update docs

Author: alessandratrapani

docs/source/api.rst

@@ -131,8 +131,8 @@ Segmentation3D
 Methods
 ^^^^^^^
 .. automethod:: ndx_microscopy.Segmentation3D.add_roi
-.. automethod:: ndx_microscopy.Segmentation3D.voxel_to_image
-.. automethod:: ndx_microscopy.Segmentation3D.image_to_voxel
+.. automethod:: ndx_microscopy.Segmentation3D.voxel_to_volume
+.. automethod:: ndx_microscopy.Segmentation3D.volume_to_voxel
 .. automethod:: ndx_microscopy.Segmentation3D.create_roi_table_region
 
 SegmentationContainer

docs/source/examples.rst

@@ -492,7 +492,7 @@ Example of volumetric imaging with 3D ROI segmentation:
     # Add 3D ROIs using image masks
     roi_mask = np.zeros((height, width, depths), dtype=bool)
     roi_mask[256:266, 256:266, 4:6] = True  # 10x10x2 ROI
-    segmentation.add_roi(image_mask=roi_mask)
+    segmentation.add_roi(volume_mask=roi_mask)
 
     # Add ROIs using voxel masks
     voxel_mask = [
@@ -512,7 +512,7 @@ Example of volumetric imaging with 3D ROI segmentation:
     num_rois = len(segmentation.id)
     responses = np.zeros((frames, num_rois))
     
-    for i, roi_mask in enumerate(segmentation.image_mask[:]):
+    for i, roi_mask in enumerate(segmentation.volume_mask[:]):
         roi_data = data[:, roi_mask]
         responses[:, i] = np.mean(roi_data, axis=1)
 
@@ -552,7 +552,7 @@ Example of volumetric imaging with 3D ROI segmentation:
         # Access ROI data
         ophys = nwbfile.processing['ophys']
         rois = ophys['volume_rois']
-        roi_masks = rois.image_mask[:]
+        roi_masks = rois.volume_mask[:]
         
         # Access responses
         responses = ophys['volume_responses']

docs/source/format.rst

@@ -464,7 +464,7 @@ For 3D segmentation data.
         neurodata_type_inc: Segmentation
         doc: Results from image segmentation of a specific volumetric imaging space.
         datasets:
-          - name: image_mask
+          - name: volume_mask
             neurodata_type_inc: VectorData
             dims:
               - - num_roi

docs/source/release_notes.rst

@@ -3,6 +3,28 @@
 *************
 Release Notes
 *************
+Version 0.3.0 (May 29, 2025)
+==============================
+
+Deprecations and Changes
+-------------------------
+
+* Changed `image_to_voxel` in `volume_to_voxel`
+* Changed `voxel_to_image` in `voxel_to_volume`
+* Changed `image_mask` in `volume_mask` in VolumetricSegmentation
+
+Features
+--------
+
+
+Improvements
+------------
+
+
+Notes
+------
+
+
 
 Version 0.2.0 (March 19, 2025)
 ==============================