From 2b11e814597de910e1e58f67a100bc7baba1c309 Mon Sep 17 00:00:00 2001
From: Brandon <brandon@asiimaging.com>
Date: Fri, 30 Oct 2026 15:06:16 -0700
Subject: [PATCH 1/2] leave the controller alone after a run refused before it
 set one up

---
 .../model/acquisitions/AcquisitionEngineScape.java         | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngineScape.java b/src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngineScape.java
index fd66d10a..b0ee80c4 100644
--- a/src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngineScape.java
+++ b/src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngineScape.java
@@ -116,6 +116,7 @@ boolean setup() {
         updateSettings();
 
         // set before any validation below can return early: finish() runs on every exit from setup()
+        controller_ = null;
         stageScanState_ = null;
         originalCoreCamera_ = null;
         originalChannelPreset_ = null;
@@ -1306,10 +1307,8 @@ void finish() {
         // TODO: figure out if we really want to return piezos to 0 position (maybe center position,
         //   maybe not at all since we move when we switch to setup tab, something else??)
         if (model_.devices().isUsingPLogic() && controller_ != null) {
-            // SCAPE: leave the imaging piezo where it is instead of driving it to 0. diSPIM 1.4
-            // passes centerPiezos=false for SCOPE (AcquisitionPanel line 4979). Parking at 0
-            // defocuses the live view and re-introduces the first-frame jump on the next run
-            // (issues #404 symptom 3 / #407).
+            // SCAPE: leave the imaging piezo where it is instead of driving it to 0. Parking at 0
+            // defocuses the live view and re-introduces the first-frame jump on the next run.
             controller_.cleanUpControllerAfterAcquisition(acqSettings_, false);
             controller_.stopSPIMStateMachines();
         }

From e7f25dcc158620ab24e48eb8dbe22e34812e0676 Mon Sep 17 00:00:00 2001
From: Brandon <brandon@asiimaging.com>
Date: Fri, 30 Oct 2026 16:25:19 -0700
Subject: [PATCH 2/2] let the image window close once the acquisition has
 finished writing

---
 .../model/acquisitions/AcquisitionEngine.java                | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngine.java b/src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngine.java
index 40559e52..df873e94 100644
--- a/src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngine.java
+++ b/src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngine.java
@@ -743,6 +743,11 @@ public boolean abortRequest() {
         if (acq == null) {
             return true; // nothing is running, so there is nothing to protect
         }
+        // the data is written and finish() is only restoring the hardware, so it is safe to
+        // close the window
+        if (cleaningUp_ && acq.getDataSink().isFinished()) {
+            return true;
+        }
         // always refuse while a run is live: closing the live window would close the datastore
         // the run is still writing. answering yes only aborts, so the close succeeds on the next
         // attempt.