TraceOverlay
go get github.com/carbocation/traceoverlay
Purpose
TraceOverlay is a tool for labeling pixels within an image with semantically
meaningful labels (semantic segmentation). The tool was written to create
training data for aortic segmentation in the following manuscript:
Pirruccello, J.P., Chaffin, M.D., Chou, E.L. et al. Deep learning enables genetic analysis of the human thoracic aorta. Nat Genet 54, 40–51 (2022). https://doi.org/10.1038/s41588-021-00962-4
Installation
cd cmd/traceoverlay
go install
cd ../../
Demos
Demo config files have relative paths that will only work if run from this
folder (the same folder as this README).
Running the basic demo
traceoverlay -config demo/basic/config.json
Then navigate in your browser to http://localhost:9019
Running the advanced demo
traceoverlay -config demo/advanced/config.json
Then navigate in your browser to http://localhost:9019
The advanced demo uses a manifest.tsv
file to specify which images should be
listed (rather than listing all images in a folder).
Demo image licensing
Note: images are used with permission from the "Pexels
License" from
https://www.pexels.com/photo/christmas-cookies-on-tray-3370704/
Output
Each traced overlay is output as the input filename with .mask.png
appended.
Screenshots