Data Directory Restructure

*This is for internal use only; if you'd like to open an issue or request a new feature, please open a bug or enhancement issue*

### Instructions
This document should be filled out prior to embarking on any project that will take more than a couple hours to complete. The goal is to make sure that everyone is on the same page for the functionality and requirements of new features. Therefore, it's important that this is detailed enough to catch any misunderstandings beforehand. For larger projects, it can be useful to first give a high-level sketch, and then go back and fill in the details. For smaller ones, filling the entire thing out at once can be sufficient.

**Relevant background**

Currently, the MALDI pipeline notebook is not scalable, as it operates only on a single slide throughout the entire notebook. This is not ideal as it requires the user to manually run and make adjustments to the notebook for each slide.

**Design overview**

In order to enhance scalability we will need to do two things:

1. Restructure the `Data` directory to store the data of multiple slides

**Directory Mockup**

```shell
data/
├── cohort/
│ ├── library.csv
│ ├── slide_1/
│ │ ├── tof/
│ │ │ ├── slide_1.ibd
│ │ │ └── slide_1.imzml
│ │ └── images/
│ │ ├── scanned_slide_image
│ │ ├── post_fleximaging_image
│ │ └── generated_mask
│ ├── slide_2/
│ │ ├── tof/
│ │ │ ├── slide_2.ibd
│ │ │ └── slide_2.imzml
│ │ └── images/
│ │ ├── scanned_slide_image
│ │ ├── post_fleximaging_image
│ │ └── generated_mask
│ ├── ...
│ └── slide_n/
│ ├── tof/
│ │ ├── slide_n.ibd
│ │ └── slide_n.imzml
│ └── images/
│ ├── scanned_slide_image
│ ├── post_fleximaging_image
│ └── generated_mask
└── extracted/
├── slide_1/
│ ├── debug/
│ └── extracted/
├── slide_2/
│ ├── debug/
│ └── extracted/
├── ...
└── slide_n/
├── debug/
└── extracted/
```

**Required inputs**

Files:
- Original Slide image (scanned image)
- `ibd`
- `imzml`
- Annotated image post flex imaging
- Generated mask for input to Albert's tiler

**Output files**

The output files are the same as they are currently, a directory for debug and extracted images per slide. We just need to account for another layer of nesting.

**Timeline**
Give a rough estimate for how long you think the project will take. In general, it's better to be too conservative rather than too optimistic.
- [ ] A couple days
- [ ] A week
- [x] Multiple weeks. For large projects, make sure to agree on a plan that isn't just a single monster PR at the end.

Estimated date when a fully implemented version will be ready for review: 11/10s

Estimated date when the finalized project will be merged in: