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Merge pull request #155 from nicost/LightSheetControl
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Added LIghtSheetControl plugin documentation.
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nicost authored Dec 9, 2024
2 parents f2d55be + a534a19 commit ab128eb
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69 changes: 69 additions & 0 deletions _pages/LightSheetControl.md
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---
autogenerated: false
title: LightSheetControl - Automated stage synchronization
layout: page
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<table>

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**Summary:**

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This plugin was developed to facilitate synchronization of two stages in
a lightsheet microscope (fixed sheet illumination from the side, main stage moves the sample through the sheet, second stage moves the objective to keep the
sheet in focus). It can be used for all uses of the [Utilities-MultiStage](Utilities)
adapter to calibrate movement of the two stages.
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**Authors:**

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Kurt Thorn, refresh by Nico Stuurman
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**License:**

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BSD

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**Platforms:**

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All supported platforms

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### Operation


![](/media/LightSheetControl.png)


The following assumes that you have two stages, set as physical stages in the [Utilities-MultiStage device](Utilities). Move the first stage, for instance to the bottom of the sample, then move the second stage to get the sample in focus. Press "Add Reference Point". Move the sample up, refocus the second stage, add as a reference point, etc.. As you add points, the locations will be added to the graph in the bottom of the plugin and the the linear fit will be shown. You probably do not gain much by adding more than ~5 or so reference points, but the graph should help you judge.

Control points can be saved to disk and re-loaded. This may be useful, for instance, when using multiple objective lenses, each of which may have its own
Multi-stage calibration.
11 changes: 10 additions & 1 deletion _pages/Utilities.md
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Expand Up @@ -89,9 +89,18 @@ Improvements to the core have fixed this issue.

Combines two physical 1D stages into a single logical 1D stage. The
scale factor and offset for both physical stages are specified as
properties. Make sure to specify the properties "PhysicalStage-1" and
properties. When setting a position, all know stages will be moved
using the formula:

<code>
physicalPos = stageScalings_[i] * position + stageTranslations_[i];
stage->SetPositionUm(physicalPos);
</code>

Make sure to specify the properties "PhysicalStage-1" and
"PhysicalStage-2" (e.g. in System-&gt;Startup group preset).


## Combo XY Stage

Combines two physical 1D stages into a single logical 2D stage. The
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1 change: 1 addition & 0 deletions _pages/Version_2.0_Plugins.md
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Expand Up @@ -20,6 +20,7 @@ applications in microscopy:
- [HCS Site Generator](HCS_Site_Generator)
- [Intelligent Acquisition](Intelligent_Acquisition)
- [Image Flipper](Image_Flipper)
- [LightSheetControl](LightSheetControl)
- [Live Replay](Live_Replay)
- [Localization Microscopy](Localization_Microscopy)
- [MicroMagellan](MicroMagellan)
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