Ok, I'm new at parts of this, so please, cut me a little slack....
Gear info: Fujifilm X-Pro1, 50mm f/2 Leitz Summitar, shortest (10mm? Not sure, I can't read Russian) LTM extension tube. ISO 200, f/11, 1/40th, -1 stop EV.
Image info: I'd shot pretty much this same (series of) image(s) half an hour or so before, then imported the set into LR. The plan was to shoot 5 images then stack, align and blend the bunch in PS, so I did. Made for a pretty decent image overall, but I noticed two serious problems: first, the closer-most elements (the moonflower seeds) were not in focus, and second, I finally saw the 'worms' others have described as being a problem with X-Trans images, and knew this would not stand. So, I took the tray of 'Fall Harvest' moonflower pods back outside and re-shot them, but this time increasing the subject-to-camera ratio very slightly, decreased exposure by a stop, and re-shot two sets of seven images to stack. Upon completion of that, I returned to my computer and imported the shots with the new Fuji-dedicated (Lite) version of Capture One. Voila! No worms! And what I wanted in focus was indeed in focus. I then proceeded to stack and process (tweaks in LR and Topaz Studio) the image to the result you see here.
A question, however: As mentioned, I'm new to Fuji. As such, Focus Peaking is new to me, and I'm finding I sometimes undershoot an area of (what I want to be) critical focus. Does anyone have any manual, non-Fuji glass focusing tips they'd be so kind as to pass along to me? I'm all for learning by trial and error, but jeez.....