The 3rd International Workshop on Monte Carlo eXtreme for Biomedical Optics Research (MCX'19)

1. Summary
2. Event agenda
3. Instructions on preparing your laptop (to be updated)
4. Organizer contact info
upload:mcx19_icon.png

1. Summary

Where
ISEC 138 (1st floor), Northeastern University, 805 Columbus Ave, Boston, MA 02115
When
Aug. 8-9, 2019
What
We are the developers of MCX and MMC, two NIH-funded high-performance Monte Carlo photon transport simulation platforms that are widely distributed among the biophotonics research community. We organize this two-day event to train our software users - particularly students and researchers in the biophotonics/imaging areas - to properly and efficiently use our photon simulation packages. We will cover various tools we have developed, including MCX, MMC, MCXLAB/MMCLAB, MCX Studio and Iso2mesh (for 3D mesh-generation). We will show our participants via interactive sessions on how to define simulation domains, setting critical parameters, running simulations, and displaying results.
How much is the registration fee
Free! We thank the funding support from the NIH/NIGMS under Award# R01-GM114365. This event is not possible without this support! (Participants are responsible for the travel and lodging cost. We have limited funding for student travel grant and subsiding on-campus housing, please see registration form for details.)
What do you need
A laptop that can be connected to the Internet using Wifi/cable. We will have a reception/poster session on Day 2 (Aug. 2), we encourage all attendees to present a poster for your related research.
How to register
Seats limited, click here to register. Registration will be closed on June 30, 2019.

2. Event agenda

Day 1 (Aug. 8)

  • 8:00-9:00 Breakfast (provided), user laptop preparation
  • 9:00-9:15 Opening (Monte Carlo algorithm, MCX project overview)
  • 9:15-11:00 MCX Studio Training
    • 9:15-9:45 Basics of MCX Studio (GUI, built-in demo, remote execution, visualization, use binary data)
    • 9:45-10:15 Designing complex domains using MCX Studio
    • 10:15-11:00 Hands-on session on MCX Studio
  • 11:00-12:30 MCXLAB Training
    • 11:00-11:15 MCXLAB Introduction
    • 11:15-11:45 MC simulation in Digimouse using MCXLAB
    • 11:45-12:30 Hands-on session on MCXLAB

  • 12:30-1:30 Lunch Break (lunch provided)

  • 1:30 - Group photo
  • 1:35 - Starting MMC/iso2mesh training session
  • 1:35-2:45 Iso2Mesh/Brain2Mesh training
    • 1:30-1:45 Introduction to Iso2Mesh and basic mesh generation
    • 1:45-2:15 Hands-on session on Iso2Mesh basic meshing features
    • 2:15-2:30 Generating high-quality human brain 3D meshes
    • 2:30-2:45 Hands-on session on Brain2mesh
  • 2:45-3:30 MMCLAB Training
    • 2:45-3:00 MMC algorithm and simulation basics
    • 3:00-4:00 Hands-on session on MMCLAB for brain simulations
  • 3:30-4:30 (NEW!) Redbird-m training - a fast MATLAB-based diffusion forward/inverse solver
    • 3:30-3:50 Redbird-m overview and demos, interact with MMCLAB
    • 3:50-4:30 Hands-on session on Redbird-m
  • 4:30-6:30 Break
  • 6:30-8:00 Dinner (location TBD)

Day 2 (Aug. 9):

  • 8:00-9:30 Breakfast (provided)
  • 9:30-11:00 Invited talks
    • 9:30-10:15 Talk 1 - TBD
    • 10:15-11:00 Talk 2 - TBD
  • 11:00-12:30 MCX/MMC advanced simulation features demo and hands-on

  • 12:30-1:30 Lunch break

  • 1:30-2:30 MCX/MMC developer guide - how to customize MCX/MMC/MCXCL
  • 2:30-4:00 Poster session, social hours
  • 4:00 Concluding Day 2

  • Collaboration/troubleshooting meetings can be arranged with the MCX/MMC team in the afternoon of Aug. 9th. Please provide the meeting request via email to the organizer to arrange for collaboration meetings.

3. Instructions on preparing your laptop (to be updated)

Our MC simulation software delivers the best efficiency when running on more capable hardware (such as later generations of GPUs). We will give users opportunities to experience fast simulations using our GPU resources in our lab. On the other hand, we also recognize that our participants will benefit the most from setting up a stand-alone simulation environment on our own computers.

For the above reason, we strongly recommend our participants to try our first approach:

  • Method A (recommended) - Running everything from your laptop (or remote server in your own lab)

This way, you will have a working system after getting back from the workshop and ready to run new simulations.

In the event that your laptop is too old, or have driver issues and unable to use the CPU/GPU for our simulations, we will ask you to try the alternative approach:

  • Method B - Use remote GPU via MCXStudio from your laptop

If the above approach (Method B) still unable to allow you to connect and run simulations, we will have to use our preconfigured Linux-based environment, this is our fall-back plan:

  • Method C - Run simulations over the remote desktop of our Linux GPU server

Because of limited network bandwidth, we do not recommend Method C to everyone, but only use it when the previous two approaches fail.

If you have difficult configuring your laptop, please consider borrowing another laptop or run a remote server in your home institution. Please test connections if you decide to run the simulations on your server.

4. Organizer contact info

If you have any questions regarding this event, please feel free to contact the organizers. Their contact info is listed below.

  • Xin Sun (workshop coordinator)
    • Email: sun.xin1 at husky.neu.edu
    • Phone: 857-272-4545 (cell)
  • Prof. Qianqian Fang
    • Email: q.fang at neu.edu
    • Phone: 617-407-5769 (cell), 617-373-3829 (office)
    • Office: ISEC 223
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