add fiji steps

ome · Aug 23, 2019 · 0d527f2 · 0d527f2
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diff --git a/docs/images/setup1.png b/docs/images/setup1.png
diff --git a/docs/images/setup2.png b/docs/images/setup2.png
diff --git a/docs/images/threshold1.png b/docs/images/threshold1.png
diff --git a/docs/images/threshold2.png b/docs/images/threshold2.png
diff --git a/docs/images/threshold3.png b/docs/images/threshold3.png
diff --git a/docs/images/threshold_script1.png b/docs/images/threshold_script1.png
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diff --git a/docs/index.rst b/docs/index.rst
@@ -1,17 +1,12 @@
-Welcome to guide template's documentation!
-==========================================
+Fiji
+====
 
 Contents:
 
 .. toctree::
-   :maxdepth: 2
-
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+   :maxdepth: 1
 
+   installation
+   manual_analysis
+   threshold_manual
+   threshold_scripting
diff --git a/docs/installation.rst b/docs/installation.rst
@@ -0,0 +1,57 @@
+How to install the OMERO plugin for Fiji/ImageJ
+===============================================
+
+Description:
+------------
+
+Fiji is a free open-source image processing package based on
+ImageJ, \ https://imagej.net/Fiji\ . The following workflow should how to
+install the OMERO plugin for Fiji and ImageJ.
+
+The OMERO plugin does not have yet and update site.
+
+**Setup step-by-step:**
+-----------------------
+
+We assume that you have already Fiji/ImageJ installed locally.
+
+In this section, we will cover the steps required to install the
+OMERO.imagej plugin for Fiji. If you wish to install it for ImageJ,
+an additional step is needed.
+
+We first describe how the common installation steps for ImageJ and Fiji.
+We then describe how to install the *Bio-Formats Package* for ImageJ.
+
+Installing the OMERO.imagej plugin also adds the dependencies
+required to connect to OMERO using the Script Editor of Fiji.
+
+Installation of the OMERO.imagej plugin for Fiji and ImageJ, the
+common steps:
+
+-  Download from \ https://www.openmicroscopy.org/omero/downloads \
+   the latest 5.x.x version of ImageJ/Fiji plugin for OMERO
+
+.. image:: images/setup1.png
+
+-  Extract the downloaded .zip archive. Remember where you extracted it to.
+
+-  Copy the extracted folder and paste it to the *plugins* folder
+   of Fiji.
+
+-  **Note:** Some Windows unzip apps create a double folder enclosing the
+   plugin. If that is the case, copy the inner OMERO.imagej-5.x.x
+   folder into *Fiji.app > plugins* folder.
+
+-  Now, restart Fiji. If you are using ImageJ, follow with the
+   additional step below.
+
+**Installation of Bio-Formats Package, ImageJ only:**
+
+-  Download the latest version of the *Bio-Formats Package* from:
+   https://www.openmicroscopy.org/bio-formats/downloads
+
+.. image:: images/setup2.png
+
+-  Move the downloaded file into the *ImageJ > plugins* folder.
+
+-  Restart ImageJ.
diff --git a/docs/manual_analysis.rst b/docs/manual_analysis.rst
@@ -0,0 +1,142 @@
+Analyze manually OMERO data using the OMERO plugin for Fiji/ImageJ
+==================================================================
+
+**Description:**
+----------------
+
+The following workflows should work
+both with ImageJ and Fiji, after these have been correctly set up with
+the OMERO plugin for Fiji/ImageJ.
+
+Using the User Interface of the OMERO plugin, we will show:
+
+-  How to connect to OMERO using the OMERO plugin for ImageJ/Fiji.
+
+-  How to open an image from OMERO.server into Fiji/ImageJ.
+
+-  How to manually save ROIs and measurements as CSV back to the
+   original image in OMERO.server.
+
+-  How to import a newly created image from Fiji/ImageJ into OMERO.
+
+**Setup:**
+----------
+
+-  Install Fiji on the local machine with the OMERO.insight-ij plugin.
+   The installation instructions can be found at :doc:`installation`.
+
+**Resources:**
+
+-  Samples images from the Image Data Resource (IDR) \ https://idr.openmicroscopy.org/webclient/?show=project-51\ .
