Participating in the 3D IP Workshop

The 3D IP Workshop follows the UBC Live-Cell Course after a rest day. Although digital image processing in one form or another, is taught in thousands of venues every week, it is unusual for these workshops to concentrate on techniques optimized for the processing of microscopical image data, and even more unusual to concentrate on processing to enhance the graphical display and measurement of image data having > 2 dimensions. The 3D IP Workshop aims to fill this gap. Proper analysis and display of such data is essential to progress in modern biological research.

The aims of the workshop

• To introduce students to all the important concepts needed to understand 3D image processing: pixels, voxels, sampling, transparency, projection, measurement, thresholding, segmentation.
• To guide students to an appreciation of the features of a representative sample of the many software packages available for optimizing the analysis and display of 3D and 4D microscopical data sets. This familiarity is important not only to let them process their own data but, even more, to enable them to make an informed choice when purchasing a system for their own lab.
• To give manufacturers a chance to introduce and explain the pertinent features of their software packages to students likely to need this abilities, and also, by working with students, to identify problem areas where improvements or additions to their products are needed.
• Instruction will include a mix of lectures on basic concepts and hands-on use of the packages available. In general, we will emphasize the hands-on aspect as this is something that the students will have more difficulty doing after they leave. We aim to have no more than 2 students to a computer. For all labs, we expect to have at least one faculty member available for 1-on-2 mentoring, for every 3 computers.
• While some elementary laboratory sessions involve following step-by step instructions, others will give only general directions for the display of data. Although most exercises are designed to operate on "canned" data, there will be some opportunity, especially in the evenings, to work on data collected by the student during the 3D Live-Cell course.
• The final section of the Workshop is set aside for students to display short PowerPoint presentations that they have assembled during the workshop.

Relationship to Live Cell Course

3D IP follows the Live-Cell Course and all Workshop students have taken the Live-Cell course at some time. As the end of this course includes about 1.5 days of 3D IP, many basic concepts will be covered there. The 3D IP Workshop covers more advanced concepts.

Role of the software vendor

Who gets invited

While we do want to expose the students to a carefully selected variety of software products, 3D IP is only 3 days: not long enough to permit an open door policy in terms of which companies are invited to participate. In general, we try to invite companies representing software that covers a wide range of differing capabilities: starting from Image-J, Photoshop and PowerPoint, and progressing to packages costing over $25,000 We cannot automatically accept every vendor that currently offers software that might be useful.

Although some consideration will be given to those vendors who provide hardware and personnel to support the 3D Live-Cell course, in general, choices are made based on what the organizers see as the value-for-money of the software offered, in terms of 3D capabilities, as well as the vendor's willingness to provide suitable hardware and experienced support personnel to help run the workshop.

What is expected

The software vendor is responsible for providing, in a timely fashion, the software, dongles, passwords and installation instructions needed to operate their packages. If they are bringing hardware, they need to be sure that it gets through customs and arrives in time for them to install it and have it working by the end of the rest day that precedes 3 D IP. (Be sure to keep the paperwork. US Customs has become increasingly fussy about allowing computers, and especially monitors, back in tot he USA.)

Because we have a limited amount of space for setting up equipment, manufacturers that bring hardware may be asked to allow their equipment to be used to demonstrate other, generally "open-source" software during the early parts of the course.

Reps who are present are also expected to help students getting their equipment working and to serve as mentors when students have trouble using elementary software.

In order to catch Live-Cell Course students that do not plan to participate in the 3D IP Workshop, some vendors of 3D software choose to participate in the last two days of the Live-cell Course as well as the Workshop.

Presentations

Each manufacturer selected to participate will be given time during the workshop (usually ~30 min) to present the strong points of their software. We realize that 30 minutes is NOT enough time for you to tell the students everything. However, it is enough time to introduce its unique or unusual capabilities, and to set the stage for the use of your equipment during the hands-on section to follow.

Given the limited time, it is recommended that presentations "compare and contrast" your software to that already presented rather than "starting from the beginning." It is also recommended that you confine your comments to describing the capabilities of the software on the machines rather than giving a prolonged introduction to the "history of the company...".

A detailed program of lectures and labs will be available before the workshop starts to help you to "tune" your presentation to that of those presented earlier.

If your AV needs spread beyond a 1024×768 digital projector, please contact the organizers.

Literature

Any manufacturer of software that is suitable for analyzing or displaying multi-dimensional image data sets is invited to submit literature for distribution to students.

Lodging

Manufacturers are responsible for making their own arrangements for lodging. In practice, there really is not alternative to staying at the Conferences and Accommodation at UBC. It is nearby, convenient and inexpensive. The nearest hotels are at least a half hour away and parking on campus is a big problem. While the single-shared-washroom accommodations are more than adequate, they are somewhat Spartan. However, they are what the faculty use because one really has very little time to spending ones room. Alternatively, studio- and one-bedroom suites are also available at Conferences and Accommodation at UBC if you reserve early.

What we provide

In general we provide a venue, students, and faculty. We also provide a fair chance for selected vendors to teach, and to learn from, interested students from many countries. We provide access to a fair share of the table space available for the Workshop for vendors to install their hardware. We provide WWW access, however, as the course takes place in a university setting, you cannot use this access for setting up commercial web sites.

Course content, lecture sequence and other pedagogical matters are entirely controlled by the organizers: Jim Pawley, Felix Margadant, Andres Kriete, Ping Chin Cheng, Glen MacDonald, Robert Murphy, and Badri Roysam.

Food

The Workshop provides lunches and 2 generous snacks to students, faculty and reps each day. Although many participants survive quite well on the generous snacks, breakfast and dinner can be purchased from a wide variety of nearby restaurants, cafeterias and pizza shops.

Tuition

$1,750.00 USD (Incl. lunches, snacks & Farewell Dinner)