im weighing on the need to manually review my feature extraction pipeline. on one hand it has gone through several revisions, suggestions given by itself and other chatbots. on the other hand i cannot verify everything it does is that consistent and accurate at the same time. im weighing my options, and i don't have much time to both decide and if i decide to manually review, get technical in the specific domain of data science and image to numerical data translation. im leaning no.
update: yeah no. that makes all technical issues i brought up for the past few entries resolved and void.
today i ran into the problem of D4 A10 being stitched incorrectly, so far the most upstream computational problem i have encountered, and also the most external of them all. the stitching doesn't originally happen on my device but the UMass one, under the Image Gen software. and after being paranoid for about like 30 minutes i got my hands dirty (aka getting claude code up lol) to build my own scikit based falty stitched tiff replacement pipeline and it works like magic. another guardrail i have fully set up to prepare for falty images, and the only thing i really have to do is to just export then import the raw brightfield microscopy that are 100% consistent, then my computer does the stitching itself while preserving the seamlessness of everything downstream, ie the segmentation pipeine.
something about hull alpha though. this is the latest concern that Claude Code raised for me, but here is what i think in response:
there comes each time when i have to look at masks with big dents or cutthroughs by the well scratches and weigh the following: do i care more about the consistency of thresholding and use of convex hull or pursue the closeness to true biological structure of the objects of interest?
with dents, with the biologically inconsistent masking by SAM3, the need for increasing the hull alpha value is strong. i try to keep it not that high until absolutely necessary. my default operation is using the prompt "dark blob" at 0.4 as my instance thresholding value, and the hull alpha is zero.
hull alpha's value increase, change in prompt or clipping sensitivity are all contingencies. and the pursuit to true biological structure/shape is more important than leaving dents that are technical errors. this is the same with my employment of my own restitching contigency plans; although restitch doesn't directly impact feature extraction. however, i would rather have slightly more unnatural smoothness than letting a falty mask go through the segmentation pipeline and be used for feature extraction.
and im today years old to figure out that all the contingencies and guardrails i have set up are a result of stochastic performance of existing tooling. Claude Code is slightly stochastic, SAM3 is stochastic, and even my intuition isn't completely consistent. so to which extent do i stop falling under the pursuit for accuracy and instead fall under the obsession for perfection, when perfection doesn't exist in the first place in a flat, 2 dimensional brightfield image, and that my physical handling of the 1x 96w from incubator room to the plate reader might affect their growth because i was simply holding it and walking at normal human speed?
my attention to detail and tendencies to design multiple layers of bulletproof guardrails might be both my biggest strength and biggest mental curse.
and when i hit that mental wall, i need to stop hitting that wall and perhaps just let something go, and tell myself "perhaps getting ALL the details are not necessary, or simply impossible. you have found your approximities, and let that satisfy your desires."