# mcDETECT Tutorial

MERSCOPE-focused walkthrough: `mcDETECT` setup, granule detection, profiling, manual subtyping, WT vs AD density, and Isocortex neuropil subdomains.

```{toctree}
:maxdepth: 2
:caption: Tutorial

tutorial_pages/README
tutorial_pages/01_what_mcdetect_expects
tutorial_pages/02_construct_mcdetect
tutorial_pages/03_granule_detection
tutorial_pages/04_profile_granules
tutorial_pages/05_manual_subtyping
tutorial_pages/06_density_wt_ad
tutorial_pages/07_neuropil_subdomains
tutorial_pages/08_checklist
```