systems) technologies in her classroom. Last year she asked that QGIS be added to the base image for public computers on campus. I didn’t know about QGIS until April pointed it out to me. QGIS is a free and open source tool that empowers users to “create, edit, visualize, analyze and publish geospatial information”. It is also cross-platform, so that means you can use it on your Mac, Windows or Linux machine. (As an educator, I really appreciate it when software is free and cross platform!) Not too long ago, April gave a little demo in her office showing me and a couple Economics professors how to import maps into QGIS and how to get started creating your own customized maps. It seemed like a great tool for teaching and research, although there is a bit of a learning curve.

All of these maps were made with free QGIS:



I should also mention that Vassar has a GIS lab (using ArcGIS) in Ely Hall 114 and that GIS is available on the SciVis Lab machines. Vassar GIS users can also arrange a consultation with Stephanie LaRose, who is a GIS specialist that comes to campus a couple days a week. If faculty or students are interested in pursuing any of these technologies or resources and would like help, please contact Academic Computing Services by emailing acs@vassar.edu.

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