From b91e8f006268edd9cd914d74ad324cfd3836498c Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Wed, 24 Jun 2026 14:25:50 -0500
Subject: [PATCH 1/2] CellSens: respect fill color setting

---
 components/formats-gpl/src/loci/formats/in/CellSensReader.java | 1 +
 1 file changed, 1 insertion(+)

diff --git a/components/formats-gpl/src/loci/formats/in/CellSensReader.java b/components/formats-gpl/src/loci/formats/in/CellSensReader.java
index 54a254e7869..d80703722cd 100644
--- a/components/formats-gpl/src/loci/formats/in/CellSensReader.java
+++ b/components/formats-gpl/src/loci/formats/in/CellSensReader.java
@@ -529,6 +529,7 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
     throws FormatException, IOException
   {
     FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
+    Arrays.fill(buf, getFillColor());
 
     if (getCoreIndex() < core.size() - 1 && getCoreIndex() < rows.size()) {
       int tileRows = rows.get(getCoreIndex());

From de810a7b00a9f11d81a8d543dc1bb0b127eac722 Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Wed, 24 Jun 2026 15:30:05 -0500
Subject: [PATCH 2/2] Parse and apply default background color for each pyramid

---
 .../formats-gpl/src/loci/formats/in/CellSensReader.java    | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/components/formats-gpl/src/loci/formats/in/CellSensReader.java b/components/formats-gpl/src/loci/formats/in/CellSensReader.java
index d80703722cd..04b90b6ea3f 100644
--- a/components/formats-gpl/src/loci/formats/in/CellSensReader.java
+++ b/components/formats-gpl/src/loci/formats/in/CellSensReader.java
@@ -545,6 +545,9 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
       int outputRowLen = w * pixel;
 
       Pyramid pyramid = getCurrentPyramid();
+      if (pyramid.fillColor != null) {
+        Arrays.fill(buf, pyramid.fillColor);
+      }
 
       for (int row=0; row<tileRows; row++) {
         for (int col=0; col<tileCols; col++) {
@@ -1958,6 +1961,9 @@ else if (tag == GREEN_OFFSET) {
               else if (tag == BLUE_OFFSET) {
                 pyramid.blueOffset = DataTools.parseDouble(value);
               }
+              else if (tag == DEFAULT_BACKGROUND_COLOR) {
+                pyramid.fillColor = Byte.parseByte(value);
+              }
               else if (tag == VALUE) {
                 if (tagPrefix.equals("Channel Wavelength ")) {
                   pyramid.channelWavelengths.add(DataTools.parseDouble(value));
@@ -2665,6 +2671,7 @@ class Pyramid {
     public Double redOffset;
     public Double greenOffset;
     public Double blueOffset;
+    public Byte fillColor;
 
     public ArrayList<String> channelNames = new ArrayList<String>();
     public ArrayList<Double> channelWavelengths = new ArrayList<Double>();