README.md

3D_tissue_visualizarion

prerequisite:

1. Download 'model' folder of Superglue to working directory. (https://github.com/magicleap/SuperGluePretrainedNetwork)
2. Crop HE from .SVS and convert to .tif
   https://iipimage.sourceforge.io/documentation/images/
   http://www.andrewjanowczyk.com/converting-an-existing-image-into-an-openslide-compatible-format/

Workflow

1)Coregister HE to HT

2)Register HT to center HT

3)Register HT-coregistered HE to center HT

4)Final HE crop with same FOV

5)Get 3D Cell & Collagen masks