+
+..
+
+**Step-by-step:**
+-----------------
+
+**Example 1: ROIs and measurement creation**
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+In this first example we show how to open an OMERO image in Fiji, draw ROIs, measure those ROIs and show how to save the ROIs and the measurement back to OMERO. 
+
+1. Launch Fiji/ImageJ.
+
+2. Go to *Plugins > OMERO > Connect* To OMERO. This will show a login
+   screen where you can enter the name of the server to connect to,
+   the username and password. The OMERO plugin will allow you to
+   browse your data in a similar manner to OMERO.web.
+
+3. In the OMERO login dialog, click the wrench icon\ |image1| and then
+   add the server address in the dialog. By default, only "localhost"
+   is listed. Click on the *plus* icon to add a new line to the list
+   and type into the line the server address.
+
+4. Click Apply.
+
+.. image:: images/manual2.png
+
+5.  Enter your credentials and click *Login*.
+
+6.  Select the **A-Fiji-dataset** Dataset.
+
+7.  Double-click on a thumbnail or on an Image in the left-hand tree to
+    open an Image in ImageJ.
+
+8.  Go to *Analyze > Tools > ROI Manager...*
+
+9.  Draw a shape using for example the Freehand selection tool.
+
+10. In the ROI manager, click the button *Add [t]* to add the shape to the
+    ROI Manager.
+
+.. image:: images/manual3.png
+
+11. Move to another channel, using the *c slider*.
+
+12. Draw other shapes if desired. Add drawing a shape. Click *Add [t]* to
+    add it to the Manager.
+
+13. When done with the drawing, click the button *Measure* in the ROI Manager.
+
+14. A dialog with measurements for each shape pops up.
+
+15. To save the ROI and the measurement back to OMERO,
+    go to *Plugins > OMERO > Save ROIs To OMERO*.
+
+16. In the dialog popping up, under the *Save* section select ROI and Measurements.
+
+17. The measurements are saved back to OMERO as a CSV file and linked to
+    the Image.
+
+.. image:: images/manual4.png
+
+18. Go back to OMERO.web, in the right-hand panel.
+
+19. Select the image opened in Fiji/ImageJ.
+
+20. Check that there is a new CSV file under the Attachments harmonica.
+
+21. Open the image in OMERO.iviewer to the see the ROIs and make sure
+    that you can interact with them.
+
+**Example 2: Cropping and import**
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+In this example, we show how to open an OMERO image, crop the image and
+import the cropped image back to OMERO as OME-TIFF.
+
+In this example we assume that the user is already logged in. If this is
+not the case, go back to the first step of Example 1.
+
+1. Select the *A-Fiji-dataset* Dataset.
+
+2. Double-click on a thumbnail or on an Image in the left-hand tree to
+   open an Image in Fiji/ImageJ.
+
+3. Draw a Rectangle on the Image.
+
+4. Select the option *Image > Crop*.
+
+5. A new Image will be displayed in a Fiji/ImageJ window.
+
+6. Go to *Plugins > OMERO > Save Image(s) To OMERO*.
+
+7. An Import dialog (specific to the OMERO Fiji/ImageJ plugin) will pop up.
+
+.. image:: images/manual5.png
+
+8.  Check that the option *Add Image from current window* is selected
+
+9.  Select where to import the cropped Image e.g. **A-Fiji-dataset** Dataset.
+
+10. Click *Add to the Queue* button.
+
+11. Then click *Import*. The import will start.
+
+12. When the import is done, go back to the Tree view in the Fiji plugin
+    or OMERO.web. Refresh. Check the new Image.
+
+.. |image1| image:: images/manual1.png
+   :width: 0.24105in
+   :height: 0.24105in
+
diff --git a/docs/threshold_manual.rst b/docs/threshold_manual.rst
@@ -0,0 +1,143 @@
+Segment manually OMERO data using Fiji/ImageJ
+=============================================
+
+**Description:**
+----------------
+
+The following workflows should work both with ImageJ and Fiji,
+after these have been correctly set up with
+the OMERO plugin for Fiji/ImageJ.
