Q: Label bands in reference to ladder?

[ericHester]

Hi, I'm not sure if it is already a feature, but is there a tool that labels the bands relative to the ladder (or a specified lane)? Currently it seems the bands are labeled 1 to N from the first one detected in the lane. Maybe something like pixel height would work?

[mattaq31]

Hi @ericHester, unfortunately the naming scheme you've mentioned is the only one currently implemented (1 to N from the top to the bottom of the lane). Options such as comparison pixel heights could potentially work, but the scheme could fall apart with gels that are crooked or with lanes that follow curved paths. I think the best solution could be to implement some form of lane detection on top of the ML segmentation, from which distances could be calculated within the lane itself. We presented a draft approach for this in Figure 5 here but this has not been implemented in GelGenie itself. I think it would be a great feature to have if integrated within GelGenie!

For now, it's also possible to manually edit band names directly (click on a band and then press enter or the 'relabel' button on the GelGenie UI).

[ericHester]

Thanks for the quick reply. Indeed I saw Fig 5 and was thinking there might be something in the works, and would rather not reinvent the wheel. Perhaps something to include as a toolbox from the community.

[mattaq31]

At this stage, we are not pushing any further feature additions to the project apart from completing the publication process of the original paper (there might be a follow-up research project in the future, but this is still in its early stages). If automated band labelling and distance measurement is something you would be interested in and would be able to contribute to the app (or even as a standalone QuPath or Python script), that would also be highly appreciated! Once such a feature is scripted, it takes relatively little time from my end to include it within the GelGenie package.