Tell Bioformats not to "flatten" pyramids (#193)

If an input image has a thumbnail or other subresolution image, this change
will allow us to read it without getting tripped up by the subresolutions.

ashlar/reg.py

@@ -226,6 +226,7 @@ def _init_metadata(self):
         metadata = service.createOMEXMLMetadata()
         self._reader = ChannelSeparator()
         self._reader.setMetadataStore(metadata)
+        self._reader.setFlattenedResolutions(False)
         # For multi-scene .CZI files, we need raw tiles instead of the
         # auto-stitched mosaic and we don't want labels or overview images
         options = DynamicMetadataOptions()