The 5th International MCX Training Workshop (MCX'24)

1. Summary
2. Event agenda
3. Laptop preparation instructions
4. Directions and logistics
5. Organizer contact info
upload:mcx24_logo.png

1. Summary

Where
Northeastern University Boston Campus, MA 02115
When
June 29-30, 2024 (EDT)
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 Cloud 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.
How to register
Limited seats are available. Please register using this link.

2. Event agenda

All time marks below are in the US Eastern Standard Time (EST).

Day 0 (Jun. 28) - ISEC 201 (second floor of ISEC)

  • 5:30-7:00PM Optional: user laptop preparation (pre-workshop)

Day 1 (Jun. 29) - Room TBD

  • 8:30-9:30 Breakfast (provided), badge pickup, user laptop preparation
  • 9:30-10:00 Opening remarks (Monte Carlo algorithm, MCX project overview)
  • 10:00-11:30 MCX Cloud - getting to know MCX basics
    • 10:00-10:30 Running build-in examples - data input/output JSON, rendering, visualization settings
    • 10:30-11:00 Exec 1: Building a customized simulation
    • 11:00-11:30 Exec 2: Building a slightly more complex simulation
  • 11:15-11:30 Break/Q&A
  • 11:30-12:30 MCX Command line (Jupyter Notebook)
    • 11:30-11:45 Benefits and ticks in the command line
    • 11:45-12:15 Running build-in examples, modify options, run batch modes
    • 12:15-12:30 Reading and processing output data
  • 12:30 PM - Group photo (at the ISEC atrium)
  • 12:35-1:30 PM Lunch Break (lunch provided)
  • 1:30-4:00 PM MCXLAB Training (Jupyter Notebook)
    • 1:30-1:45 PM Understanding MCXLAB in 15 min, using a basic simulation
    • 1:45-2:30 PM Exec 1: simulating complex sources, and multiple sources
    • 2:30-3:00 PM Exec 2: detecting photons and processing partial-path data
    • 2:30-2:45 PM Exec 3: handling low-scattering medium using SVMC
    • 2:45-3:15 PM Exec 4: obtaining diffuse reflectance and hyperspectral simulations (Steve Jacques)
    • 3:15-3:45 PM Exec 5: MC based reconstructions
    • 3:45-4:00 QA: in-person or online joint QA session
  • 4:00-5:00 PM PMCX training (Jupyter Notebook)
    • 4:00-4:30 PM Exec 1: Running a basic pmcx simulation, modifying options, reading outputs
    • 4:30-5:00 PM Exec 2: pmcx data exchange with mcxlab/mcx command line
  • 5:00-5:30 QA: in-person or online joint QA session
  • 5:30-6:30 PM Break
  • 6:30-8:00 PM Dinner (Location TBD)

Day 2 (Jun. 30) Room TBD

  • 8:30-9:30 Breakfast (provided)
  • 9:30-11:30 MMCLAB training (Jupyter Notebook)
    • 9:30-10:15 Exec 1: Meshing using iso2mesh, (demo-only): meshing using BlenderPhotonics
    • 10:15-10:45 Exec 2: Light simulations in human head
    • 11:45-11:15 Exec 3: Wide-field source modeling in a multi-layered domain
  • 11:15-11:30 Break
  • 11:30-12:30 PM Redbird Introduction (Jupyter Notebook)
    • 11:30-12:00 Exec 1: Basic forward modeling
    • 12:00-12:30 Exec 2: Iterative DOT reconstructions
  • 12:30-1:30 PM Lunch break (lunch provided)
  • 1:30-3:30 PM MMCLAB and Redbird practices
    • 1:30-2:30: MMCLAB exercises
    • 2:30-3:30: Redbird DOT reconstruction exercises
  • 3:30 PM MCX workshop closing remarks
  • 3:30-4:30 PM Poster session, social hours, developer meetings
  • 4:30 PM Concluding Day 2

  • Collaboration/troubleshooting meetings can be arranged with the MCX/MMC team in the afternoon of June 30 after conclusion of Day 2. Please provide the meeting request via email to the organizer to arrange for collaboration meetings.

3. Laptop preparation instructions

Please follow the instructions in Workshop/MCX24Preparation to prepare your laptop before attending the conference. Although we will primarily use Google Colab and Jupyter Notebook for the training, we also encourage in-person participants to install our software on your own laptop as a backup plan.

4. Directions and logistics

If you have booked the on-campus housing, or require location transportation to arrive at NU campus, please read our Logistics Letter on the directions and check-in information.

For those of you who will travel locally to attend this event, please try to utilize the subway (the "T") if possible. The ISEC building is just a short walk from the "Ruggles" Orange Line T station.

If you have to drive, please check out the parking information in the Logistics Letter. If you need a parking voucher, please contact Dr. Fang ahead of the event. The address for the ISEC building is 805 Columbus Ave, Boston, MA, and the address for the Renaissance Parking garage is at 835 Columbus Ave, Boston, MA 02120.

5. Organizer contact info

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

  • Ashlyn McCann (workshop coordinator)
    • Email: mccann.as at northeastern.edu
  • 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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