Hi @vianamp , I very much appreciate the additional features and documentation, this is cool stuff. If you would like feedback, I have a few suggestions that might improve things from my perspective as an external user:
Glad to see there are plans to add a config file - this would be great for things like microscope resolution in xy, which seems to be hard-coded in a few places (edit: I think I misremembered this, it might actually have been in
cvapipe that I saw this). Would also be useful if the config file could define where the
local_staging directory is created, which defaults to the current working directory in my hands.
datastep seems to suggest that this could be provided in a config file but I haven’t yet figured out how to do this.
loaddata step seems geared toward downloading Quilt data (which makes sense for the purposes of the Institute). I was able to work around this, but it would be useful if the data loading step were more agnostic to where the data are coming from. Not sure what the best solution is, but it might be good enough to have the option to use local data and indicate where the data are stored on the command line (hm, maybe I will try to implement this on my local repo).
Right now, some steps are dependent on having membrane, DNA, and structures labeled - but some users may want only to analyze shapemodes on images with only the membrane and/or DNA channel, for instance. I have a branch that I’ve been tweaking to work on “membrane-only” images for the time being, but it’s more of a workaround than a robust solution. I think it would be more ideal if the user could specify this at the beginning and have subsequent steps adapt. This might be more challenging to implement, though, and I’d understand if it’s not a priority at this time.
Not sure if this is the kind of feedback you all are looking for, feel free to ignore if it’s not, haha. Again, very cool stuff, and I’m thankful to have access to the code as it’s being developed, it’s already been helpful for my work. I don’t know if there’s much I can do to help given my skill level, but I will definitely be keeping an eye on this project in the near future.