general update (mostly read through)

ome · Aug 31, 2023 · 2cc7195 · 2cc7195
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diff --git a/.gitignore b/.gitignore
@@ -1,2 +1,3 @@
 data.zarr
 METADATA.ome.xml
+a.ome.tiff
diff --git a/3_POSIX_Bash.ipynb b/3_POSIX_Bash.ipynb
@@ -1227,7 +1227,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 35,
    "id": "f709974e-a12d-46e5-86bb-324e8ba00642",
    "metadata": {},
    "outputs": [],
@@ -2215,6 +2215,27 @@
     "</table>\n"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "97256625-31f7-4d88-8faa-12b8d11df986",
+   "metadata": {},
+   "source": [
+    "## Excercise 2:\n",
+    "### Use the tools above to find inspect the data you chose, and convert it to OME-TIFF."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 36,
+   "id": "3d2aa171-0191-428a-8dc0-06a5fea0ccb2",
+   "metadata": {
+    "jp-MarkdownHeadingCollapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "## Do something here or on the command-line. If you are having issues, ask."
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "c1a3d89a-e7f3-4180-b506-69865c12db9b",

diff --git a/4_OMETiff_Python.ipynb b/4_OMETiff_Python.ipynb
@@ -21,12 +21,49 @@
     "\n",
     "## Day 2 - Session 1: Image Data Management - 10:15 to 11:15 \"Get set\"\n",
     "\n",
-    "### Continuing from `3_Bash` in Python!..."
+    "### Continuing from `3_Bash` in Python!...\n",
+    "\n",
+    "Quick introduction to / comparison of:\n",
+    " * scikit-image\n",
+    " * aicsimageio\n",
+    " * tifffile\n",
+    " * and ome-types"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 48,
+   "execution_count": 9,
+   "id": "c65afca4-27bd-41f6-b59a-ce2fc7d9cd88",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import skimage as ski\n",
+    "image  = ski.io.imread(\"a.ome.tiff\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "bc8764bc-151a-46e0-8444-7344f5f65cd6",
+   "metadata": {},
+   "source": [
+    "https://datacarpentry.org/image-processing/"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 59,
+   "id": "b9ec37a2-5bd0-42a2-89a7-07bc03a614db",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from aicsimageio import AICSImage\n",
+    "\n",
+    "img = AICSImage(\"a.ome.tiff\") "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
    "id": "79ded011-475a-4320-993d-2227b620681c",
    "metadata": {},
    "outputs": [],
@@ -39,15 +76,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 55,
+   "execution_count": 11,
    "id": "8a8d96dc-e6d3-4e9d-944c-b66160811305",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "id='Image:0' name='data/a' pixels={'channels': [{'annotation_refs': [], 'light_path': {'excitation_filters': [], 'emission_filters': [], 'annotation_refs': []}, 'id': 'Channel:0:0', 'samples_per_pixel': 1, 'color': Color('white', rgb=(255, 255, 255))}], 'bin_data_blocks': [], 'tiff_data_blocks': [{'uuid': {'value': 'urn:uuid:0cc95cd0-950f-40bb-bc97-77a3fe7f7b64', 'file_name': 'a.ome.tiff'}, 'plane_count': 1}], 'planes': [], 'id': 'Pixels:0', 'dimension_order': <Pixels_DimensionOrder.XYZCT: 'XYZCT'>, 'type': <PixelType.UINT8: 'uint8'>, 'significant_bits': 8, 'interleaved': False, 'big_endian': False, 'size_x': 512, 'size_y': 512, 'size_z': 1, 'size_c': 1, 'size_t': 1}\n"
+      "id='Image:0' name='data/a' pixels={'channels': [{'annotation_refs': [], 'light_path': {'excitation_filters': [], 'emission_filters': [], 'annotation_refs': []}, 'id': 'Channel:0:0', 'samples_per_pixel': 1, 'color': Color('white', rgb=(255, 255, 255))}], 'bin_data_blocks': [], 'tiff_data_blocks': [{'uuid': {'value': 'urn:uuid:d8f35575-5655-4b0e-8885-a952f05ebaeb', 'file_name': 'a.ome.tiff'}, 'plane_count': 1}], 'planes': [], 'id': 'Pixels:0', 'dimension_order': <Pixels_DimensionOrder.XYZCT: 'XYZCT'>, 'type': <PixelType.UINT8: 'uint8'>, 'significant_bits': 8, 'interleaved': False, 'big_endian': False, 'size_x': 512, 'size_y': 512, 'size_z': 1, 'size_c': 1, 'size_t': 1}\n"
      ]
     }
    ],
@@ -60,15 +97,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 56,
-   "id": "289f0d8b-a10a-4bf4-8f8f-909117954b5f",
-   "metadata": {},
+   "execution_count": 12,
+   "id": "2869cf30-3f91-44ef-8fc3-bdbc45ba242c",
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "id='Image:0' name='data/a' pixels={'channels': [{'annotation_refs': [], 'light_path': {'excitation_filters': [], 'emission_filters': [], 'annotation_refs': []}, 'id': 'Channel:0:0', 'samples_per_pixel': 1, 'color': Color('white', rgb=(255, 255, 255))}], 'bin_data_blocks': [], 'tiff_data_blocks': [{'uuid': {'value': 'urn:uuid:0cc95cd0-950f-40bb-bc97-77a3fe7f7b64', 'file_name': 'a.ome.tiff'}, 'plane_count': 1}], 'planes': [], 'id': 'Pixels:0', 'dimension_order': <Pixels_DimensionOrder.XYZCT: 'XYZCT'>, 'type': <PixelType.UINT8: 'uint8'>, 'significant_bits': 8, 'interleaved': False, 'big_endian': False, 'size_x': 512, 'size_y': 512, 'size_z': 1, 'size_c': 1, 'size_t': 1}\n"
+      "id='Image:0' name='data/a' pixels={'channels': [{'annotation_refs': [], 'light_path': {'excitation_filters': [], 'emission_filters': [], 'annotation_refs': []}, 'id': 'Channel:0:0', 'samples_per_pixel': 1, 'color': Color('white', rgb=(255, 255, 255))}], 'bin_data_blocks': [], 'tiff_data_blocks': [{'uuid': {'value': 'urn:uuid:d8f35575-5655-4b0e-8885-a952f05ebaeb', 'file_name': 'a.ome.tiff'}, 'plane_count': 1}], 'planes': [], 'id': 'Pixels:0', 'dimension_order': <Pixels_DimensionOrder.XYZCT: 'XYZCT'>, 'type': <PixelType.UINT8: 'uint8'>, 'significant_bits': 8, 'interleaved': False, 'big_endian': False, 'size_x': 512, 'size_y': 512, 'size_z': 1, 'size_c': 1, 'size_t': 1}\n"
      ]
     }
    ],
@@ -78,15 +117,11 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": 59,
-   "id": "b9ec37a2-5bd0-42a2-89a7-07bc03a614db",
+   "cell_type": "markdown",
+   "id": "4db4f9ea-8e2b-42d4-a0e5-9216774e9940",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "from aicsimageio import AICSImage\n",
-    "\n",
-    "img = AICSImage(\"a.ome.tiff\") "
+    "## Exercise 3: Play! (Time-permitting)"
    ]
   },
   {