Add --rgb flag to raw2ometiff for H&E images with pyvips thumbnails

modules/bioformats2ometiff.nf

@@ -15,8 +15,9 @@ process bioformats2ometiff {
   touch "${image.simpleName}.ome.tiff"
   """
   script:
+  def rgb_flag = meta.he ? '--rgb' : ''
   """
   bioformats2raw $image 'raw_dir'
-  raw2ometiff 'raw_dir' "${image.simpleName}.ome.tiff"
+  raw2ometiff ${rgb_flag} 'raw_dir' "${image.simpleName}.ome.tiff"
   """
 }

modules/make_miniature.nf

@@ -17,15 +17,45 @@ process make_miniature {
     """
     #!/usr/bin/env python
 
-    from tiffslide import TiffSlide
-    import matplotlib.pyplot as plt
-    import os
+    import tifffile
+    from PIL import Image
+    import numpy as np
 
-    slide = TiffSlide('$image')
-
-    thumb = slide.get_thumbnail((512, 512))
-    if thumb.mode in ("RGBA", "P"): 
+    # Open the OME-TIFF file
+    with tifffile.TiffFile('$image') as tif:
+        # For pyramidal images, use the smallest level for efficiency
+        if len(tif.series) > 0 and hasattr(tif.series[0], 'levels') and len(tif.series[0].levels) > 1:
+            # Get the smallest pyramid level
+            level = tif.series[0].levels[-1]
+            img_array = level.asarray()
+        else:
+            # No pyramid or single level, read the full resolution
+            img_array = tif.asarray()
+
+    # Ensure proper data type for PIL (uint8)
+    if img_array.dtype != np.uint8:
+        # Scale to uint8 range if needed
+        img_min = img_array.min()
+        img_max = img_array.max()
+        if img_max > 255:
+            # Avoid division by zero
+            if img_max > img_min:
+                img_array = ((img_array - img_min) / (img_max - img_min) * 255).astype(np.uint8)
+            else:
+                img_array = np.zeros_like(img_array, dtype=np.uint8)
+        else:
+            img_array = img_array.astype(np.uint8)
+
+    # Convert numpy array to PIL Image
+    thumb = Image.fromarray(img_array)
+
+    # Create thumbnail (maintains aspect ratio)
+    thumb.thumbnail((512, 512))
+
+    # Ensure RGB mode
+    if thumb.mode != "RGB": 
       thumb = thumb.convert("RGB")
+
     thumb.save('miniature.jpg')
     """
   } else {