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fix piezo settings for stage scan #342

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Merged
bls337 merged 1 commit into from
Dec 11, 2025
Merged

fix piezo settings for stage scan #342

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2 changes: 1 addition & 1 deletion src/main/java/org/micromanager/lightsheetmanager/LightSheetManagerPlugin.java
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ public class LightSheetManagerPlugin implements MenuPlugin, SciJavaPlugin {
public static final String copyright = "Applied Scientific Instrumentation (ASI), 2022-2026";
public static final String description = "A plugin to control various types of light sheet microscopes.";
public static final String menuName = "Light Sheet Manager";
public static final String version = "0.5.2";
public static final String version = "0.5.3";

private Studio studio_;
private LightSheetManager model_;
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16 changes: 10 additions & 6 deletions src/main/java/org/micromanager/lightsheetmanager/model/PLogicSCAPE.java
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Expand Up @@ -441,7 +441,7 @@ public boolean prepareControllerForAcquisitionSide(
// for stage scanning we define the piezo position to be the home position (normally 0)
// this is basically required for interleaved mode (otherwise piezo would be moving every slice)
// and by convention we'll do it for all stage scanning
piezoCenter = piezo_.getHomePosition();
piezoCenter = piezo_.getHomePosition() * 1000.0; // convert to mm
} else {
// TODO: add centerAtCurrentZ to acqSettings
final boolean centerAtCurrentZ = false;
Expand All @@ -465,13 +465,17 @@ public boolean prepareControllerForAcquisitionSide(
// we modify it if we are taking "extra slice" for synchronous/overlap
int numSlicesHW = settings.volumeSettings().slicesPerView();

// tweak the parameters if we are using synchronous/overlap mode
// object is to get exact same piezo/scanner positions in first
// N frames (piezo/scanner will move to N+1st position but no image taken)
// tweak the piezo parameters if we are using synchronous/overlap mode
// object is to get exact same piezo/scanner positions in first N frames (piezo/scanner will move to N+1st position but no image taken)
// amplitude is (N-1)*stepSize and artificially make N*stepSize instead => multiply amplitude by (N)/(N-1)
// offset shifts by half a step
final CameraMode cameraMode = settings.cameraMode();
if (cameraMode == CameraMode.OVERLAP) {
piezoAmplitude *= numSlicesHW / (numSlicesHW - 1.0);
piezoCenter += piezoAmplitude / (2 * numSlicesHW);
if (settings.volumeSettings().slicesPerView() > 1) {
piezoAmplitude *= numSlicesHW / (numSlicesHW - 1.0);
}
// was piezoCenter += piezoAmplitude/(2*numSlicesHW) which isn't quite the same but close enough that nobody probably noticed
piezoCenter += settings.volumeSettings().sliceStepSize() / 2;
numSlicesHW += 1;
}

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