Sample holder
By the end of this page fibsemOS knows which holder is in the chamber, which grid is in each of its slots and where each slot sits on the stage, and you can move between grids by name.
Before you start
- You are connected and can image and move.
- The grids are loaded in the holder and you know which slot each is in.
1. The Sample tab
Open the Sample tab in the control panel. It is the instrument’s view of the grids: the holder, its slots, and what is in them.
- (1) The holder’s facts: how many slots, how many are calibrated, and the pre-tilt and reference rotation it was calibrated against. The holder is saved with the microscope configuration.
- (2) One row per slot: a dot that is green once the slot has a calibrated position, the slot’s name, and the grid in it.
- (3) Move to this slot. Greyed out until the slot is calibrated.
- (4) The pencil: edit the holder’s name and slot count, and calibrate the slots.
The hint below the rows says what is missing. On a fresh install nothing is calibrated, so nothing can move to a slot yet.
2. Say which grid is where
Type a name into a slot’s row and press Enter. The name is the grid’s identity from here on: the views’ stage line shows it, positions and lamellae are recorded against it, and the Grids view of an experiment lists grids by it. Clear the name when the grid comes out.
What is in the holder is remembered between sessions, so name grids when you load them and the next session starts knowing.
With an experiment open, naming a slot also renames that grid’s record on the Grids tab. Once a grid has run in the grid workflow its name is fixed, because its folder and images carry it, and naming its slot is refused.
3. Calibrate the slots
A slot’s position is where its grid centre sits on the stage. It is measured once per holder, not per session, because the holder’s geometry does not change: only the grids in it do. Press the pencil to open the calibration.
Check the name and the slot count. Two for a standard shuttle.
Positions are captured at the SEM orientation, flat and pre-tilted, and the other orientations are derived from them, so the dialog refuses to capture anywhere else. Press Move to SEM orientation and wait for the green line.
For each slot, drive the stage until the centre of that slot’s grid is under the electron beam. Use the Movement tab, or double-click in the SEM image at a low magnification where the whole grid is visible, then press Capture. The stage’s x, y and z are recorded; rotation and tilt come from the orientation. Move to slot drives back to what was captured, to check it.
A slot with no grid in it can be skipped and calibrated later.
Save writes the holder into the microscope configuration. Both slots now show a green dot, and the facts line says so.
4. Move between grids
Press a slot’s move button. The stage drives to that slot’s grid centre at the SEM orientation, the views are re-imaged, and the stage line names the grid you are now on. At a wide field of view you see the whole grid, its rim, and the holder around it.
The AutoLamella overview uses the same positions to draw an outline for each grid, which is why the hint on an uncalibrated holder mentions overviews.
5. Where it lives
The holder, with its slot positions, is saved in the microscope
configuration that was connected when it was calibrated, under
calibration: every holder the instrument has, and which one is on the
stage. The grid names are kept in that configuration’s session state,
config/session/<configuration file>.yaml. A sample-holder.yaml from an
earlier version, beside the configuration files, is imported when the
configuration has no holder of its own, and is carried into the
configuration the next time it is saved.
If a different holder is fitted, edit the name and slot count with the pencil and calibrate it; the old positions are discarded because they no longer apply. A position captured against a different pre-tilt or reference rotation is also treated as uncalibrated, which is what the facts line’s “pre-tilt” and “reference rotation” are telling you.
6. The Arctis: holder and loader
On an Arctis the Sample tab has two panels. The holder is the compustage’s one working slot, where the autoloader puts every grid. Below it is the Loader: the autoloader’s magazine, with its twelve slots and the grid in each.
- (1) The holder: the working slot.
- (2) The Loader: one row per magazine slot, with the grid’s name and a button that loads the grid into the working slot, or sends the loaded grid back to the magazine. An exchange, unloading one grid and loading the next, takes about 3 minutes.
- (3) Scan the magazine: the autoloader checks every slot for a grid. A scan takes about 10 minutes, with the magazine shut. After the magazine is undocked its slots read as unknown until the next scan.
- (4) The pencil: calibrate the working slot.
Name grids in the magazine’s rows as in a shuttle slot. The name is written to the autoloader’s slot description, so it stays with the slot between sessions.
Calibrate the working slot
Until it is calibrated, the working slot is the stage origin. A grid the autoloader loads sits off the origin in x, y and z, by the same amount on every load, and out of coincidence. Grid tasks centre their overviews on the working slot, so calibrate it once per instrument.
Load a grid, then press the pencil. The calibration is the one in section 3, for one slot: the holder’s name and slot count are fixed.
Move to the SEM orientation as for a shuttle. Then drive the stage until the centre of the grid is under the electron beam, with the beams in coincidence there, and press Capture. The height is captured as well as x and y. Move to slot drives back to what was captured, to check it.
Check and save. The working slot’s dot turns green, and the calibration is kept across connections.
A calibration captured against a different pre-tilt or reference rotation is dropped with a warning when the instrument connects, and the working slot is the origin again until it is recalibrated.
Next
Fluorescence imaging on an Arctis, or straight on to the AutoLamella workflow.