Merge pull request #8 from zoccoler/add_notebooks

minor fixes to images and notebook paths
haesleinhuepf · May 10, 2022 · 2ddeb66 · 2ddeb66
2 parents 417aeb8 + fc6a38a
commit 2ddeb66
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Showing 5 changed files with 31 additions and 26 deletions.
diff --git a/notebooks_and_napari/batch_segmentation_workflow.ipynb b/notebooks_and_napari/batch_segmentation_workflow.ipynb
diff --git a/notebooks_and_napari/data/nuclei3d.tif b/notebooks_and_napari/data/nuclei3d.tif
diff --git a/notebooks_and_napari/data/nuclei3d_cropped.tif b/notebooks_and_napari/data/nuclei3d_cropped.tif
diff --git a/notebooks_and_napari/my_segmentation_workflow.ipynb b/notebooks_and_napari/my_segmentation_workflow.ipynb
diff --git a/notebooks_and_napari/save_image_locally.ipynb b/notebooks_and_napari/save_image_locally.ipynb
@@ -18,7 +18,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 5,
    "id": "7821bc45-75ae-4968-b432-007646a73525",
    "metadata": {},
    "outputs": [],
@@ -29,18 +29,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 6,
    "id": "b4ff20e4-3190-4e89-ace9-20149bf68fea",
    "metadata": {},
    "outputs": [],
    "source": [
-    "image = cells3d()[:,0]\n",
+    "image = cells3d()[:,1]\n",
     "image_cropped = image[:,45:230,25:220]"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 7,
    "id": "5829401d-833e-4322-9d72-6e1ea12ba59c",
    "metadata": {},
    "outputs": [],
@@ -50,7 +50,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 8,
    "id": "bcb856e6-a03c-4ba8-8b55-7d60be3f3fbc",
    "metadata": {},
    "outputs": [],