Merge pull request #25 from guiwitz/bioio

Bioio
guiwitz · Dec 13, 2024 · f78e55f · f78e55f
2 parents c0666e1 + 200483f
commit f78e55f
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 4 deletions.
diff --git a/microfilm/dataset/dataset.py b/microfilm/dataset/dataset.py
@@ -229,7 +229,8 @@ def __init__(
 
     def initialize(self):
 
-        from aicsimageio import AICSImage, readers
+        from bioio import BioImage
+        import bioio_tifffile
 
         # if no channel names are provided, consider all folders as channel
         if self.channel_name is None:
@@ -240,7 +241,7 @@ def initialize(self):
         self.channelfile = self.channel_name
 
         self.channel_imobj = [
-            AICSImage(os.path.join(self.expdir, x), dim_order="TYX", reader=readers.TiffReader)
+            BioImage(os.path.join(self.expdir, x), dim_order="TYX", reader=bioio_tifffile.Reader)
             for x in self.channel_name
         ]
 

diff --git a/setup.cfg b/setup.cfg
@@ -44,14 +44,16 @@ install_requires =
 
 [options.extras_require]
 multipage =
-    aicsimageio
+    bioio
+    bioio-tifffile
 nd2 =
     nd2reader
 animation =
     imageio-ffmpeg
     ipywidgets
 all =
-    aicsimageio
+    bioio
+    bioio-tifffile
     nd2reader
     imageio-ffmpeg
     ipywidgets