Identify Pores: Pore Reconnection Issues

[jdrunner]

Good afternoon,

I have been utilizing Identify pores to help with pore analysis on one of my samples. Some of the pores weren't fully recognized in our scan, leading to holes in the segmented pores. When editing the settings of the Identify Pores module, I adjusted the fragmented pores reconnectivity near to the maximum to help mitigate issues, but they persisted.

Currently, multiple pores are being assigned to one in our segmented dataset. I was curious if there were other settings that could be altered to help alleviate these issues? Thank you.

Respectfully,
Jack Davis

[Anne Blumer]

Dear Jack,

there is indeed another setting that could influence the connectivity of the found pores.
In the "Initialization" panel you can define the Minimal Pore Diameter in Voxel or meters.
All unconnected (isolated) pores which have a diameter smaller than this value are neglected from the analysis.
Connected pores, that touch other pores with a larger diameter (larger than the minimal diameter) are merged with the larger pore. Thus, both pores are treated as one.

This also means that they cannot be separated by modifying the interface threshold for Reconnect Fragmented Pores.
This feature only has influence on two different pores that touch.

Please find a small example for the Minimal Pore Diameter in our User Guide (Expand the "Minimal Pore Diameter" section): https://geodict-userguide.math2market.de/2025/porodict_identifypores_poresegmentation_initialization.html

We recommend to set the Minimal Pore Diameter to the default of 2 Voxels.
Then, you can do a post-processing step (Threshold by Scalar Value), which you can use to seperate pores of different sizes and do analysis again on a subset of pores.

Please let me know if you have further questions.

Best regards
Anne

[jdrunner]

Sorry to re-enter this thread later,

I was able to utilize the aforementioned settings. I was able to get 1 of my samples clean (see Image 1). However, most of my other samples were not clean, with Image 2 having the worst reconnectivity.

I altered the settings, and the current outputs I have are optimized. If there are more settings to be changed or anything additional that can help with pore identification accuracy, that would be great. I would also be happy to send over the datasets if that would help if you reach out via email. Thank you.

Respectfully,
Jack Davis

[Anne Blumer]

Dear Jack,

at a first glance it seems to me that there are isolated pores which are fragmented and need to be merged.
You can set the Interface Threshold parameter to 0% (or close to 0%) to merge all pore fragments.
Remember that you can (and maybe have to) use different values for the different samples.

Could you please test varying the Interface Threshold and see if it is helpful?
Otherwise I would need more information about the settings you used for the analysis.

Best regards
Anne