From 6b1da5172b3f85b109dc27ea6edcfe0b8cfe84c3 Mon Sep 17 00:00:00 2001
From: David Gault <d.gault@dundee.ac.uk>
Date: Fri, 3 Nov 2023 15:44:22 +0000
Subject: [PATCH] Ensure WellSampleIndex is used when comparing to OME-XML

---
 src/loci/formats/in/ZarrReader.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/loci/formats/in/ZarrReader.java b/src/loci/formats/in/ZarrReader.java
index 99899a3..2b239fd 100644
--- a/src/loci/formats/in/ZarrReader.java
+++ b/src/loci/formats/in/ZarrReader.java
@@ -983,8 +983,8 @@ private void parseOMEXML(Location omeMetaFile, MetadataStore store, ArrayList<St
         NonNegativeInteger row = omexmlMeta.getWellRow(plateIndex, wellIndex);
 
         String rowLetter = getRowString(row.getValue());
-        String expectedPath = rowLetter + File.separator + (col.getValue() + 1) + File.separator  + "0";
         for (int wellSampleIndex = 0; wellSampleIndex < omexmlMeta.getWellSampleCount(plateIndex, wellIndex); wellSampleIndex++) { 
+          String expectedPath = rowLetter + File.separator + (col.getValue() + 1) + File.separator  + wellSampleIndex;
           String imageRef = omexmlMeta.getWellSampleImageRef(plateIndex, wellIndex, wellSampleIndex);
           imageRefPaths.put(imageRef, expectedPath);
         }