notebook updates

templates/3a_monitor_MIBI_run.ipynb

@@ -93,7 +93,9 @@
  "\n",
  "* The `plot_mph_metrics` run callback will compute the median pulse height data for each FOV, and plot the results once the run has completed. Additional arguments are: `regression` which when set to True will also plot the linear regression line for the data. <br/> (See [3d_compute_median_pulse_height](./3d_compute_median_pulse_height.ipynb) for more details.)\n",
  "\n",
- "* The `image_stitching` run callback will create a single image, which stitched together all FOV images for a specific channel. Additional arguments are: `channels`. <br/> (See [3e_stitch_images](./3e_stitch_images.ipynb) for more details.)"
+ "* The `image_stitching` run callback will create a single image, which stitched together all FOV images for a specific channel. Additional arguments are: `channels`. <br/> (See [3e_stitch_images](./3e_stitch_images.ipynb) for more details.)\n",
+ "\n",
+ "* The `check_incomplete_fovs` run callback will check the run for any partially generated images. <br/> (See [3b_extract_images_from_bin](./3b_extract_images_from_bin.ipynb) for more details.)"
  ]
  },
  {
@@ -103,7 +105,7 @@
  "outputs": [],
  "source": [
  "fov_callback, run_callback, intermediate_callback = build_callbacks(\n",
- " run_callbacks = ['image_stitching'],\n",
+ " run_callbacks = ['image_stitching', 'check_incomplete_fovs'],\n",
  " intermediate_callbacks = ['plot_qc_metrics', 'plot_mph_metrics'],\n",
  " fov_callbacks = ['extract_tiffs', 'generate_pulse_heights'],\n",
  " tiff_out_dir=extraction_dir,\n",

templates/3b_extract_images_from_bin.ipynb

@@ -24,7 +24,7 @@
  "import os\n",
  "\n",
  "from toffy.panel_utils import load_panel\n",
- "from toffy.bin_extraction import extract_missing_fovs"
+ "from toffy.bin_extraction import extract_missing_fovs, incomplete_fov_check"
  ]
  },
  {
@@ -99,6 +99,25 @@
  "source": [
  "extract_missing_fovs(base_dir, extraction_dir, panel)"
  ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "3c7985e3-7f9a-499c-bb42-13e72cd340e5",
+ "metadata": {},
+ "source": [
+ "## Check for any incomplete FOVs\n",
+ "If the instrument is shut off part way through a run, this can result in output FOVs which are generated, but missing counts in parts of the images. The cell below will check for any incompete FOVs and warn you if any exist."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "5cdf46cf-edf3-4889-b1b5-08601b5b3496",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "incomplete_fov_check(bin_file_dir, extraction_dir)"
+ ]
  }
  ],
  "metadata": {
@@ -117,7 +136,7 @@
  "name": "python",
  "nbconvert_exporter": "python",
  "pygments_lexer": "ipython3",
- "version": "3.8.16"
+ "version": "3.9.16"
  }
  },
  "nbformat": 4,