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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.....  

 

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Edited by Cany143
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You could use a wide angle lens set to infinity focus -- everything will be in focus :).

Set the focus peaking to use a color that will give you the best contrast. Decide whether you like using the viewfinder or the back screen better. Then play with it. The in-focus part can seem like a blanket laid over the image and as you twist the focus ring, the blanket will move around. With some practice, the part you want to be in focus will pop into place. 

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