diff --git a/docs/notebooks/basic_usage.ipynb b/docs/notebooks/basic_usage.ipynb index 45afc49..ae5aba9 100644 --- a/docs/notebooks/basic_usage.ipynb +++ b/docs/notebooks/basic_usage.ipynb @@ -145,7 +145,7 @@ "roi_table = ngff_image.table.get_table(\"FOV_ROI_table\")\n", "\n", "print(f\"{roi_table.list_field_indexes=}\")\n", - "print(f\"{roi_table.get_roi(\"FOV_1\")=}\")\n", + "print(f\"{roi_table.get_roi('FOV_1')=}\")\n", "\n", "roi_table.table" ] @@ -175,6 +175,13 @@ "print(f\"{new_ngff_image.num_levels=}\")" ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, { "cell_type": "code", "execution_count": null, @@ -199,7 +206,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.7" + "version": "3.11.10" } }, "nbformat": 4, diff --git a/docs/notebooks/image.ipynb b/docs/notebooks/image.ipynb index 618034b..06a0014 100644 --- a/docs/notebooks/image.ipynb +++ b/docs/notebooks/image.ipynb @@ -330,7 +330,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.7" + "version": "3.11.10" } }, "nbformat": 4, diff --git a/docs/notebooks/processing.ipynb b/docs/notebooks/processing.ipynb index da1c57d..30e5550 100644 --- a/docs/notebooks/processing.ipynb +++ b/docs/notebooks/processing.ipynb @@ -90,7 +90,7 @@ "# - calculate the MIP\n", "# - set the data in the MIP image\n", "for roi in roi_table.list_rois:\n", - " print(f\" - Processing ROI {roi.infos.get(\"field_index\")}\")\n", + " print(f\" - Processing ROI {roi.infos.get('field_index')}\")\n", " patch = source_image.get_array_from_roi(roi)\n", " mip_patch = patch.max(axis=1, keepdims=True)\n", " mip_image.set_array_from_roi(patch=mip_patch, roi=roi)\n", @@ -162,7 +162,7 @@ "\n", "roi_list = []\n", "for roi in roi_table.list_rois:\n", - " print(f\" - Processing ROI {roi.infos.get(\"field_index\")}\")\n", + " print(f\" - Processing ROI {roi.infos.get('field_index')}\")\n", " roi.z_length = 1 # In the MIP image, the z dimension is 1\n", " roi_list.append(roi)\n", "\n", @@ -243,7 +243,7 @@ "print(\"Source image loaded with shape:\", source_image.shape)\n", "\n", "# Get a ROI table\n", - "roi_table = mip_ngff.table.get(\"FOV_ROI_table\")\n", + "roi_table = mip_ngff.table.get_table(\"FOV_ROI_table\")\n", "print(\"ROI table loaded with\", len(roi_table.list_rois), \"ROIs\")\n", "\n", "# Find the DAPI channel\n", @@ -255,8 +255,8 @@ "# - set the data in segmentation image\n", "max_label = 0\n", "for roi in roi_table.list_rois:\n", - " print(f\" - Processing ROI {roi.infos.get(\"field_index\")}\")\n", - " patch = source_image.array_from_roi(roi, c=dapi_idx)\n", + " print(f\" - Processing ROI {roi.infos.get('field_index')}\")\n", + " patch = source_image.get_array_from_roi(roi, c=dapi_idx)\n", " segmentation = otsu_threshold_segmentation(patch, max_label)\n", "\n", " # Add the max label of the previous segmentation to avoid overlapping labels\n", @@ -303,7 +303,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.7" + "version": "3.11.10" } }, "nbformat": 4,