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Minor edits to BoneJ use case
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@gselzer
gselzer committed Jun 16, 2023
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91 changes: 56 additions & 35 deletions doc/examples/bonej.rst
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Expand Up @@ -6,29 +6,39 @@ Here we adapt a workflow from `the BoneJ2 paper <https://wellcomeopenresearch.or
napari Setup
------------

We will install one additional plugin to support this use case. Instructions for finding and installing a napari plugin are `here <https://napari.org/stable/plugins/find_and_install_plugin.html>`_
We will install one additional napari plugin, `napari-segment-blobs-and-things-with-membranes <https://github.com/haesleinhuepf/napari-segment-blobs-and-things-with-membranes>`_, to support this use case. Instructions for finding and installing a napari plugin are `here <https://napari.org/stable/plugins/find_and_install_plugin.html>`__

Please follow these instructions to install the plugin ``napari-segment-blobs-and-things-with-membranes``. More information
on this plugin can be found `here <https://github.com/haesleinhuepf/napari-segment-blobs-and-things-with-membranes>`_
To install ``napari-segment-blobs-and-things-with-membranes``, simply ensure that your napari environment is active and paste the following into your terminal:

.. code-block:: bash
pip install napari-segment-blobs-and-things-with-membranes
Once the plugin has been installed correctly, ``napari-segment-blobs-and-things-with-membranes`` will appear as an option within the ``Plugins`` menu of napari, and the ``Tools`` menu will be populated with the various functions of the plugin.

BoneJ2 Setup
------------

We need to first specify the endpoint that we will use to access BoneJ2.

We can configure napari-imagej to use a Fiji installation by opening the settings dialog and changing the ``imagej distribution_or_endpoint`` (described `here <../Configuration.html#imagej-directory-or-endpoint>`_). This example was created using an endpoint of ``sc.fiji:fiji:2.13.0+org.bonej:bonej-ops:MANAGED+org.bonej:bonej-plugins:MANAGED+org.bonej:bonej-utilities:MANAGED``.
We can configure napari-imagej to use BoneJ2 by opening the settings dialog and changing the ``imagej directory or endpoint`` (described `here <../Configuration.html#imagej-directory-or-endpoint>`__). Within the napari-imagej settings dialog, paste the following into the ``imagej directory or endpoint`` field, and click ``OK``:

.. code-block::
sc.fiji:fiji:2.13.0+org.bonej:bonej-ops:MANAGED+org.bonej:bonej-plugins:MANAGED+org.bonej:bonej-utilities:MANAGED
**Note that napari must be restarted for these changes to take effect!**

Preparing and Opening the Data
------------------------------

We will use the same data that was used in the BoneJ2 paper. Go ahead and download umzc_378p_Apteryx_haastii_head.tif.bz2 from doi:10.6084/m9.figshare.7257179. Here is a direct link to the specific image: https://figshare.com/ndownloader/files/13369043
We will use the same data that was used in the BoneJ2 paper. Go ahead and download ``umzc_378p_Apteryx_haastii_head.tif.bz2`` from ``doi:10.6084/m9.figshare.7257179``, linked directly `here <https://figshare.com/ndownloader/files/13369043>`__.

Opening Data in napari
^^^^^^^^^^^^^^^^^^^^^^

If you haven't already unzipped the file, then unzip the file. Once that is complete you can drag-and-drop the image onto napari to open it.
Once you've unzipped the downloaded file, you can drag-and-drop the image onto napari to open it.

.. figure:: https://media.imagej.net/napari-imagej/bonej2_open_data.png

Expand All @@ -51,8 +61,9 @@ First, we will blur the image to smooth intensity values and filter noise.

Setting the parameters for the Gaussian.

2. When the widget comes up, change the `sigma` value to 2 and ensure that the image layer is correctly set to the image that was opened.
Run the widget!
2. When the widget comes up, change the ``sigma`` value to ``2`` and ensure that the ``image`` layer is correctly set to the image that was opened.

3. Run the widget! When the blurring is complete, a new ``Image`` layer will appear in the napari viewer.

Now we will threshold the image to make it binary.

Expand All @@ -63,101 +74,111 @@ Now we will threshold the image to make it binary.
1. Within napari's menus choose: ``Tools > Segmentation / binarization > Threshold (Li et al 1993, scikit image, nsbatwm)``

2. When the widget comes up, ensure that the layer that is selected is the result of step 1.
Run the widget!

The result of thresholding is a Labels layer, but we will convert it to an Image layer to work with BoneJ2.
3. Run the widget! When the thresholding is complete, a new ``Labels`` layer will appear in the napari viewer.