+
+Using the User Interface of the OMERO plugin, we will show:
+
+-  How to connect to OMERO using the OMERO plugin for Fiji/ImageJ.
+
+-  How to open an image from OMERO.server into Fiji/ImageJ.
+
+-  How to manually segment an image opened from OMERO in Fiji/ImageJ
+   using the plugin *Thresholding and Analyze particles* in Fiji/ImageJ.
+
+-  How to record this workflow in Fiji/ImageJ, using the *Recorder* plugin, for later use.
+
+**Setup:**
+----------
+
+-  Fiji has been installed on the local machine with the
+   OMERO.insight-ij plugin. The installation instructions can be
+   found at :doc:`installation`.
+
+**Resources:**
+
+-  Samples images from the Image Data Resource (IDR) \ https://idr.openmicroscopy.org/webclient/?show=project-51
+
+**Step-by-step:**
+-----------------
+
+1. Launch Fiji/ImageJ.
+
+2. Go to *Plugins > OMERO > Connect* To OMERO. This will show a login
+   screen where you can enter the name of the server to connect to,
+   the username and password. The OMERO plugin will allow you to
+   browse your data in a similar manner to OMERO.web.
+
+3. In the OMERO login dialog, click the wrench icon\ |image0| and then
+   add the server address in the dialog. By default, only "localhost"
+   is listed. Click on the *plus* icon to add a new line to the list
+   and type into the line the server address.
+
+4. Click Apply.
+
+..
+
+   |image1|
+
+5. Enter your credentials and click *Login*.
+
+6. Browse to the Project **idr0021**, open any Dataset and double-click once
+   on an Image to open it in Fiji. Bio-Formats is used to view the
+   Image.
+
+   - Make sure to select *View stack with: Hyperstack* in the *Bio-Formats
+     Import Options* dialog.
+
+   - Note that each plane will be transferred from the server to the
+     client machine so this may take a few moments.
+
+7. To open the Recorder, go *Plugins > Macros > Record...*, select
+   Macros to record the actions. The steps will then be used in
+   the Scripting workflow.
+
+8. Convert floating-point pixel-type to 8-bit using *Image > Type > 8-bit*.
+
+9. Go to *Image > Adjust > Auto Threshold*, to open the *Auto Threshold* dialog:
+
+   - Select *MaxEntropy* for the *Method* parameter.
+
+   - Check the checkbox *Stack*.
+
+..
+
+   |image2|\ |image3|
+
+10. Click *OK*.
+
+11. Then open *Analyze > Analyze Particles...*.
+
+12. In the dialog
+
+    - Set *Size* to *10-Infinity* and check *Pixel units*.
+
+    - Check the following checkboxes:
+
+       i.   *Display results*
+
+       ii.  *Clear results*
+
+       iii. *Add to Manager*
+
+    - Click *OK* then *Yes* in the popup dialog indicating asking to
+       *Process all X images?*.
+
+..
+
+   |image4|
+
+13. To save the thresholded Image back to OMERO with the generated ROIs
+    and the measurements:
+
+    -  Select *Plugins > OMERO > Save Image(s) to OMERO*.
+
+    -  Create a New Dataset for the image
+
+       i.   Click the *New...* button next to the selection box on the
+            Dataset row.
+
+       ii.  In the dialog that pops up, enter a name and a description
+            (optional).
+
+       iii. Click Create.
+
+    -  The newly created Dataset will automatically be selected.
+
+    -  Click *Add to the Queue* then *Import*.
+
+    -  Go to OMERO.web and check that the measurements have been saved
+       in a CSV file and attached to the Images. The attachment can
+       then be downloaded at any time.
+
+
+.. |image0| image:: images/manual1.png
+   :width: 0.24105in
+   :height: 0.24105in
+.. |image1| image:: images/manual2.png
+   :width: 5.10938in
+   :height: 2.5465in
+.. |image2| image:: images/threshold1.png
+   :width: 3.33854in
+   :height: 3.32695in
+.. |image3| image:: images/threshold2.png
+   :width: 2.25521in
+   :height: 2.69626in
+.. |image4| image:: images/threshold3.png
+   :width: 2.57813in
+   :height: 2.5947in