- read ome xml tiff

ndbioimage/Cargo.toml

@@ -33,7 +33,7 @@ libczirw-sys = { version = "0.5", optional = true }
 ndarray = { version = "0.17", features = ["serde"] }
 num = "0.4"
 numpy = { version = "0.29", optional = true }
-ome-metadata = "0.5"
+ome-metadata = "0.6"
 ordered-float = { version = "5", optional = true }
 phf = { version = "0.14", features = ["macros"] }
 postcard = { version = "1", features = ["use-std"], optional = true }

ndbioimage/src/readers/tiff.rs

@@ -156,6 +156,18 @@ impl Reader for TiffReader {
             .unwrap_or(1)
             == 2;
 
+        let image_description = reader.current_ifd().get_tag(Tag::ImageDescription);
+        let p_ndim = if n_samples > 1 { 3u8 } else { 2u8 };
+        let (size_c, size_t, size_z) = if let Ok(Value::Ascii(xml)) = image_description
+            && xml.starts_with("<?xml")
+        {
+            let ome = Ome::from_xml(xml)?;
+            (
+                ome.image[0].pixels.size_c as usize,
+                ome.image[0].pixels.size_t as usize,
+                ome.image[0].pixels.size_z as usize,
+            )
+        } else {
             let imagej_bytes = reader
                 .current_ifd()
                 .get_tag(Tag::Unknown(50839))
@@ -166,7 +178,7 @@ impl Reader for TiffReader {
             };
             let metadata_str = String::from_utf8_lossy(&imagej_bytes);
             let metadata_map = parse_imagej_metadata(&metadata_str);
-        let p_ndim = if n_samples > 1 { 3u8 } else { 2u8 };
+
             let size_c = if p_ndim == 3 {
                 n_samples
             } else {
@@ -198,6 +210,8 @@ impl Reader for TiffReader {
             } else {
                 size_z
             };
+            (size_c, size_t, size_z)
+        };
         drop(reader);
 
         new.shape = Shape {
@@ -220,6 +234,12 @@ impl Reader for TiffReader {
 
     fn metadata(&self) -> Result<Ome, Error> {
         let mut reader = self.get_reader()?;
+        let image_description = reader.current_ifd().get_tag(Tag::ImageDescription);
+        if let Ok(Value::Ascii(xml)) = image_description
+            && xml.starts_with("<?xml")
+        {
+            Ok(Ome::from_xml(xml)?)
+        } else {
             let imagej_bytes = reader
                 .current_ifd()
                 .get_tag(Tag::Unknown(50839))
@@ -354,6 +374,7 @@ impl Reader for TiffReader {
             });
             Ok(ome)
         }
+    }
 
     fn get_frame(&self, c: usize, z: usize, t: usize) -> Result<Frame, Error> {
         let (page_idx, offset, stride) = if self.p_ndim == 3 {
@@ -521,6 +542,8 @@ mod tests {
         metadata_e: "tiff/1xp53-01-AP1.tiff",
         metadata_f: "tiff/test.tif",
         metadata_g: "tiff/YTL1849A111_2023_05_04__14_46_19_cellnr_1_track.tif",
-        metadata_h: "tiff/Wapl-AID_C46_13_tagRFPt_MCP_well1_video1_1_max.tif"
+        metadata_h: "tiff/Wapl-AID_C46_13_tagRFPt_MCP_well1_video1_1_max.tif",
+        metadata_i: "tiff/R1_NRF1_Gtf3a500nM_REAL_20260731_25pct_500ms_001_MMStack_PosR1_NRF1_Gtf3a500nM_REAL_20260731_25pct_500ms_001.ome.tif"
+        metadata_j: "tiff/20260922_Pos0_max.tif"
     }
 }