Separate the reconstruction from downstream analyses

[lim185]

Reconstruction files should serve as ground truth to replace the raw images for efficiency, since it is MUCH faster to compress/extract the reconstruction blocks compared to images due to significantly reduced indexing overhead (since there are on the order of 1000s of images per block.

The file organization should go as follows:

YYYYMMDDI
> LOOP ID
> Images

YYYYMMDDI_R
> LOOP ID
> Reconstruction stack files
YYYYMMDDI_A
> LOOP ID
> Analysis output (OCI, MCI, Spectra, Spectrograms etc.)