Boundary mask of CREMI?

[wlsdzyzl]

Hello, how did you get the boundary mask of CREMI? It only provides the neuron_ids. I can extract the boundaries by applying skimage.segmentation.find_boundarys on neuron_ids. But I got boundaries which seem thinner than what you have shown in paper. Did you add something such as a Gaussian blur? Thanks!

[jocpae]

Hi, we used the code provided by CREMI github repository https://github.com/cremi/cremi_python/blob/aa6d211f177ad7f0364ed027ea0314803d114c04/cremi/evaluation/border_mask.py
The authors provide a function called "create_border_mask_2d" to draw the boundaries. There you can also specify how thick you want to draw the neuron boundaries.