diff --git a/notebooks/stitching_multi_view.ipynb b/notebooks/stitching_multi_view.ipynb index 00356ad..87e2d67 100644 --- a/notebooks/stitching_multi_view.ipynb +++ b/notebooks/stitching_multi_view.ipynb @@ -34,7 +34,7 @@ "%matplotlib notebook\n", "\n", "# the package napari-stitcher is required for visualization with napari\n", - "VISUALIZE_USING_NAPARI = False\n", + "VISUALIZE_USING_NAPARI = True\n", "\n", "if VISUALIZE_USING_NAPARI:\n", " import napari\n", @@ -188,21 +188,48 @@ "metadata": {}, "outputs": [], "source": [ - "# import skimage.registration\n", + "registration.register?" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ "from multiview_stitcher import registration\n", "\n", "with dask.diagnostics.ProgressBar():\n", "\n", + " # phase shift registration\n", " params = registration.register(\n", - " # [msi_utils.get_sim_from_msim(msim) for msim in msims],\n", " msims,\n", " registration_binning={'z': 2, 'y': 8, 'x': 8},\n", " reg_channel_index=0,\n", " transform_key='affine_manual',\n", + " new_transform_key='translation_registered',\n", + " pre_registration_pruning_method=None,\n", + " groupwise_resolution_kwargs={\n", + " 'transform': 'translation',\n", + " }\n", " )\n", - " \n", - "for msim, param in zip(msims, params):\n", - " msi_utils.set_affine_transform(msim, param, transform_key='affine_registered', base_transform_key='affine_manual')" + "\n", + " # affine registration\n", + " params = registration.register(\n", + " msims,\n", + " registration_binning={'z': 2, 'y': 8, 'x': 8},\n", + " reg_channel_index=0,\n", + " transform_key='translation_registered',\n", + " new_transform_key='affine_registered',\n", + " pre_registration_pruning_method=None,\n", + " pairwise_reg_func=registration.registration_ANTsPy,\n", + " pairwise_reg_func_kwargs={\n", + " 'transform_types': ['Rigid', 'Affine'],\n", + " },\n", + " groupwise_resolution_kwargs={\n", + " 'transform': 'affine',\n", + " }\n", + " )" ] }, { @@ -223,16 +250,10 @@ " viewer = napari.Viewer(ndisplay=3)\n", "\n", " lds = viewer_utils.create_image_layer_tuples_from_msims(\n", - " msims, transform_key='affine_manual', n_colors=4,\n", - " name_prefix='pre-registered view',\n", - " contrast_limits=[0, 1000],\n", - " )\n", - " mlayers = viewer_utils.add_image_layer_tuples_to_viewer(viewer, lds, do_link_layers=True)\n", - "\n", - " lds = viewer_utils.create_image_layer_tuples_from_msims(\n", " msims, transform_key='affine_registered', n_colors=4,\n", " name_prefix='registered view',\n", " contrast_limits=[0, 1000],\n", + " positional_cmaps=False,\n", " )\n", " rlayers = viewer_utils.add_image_layer_tuples_to_viewer(viewer, lds, do_link_layers=True)" ]