Segmentation

[tkcaccia]

How can I start from a predefined segmentation image?

[ArtemSokolov]

You can organize your project folder following the output structure of segmentation.
For example.

myproject/
├── params.yml
├── registration/
│   └── myimage.ome.tiff
└── segmentation/
    └── unmicst-myimage/
        ├── cell.ome.tif
        └── nuclei.ome.tif

The important aspects are:

• The folder should be named unmicst-myimage/, where the second part (myimage) should match the name of the original .ome.tiff image file, because that's how MCMICRO will match the mask to it.
• The folder must contain a file called cell.ome.tif, because that's what MCMICRO will look to quantify by default. If you name the file differently, you will need to tell MCMICRO what that name is.

After structuring your project directory as above, you can then have your run start from quantification by adding the following to params.yml:

workflow:
  start-at: quantification