diff --git a/build.gradle b/build.gradle
index 0f249663..afeff82e 100644
--- a/build.gradle
+++ b/build.gradle
@@ -48,7 +48,7 @@ dependencies {
     implementation 'ome:formats-gpl:6.9.1'
     implementation 'info.picocli:picocli:4.6.1'
     implementation 'com.univocity:univocity-parsers:2.8.4'
-    implementation 'com.bc.zarr:jzarr:0.3.3-gs-SNAPSHOT'
+    implementation 'com.bc.zarr:jzarr:0.3.5'
     // implementation 'org.carlspring.cloud.aws:s3fs-nio:1.0-SNAPSHOT'
     // implementation 'io.nextflow:nxf-s3fs:1.1.0'
     implementation 'org.lasersonlab:s3fs:2.2.3'
diff --git a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
index 8fdf84c1..bae8e811 100644
--- a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
+++ b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
@@ -69,6 +69,7 @@
 import com.bc.zarr.ArrayParams;
 import com.bc.zarr.CompressorFactory;
 import com.bc.zarr.DataType;
+import com.bc.zarr.DimensionSeparator;
 import com.bc.zarr.ZarrArray;
 import com.bc.zarr.ZarrGroup;
 import com.glencoesoftware.bioformats2raw.MiraxReader.TilePointer;
@@ -1217,7 +1218,7 @@ public void saveResolutions(int series)
           .chunks(new int[] {1, 1, activeChunkDepth, activeTileHeight,
             activeTileWidth})
           .dataType(dataType)
-          .nested(nested)
+          .dimensionSeparator(getDimensionSeparator())
           .compressor(CompressorFactory.create(
               compressionType.toString(), compressionProperties));
       ZarrArray.create(getRootPath().resolve(resolutionString), arrayParams);
@@ -1853,6 +1854,10 @@ public static DataType getZarrType(int type) {
     }
   }
 
+  private DimensionSeparator getDimensionSeparator() {
+    return nested ? DimensionSeparator.SLASH : DimensionSeparator.DOT;
+  }
+
   private void checkOutputPaths() {
     if (pyramidName != null || !scaleFormatString.equals("%d/%d")) {
       LOGGER.info("Output will be incompatible with raw2ometiff " +
diff --git a/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java b/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
index ef975e97..ae2774c8 100644
--- a/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
+++ b/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
@@ -240,7 +240,12 @@ public void testDefaultLayoutIsSetAndIsNested() throws Exception {
     Integer layout = (Integer)
         z.getAttributes().get("bioformats2raw.layout");
     ZarrArray series0 = ZarrGroup.open(output.resolve("0")).openArray("0");
-    assertTrue(series0.getNested());
+
+    // no getter for DimensionSeparator in ZarrArray
+    // check that the correct separator was used by checking
+    // that the expected first chunk file exists
+    assertTrue(output.resolve("0/0/0/0/0/0/0").toFile().exists());
+
     // Also ensure we're using the latest .zarray metadata
     ObjectMapper objectMapper = new ObjectMapper();
     JsonNode root = objectMapper.readTree(
@@ -878,6 +883,12 @@ public void testDownsampleTypes(Downsampling type) throws IOException {
   public void testNestedStorage(boolean nested) throws IOException {
     input = fake();
     assertTool(nested ? "--nested" : "--no-nested");
+    if (nested) {
+      assertTrue(output.resolve("0/0/0/0/0/0/0").toFile().exists());
+    }
+    else {
+      assertTrue(output.resolve("0/0/0.0.0.0.0").toFile().exists());
+    }
   }
 
   /**