Acquire a Z-stack
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Learning-oriented, for users. A Z-stack captures the same field at several focus depths, so nothing thick is ever fully out of focus. In this tutorial you'll acquire a stack at one position and then across a small grid.
Why a Z-stack
- Thick / uneven samples; capturing the sharpest plane; later extended-depth-of-field.
Step 1 — Set the Z-range and step count
- How to set the centre plane, the Z-range, and the number of steps.
- Note the automatic stop at the upper/lower stage limits.
TODO image
Z-stack parameter panel. Notion source:
FRAME_DOKU_FROM_NOTION/FAT FRAME #0007 Korea - Part 8 (1)
("testing Z-Stack at one position with 20x and diffusor").
Step 2 — Acquire at a single position
- Run; scroll through the resulting planes.
Step 3 — Acquire a Z-stack across a grid
- Combine Z-stack with a small (e.g. 3x3) area scan.
- Note file size growth and OME-TIFF output.
TODO image
Notion source: FAT FRAME #0007 Korea - Part 8 (1) ("Z-Stack at array 3x3 ... and
OME TIFF output").
Choosing step size
- Rule of thumb relating step size to objective NA / depth of field.
- Link: How a microscope works / NA.