4. Right click on the new ``Labels`` layer and select ``Convert to Image``. This will allow us to pass the result, now an ``Image`` layer, to BoneJ2.

.. figure:: https://media.imagej.net/napari-imagej/bonej2_convert_to_image.png

Converting the Labels layer to an Image layer for processing in BoneJ2.

1. Right click on the layer that was created by step 2 and select ``Convert to Image``.

Processing Data in napari with BoneJ2 and napari-imagej
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

**Calculating the degree of anisotropy:**

1. In the napari-imagej search bar type ``anisotropy``
1. In the napari-imagej search bar type ``anisotropy``, and select the ``Anisotropy`` Command from the search results.

2. Click ``Run``
2. Click ``Run``.

3. Select the ``inputImage`` that corresponds to the theshold layer created previously.

4. Check the ``Recommended minimums`` box.
4. Enter ``1.73`` as the samplingInterval.

5. Enter ``1.73`` as the samplingInterval.
5. Check the ``Recommended minimums`` box.

6. Click ``OK``.

This will output the degree of anisotropy measurement for the image.

.. figure:: https://media.imagej.net/napari-imagej/bonej2_anisotropy_parameters.png

Setting the parameters of BoneJ2's Anisotropy command.

This will output the degree of anisotropy measurement for the image.


**Calculating the fractal dimension:**

1. In the napari-imagej search bar type ``fractal dimension``
1. In the napari-imagej search bar type ``fractal dimension``, and select the ``Fractal dimension`` Command from the search results.

2. Click ``Run``
2. Click ``Run``.

3. Select the ``inputImage`` that corresponds to the theshold layer created previously.

4. Check the ``Automatic parameters`` box.

5. Click ``OK``.

This will output the fractal dimension of the image.

.. figure:: https://media.imagej.net/napari-imagej/bonej2_fractal_dimension.png

Setting the parameters of BoneJ2's fractal dimension command.

This will output the fractal dimension of the image.


**Calculating the surface area:**

1. In the napari-imagej search bar type ``surface area``
1. In the napari-imagej search bar type ``surface area``, and select the ``Surface area`` Command from the search results.

2. Click ``Run``
2. Click ``Run``.

3. Select the ``inputImage`` that corresponds to the theshold layer created previously.

.. figure:: https://media.imagej.net/napari-imagej/bonej2_surface_area.png
4. Click ``OK``.

Running BoneJ2's surface area command.

This command may take some time, because it runs a computationally costly algorithm called
**Note:** This command may take some time, because it runs a computationally costly algorithm called
"Marching Cubes" that creates a surface mesh of the image before computing the surface area.
This will output the surface area of the thresholded regions.

.. figure:: https://media.imagej.net/napari-imagej/bonej2_surface_area.png

Running BoneJ2's surface area command.


**Calculating the area/volume fraction:**

1. In the napari-imagej search bar type ``volume fraction``
1. In the napari-imagej search bar type ``volume fraction``, and select the ``Area/Volume fraction`` Command from the search results.

2. Click ``Run``
2. Click ``Run``.

3. Select the ``inputImage`` that corresponds to the theshold layer created previously.

4. Click ``OK``.

This will output the Bone Volume Fraction (BV/TV) measurement for the image.

.. figure:: https://media.imagej.net/napari-imagej/bonej2_area_volume_fraction.png

Running BoneJ2's area/volume fraction command.

This will output the Bone Volume Fraction (BV/TV) measurement for the image.


**Calculating the connectivity:**

1. In the napari-imagej search bar type ``connectivity``
1. In the napari-imagej search bar type ``connectivity``, and select the ``Connectivity (Modern)`` Command from the search results.

2. Click ``Run``
2. Click ``Run``.

3. Select the ``inputImage`` that corresponds to the theshold layer created previously.

4. Click ``OK``.

This will output the Euler characteristic and Conn.D for the image.

.. figure:: https://media.imagej.net/napari-imagej/bonej2_connectivity.png

Running BoneJ2's connectivity command.

This will output the Euler characteristic and Conn.D for the image.


The final measurements
^^^^^^^^^^^^^^^^^^^^^^
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