![Workshop Logo](https://mcx.space/wiki/upload/mcx24_logo.png)

# MCX 2024 Training Workshop

- URL: https://mcx.space/#mcx24

The 5th International MCX/MMC Training Workshop, joint with the 1st NeuroJSON Training Workshop
will be held between Jun. 29 and July 2, 2024 on the Boston campus of Northeastern University,
USA.

## Training Workshop Agenda
### Day 1 (Jun. 29) - [Snell Library 125 (SL125)](https://www.google.com/maps/place/Snell+Library/@42.3383134,-71.0883827,18z/data=!4m6!3m5!1s0x89e37a1999cf5ce1:0x46e17e056ed496c3!8m2!3d42.338587!4d-71.0881225!16s%2Fg%2F11h0gv2c4?entry=ttu)
- 8:30-9:30 Breakfast (provided), badge pickup, user laptop preparation
- 9:30-10:00 Opening remarks (Monte Carlo algorithm, MCX project overview, **Unit 1A**, [Jupyter Notebook](Training/MCX2024_1A_jupyter_notebook_basics.ipynb))  (**Lead by Dr. Qianqian Fang**)
- 10:00-11:30 MCX Cloud - getting to know MCX basics (**Unit 1B**) (**Lead by Dr. Qianqian Fang**)
  - 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 (**Unit 1C**, [Jupyter Notebook](Training/MCX2024_1C_mcx_command_line.ipynb)) (**Lead by Dr. Qianqian Fang**)
  - 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 (**Unit 1D**, [Jupyter Notebook](Training/MCX2024_1D_mcxlab_training.ipynb)) (**Co-Lead by Rahul Ragunathan and Dr. Qianqian Fang**)
  - 1:30-1:45 PM Understanding MCXLAB in 15 min, starter examples
  - 1:45-2:30 PM Exec 1: simulating complex sources, and multiple sources
  - 2:30-2:45 PM Exec 2: detecting photons and processing partial-path data
  - 2:45-3:00 PM Exec 3: handling low-scattering medium using SVMC
  - 3:00-3:15 PM Exec 4: obtaining diffuse reflectance and hyperspectral simulations (**Lead by Dr. 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 (**Unit 1E**, [Jupyter Notebook](Training/MCX2024_1E_pmcx_training.ipynb)) (**Lead by Ivy Yen**)
  - 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

### Day 2 (Jun. 30) - [Snell Library 125 (SL125)](https://www.google.com/maps/place/Snell+Library/@42.3383134,-71.0883827,18z/data=!4m6!3m5!1s0x89e37a1999cf5ce1:0x46e17e056ed496c3!8m2!3d42.338587!4d-71.0881225!16s%2Fg%2F11h0gv2c4?entry=ttu)
- 8:30-9:30 Breakfast (provided)
- 9:30-10:15 Meshing using iso2mesh and (demo-only) BlenderPhotonics (**Unit 2A**, [Jupyter Notebook](Training/MCX2024_2A_iso2mesh_training.ipynb)) (**Lead by Aiden Lewis**)
- 10:15-11:30 MMCLAB Training (**Unit 2B**, [Jupyter Notebook](Training/MCX2024_2B_mmc_training.ipynb))
  - 10:15-10:45 Exec 1: Light simulations in human head
  - 11:45-11:15 Exec 2: Wide-field source modeling in a multi-layered domain
- 11:15-11:30 Break
- 11:30-12:30 PM MMCLAB (**Unit 2B** continued, [Jupyter Notebook](Training/MCX2024_2B_mmc_training.ipynb)) (**Lead by Dr. Qianqian Fang**)
  - 11:30-12:00 Exec 3: Mesh-data import and export
  - 12:00-12:30 Exec 4: Loading brain mesh library from NeuroJSON.io
- 12:30-1:30 PM Lunch break (lunch provided)
- 1:30-3:30 PM Redbird-m Training (**Lead by Dr. Miguel Mireles**)
  - 1:30-2:30: Basic forward simulations and DOT reconstructions with Redbird-m (**Unit 2C**, [Jupyter Notebook](Training/MCX2024_2C_redbird_training.ipynb))
  - 2:30-3:30: Multi-spectral forward reconstruction using Redbird-m (**Unit 2D**, [Jupyter Notebook](Training/MCX2024_2D_multi-spectral_redbird.ipynb))
- 3:30 PM MCX workshop closing remarks
- 3:30-4:30 PM Poster session, social hours, developer meetings
- 4:30 PM Concluding Day 2
