Segtools

Tools to create and work with segmentations, including tiling.

How to tile images

Setup

Make sure you have installed:

• https://github.com/mrmh2/mrepo
• https://github.com/mrmh2/runtools

and that they are in the Python path:

export PYTHONPATH=~/projects/mylibs/mrepo:~/projects/runtools/

Then you will need to create a YAML file to guide the tiling. There is an example in the example_input folder. The contents of the YAML file will look like this:

mrepo_dirpath: /Users/mhartley/workingdata/da1-mrepo
position: FR
genotype: WT
tp: 252
ordering: [[1, 2], [0, 3]]

mrepo_dirpath should point at the working data directory. Ordering is the order of the tiles.

Then run:

python scripts/autotile_from_yaml.py tile_wt_fr_288.yml --guide

This will output test .png files which you can use to check the ordering. Rerrange the ordering list, then run

python scripts/autotile_from_yaml.py tile_wt_fr_288.yml

ordering is a list,

This creates the -finalprojection.png and -final-segmentation.png files