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add z-step_um metadata for the deskew plugin #343

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Merged
bls337 merged 1 commit into from
Dec 12, 2025
Merged

add z-step_um metadata for the deskew plugin #343

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5 changes: 4 additions & 1 deletion src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngine.java
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Original file line number Diff line number Diff line change
Expand Up @@ -237,7 +237,10 @@ protected DefaultSummaryMetadata addMMSummaryMetadata(JSONObject summaryMetadata
}
summaryMetadata.put(PropertyKey.AXIS_ORDER.key(), axes);

DefaultSummaryMetadata dsmd = (DefaultSummaryMetadata) dsmb.build();
// add "z-step_um" metadata to the image viewer (used in the deskew plugin)
DefaultSummaryMetadata dsmd = (DefaultSummaryMetadata) dsmb
.zStepUm(acqSettings_.volumeSettings().sliceStepSize())
.build();

summaryMetadata.put(PropertyKey.MICRO_MANAGER_VERSION.key(),
dsmd.getMicroManagerVersion());
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6 changes: 6 additions & 0 deletions ...in/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngineSCAPE.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
package org.micromanager.lightsheetmanager.model.acquisitions;

import mmcorej.StrVector;
import mmcorej.org.json.JSONException;
import mmcorej.org.json.JSONObject;
import org.micromanager.MultiStagePosition;
import org.micromanager.PositionList;
Expand Down Expand Up @@ -251,6 +252,11 @@ boolean run() {
currentAcquisition_ = new Acquisition(sink);

JSONObject summaryMetadata = currentAcquisition_.getSummaryMetadata();
try {
summaryMetadata.put("z-um_step", acqSettings_.volumeSettings().sliceStepSize());
} catch (JSONException e) {
studio_.logs().logError("Failed to add z-um_step metadata: " + e.getMessage());
}
DefaultSummaryMetadata dsmd = addMMSummaryMetadata(summaryMetadata, projectionMode);

// TODO(Brandon): where should i get this from?
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