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fix numbering and display of text
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jburel committed Aug 26, 2019
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82 changes: 38 additions & 44 deletions docs/manual_analysis.rst
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Expand Up @@ -39,65 +39,61 @@ Using the User Interface of the OMERO plugin, we will show:

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.
#. Launch Fiji/ImageJ.

2. Go to *Plugins > OMERO > Connect* To OMERO. This will show a login
#. 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
#. 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.
#. Click Apply.

.. image:: images/manual2.png
.. image:: images/manual2.png

5. Enter your credentials and click *Login*.
#. Enter your credentials and click *Login*.

6. Select the **A-Fiji-dataset** Dataset.
#. Select the **A-Fiji-dataset** Dataset.

7. Double-click on a thumbnail or on an Image in the left-hand tree to
#. 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...*
#. Go to *Analyze > Tools > ROI Manager...*

9. Draw a shape using for example the Freehand selection tool.
#. 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.
#. In the ROI manager, click the button *Add [t]* to add the shape to the
ROI Manager.

.. image:: images/manual3.png
.. image:: images/manual3.png

11. Move to another channel, using the *c slider*.
#. 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.
#. 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.
#. When done with the drawing, click the button *Measure* in the ROI Manager.

14. A dialog with measurements for each shape pops up.
#. 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*.
#. 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.
#. 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.
#. The measurements are saved back to OMERO as a CSV file and linked to the Image.

.. image:: images/manual4.png
.. image:: images/manual4.png

18. Go back to OMERO.web, in the right-hand panel.
#. Go back to OMERO.web, in the right-hand panel.

19. Select the image opened in Fiji/ImageJ.
#. Select the image opened in Fiji/ImageJ.

20. Check that there is a new CSV file under the Attachments harmonica.
#. 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.
#. 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**
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand All @@ -108,33 +104,31 @@ 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.
#. 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.
#. 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.
#. Draw a Rectangle on the Image.

4. Select the option *Image > Crop*.
#. Select the option *Image > Crop*.

5. A new Image will be displayed in a Fiji/ImageJ window.
#. A new Image will be displayed in a Fiji/ImageJ window.

6. Go to *Plugins > OMERO > Save Image(s) To OMERO*.
#. Go to *Plugins > OMERO > Save Image(s) To OMERO*.

7. An Import dialog (specific to the OMERO Fiji/ImageJ plugin) will pop up.
#. An Import dialog (specific to the OMERO Fiji/ImageJ plugin) will pop up.

.. image:: images/manual5.png
.. image:: images/manual5.png

8. Check that the option *Add Image from current window* is selected
#. 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.
#. Select where to import the cropped Image e.g. **A-Fiji-dataset** Dataset.

10. Click *Add to the Queue* button.
#. Click *Add to the Queue* button.

11. Then click *Import*. The import will start.
#. 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.
#. 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
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38 changes: 16 additions & 22 deletions docs/threshold_manual.rst
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Expand Up @@ -33,27 +33,25 @@ Using the User Interface of the OMERO plugin, we will show:
**Step-by-step:**
-----------------

1. Launch Fiji/ImageJ.
#. Launch Fiji/ImageJ.

2. Go to *Plugins > OMERO > Connect* To OMERO. This will show a login
#. 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
#. 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.
#. Click Apply.

..
.. image:: images/manual2.png

|image1|
#. Enter your credentials and click *Login*.

5. Enter your credentials and click *Login*.

6. Browse to the Project **idr0021**, open any Dataset and double-click once
#. 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.

Expand All @@ -63,27 +61,27 @@ Using the User Interface of the OMERO plugin, we will show:
- 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
#. 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*.
#. 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:
#. 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*.
#. Click *OK*.

11. Then open *Analyze > Analyze Particles...*.
#. Then open *Analyze > Analyze Particles...*.

12. In the dialog
#. In the dialog

- Set *Size* to *10-Infinity* and check *Pixel units*.

Expand All @@ -98,12 +96,11 @@ Using the User Interface of the OMERO plugin, we will show:
- 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:
#. To save the thresholded Image back to OMERO with the generated ROIs and the measurements:

- Select *Plugins > OMERO > Save Image(s) to OMERO*.

Expand All @@ -129,9 +126,6 @@ Using the User Interface of the OMERO plugin, we will show:
.. |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
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55 changes: 26 additions & 29 deletions docs/threshold_scripting.rst
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Expand Up @@ -54,59 +54,56 @@ the UI steps.
This script explores the JAVA API using Groovy.
See \ https://docs.openmicroscopy.org/latest/omero/developers/Java.html\ ,

1. In your browser, go to the server address provided.
#. In your browser, go to the server address provided.

2. Log in using the credentials provided.
#. Log in using the credentials provided.

3. Make sure you are selecting your own data. Select the Dataset **A-Fiji-dataset**.
#. Make sure you are selecting your own data. Select the Dataset **A-Fiji-dataset**.

4. Launch Fiji.
#. Launch Fiji.

5. Go to *File > New > Script...*.
#. Go to *File > New > Script...*.

6. A dialog pops up. In the *Language* menu, select *Groovy*.
#. A dialog pops up. In the *Language* menu, select *Groovy*.

7. Copy, into the text script editor of Fiji, the content of the script \ https://raw.githubusercontent.com/ome/training-scripts/master/practical/groovy/analyse_dataset_save_rois_and_summary_table.groovy\.
#. Copy, into the text script editor of Fiji, the content of the script \ https://raw.githubusercontent.com/ome/training-scripts/master/practical/groovy/analyse_dataset_save_rois_and_summary_table.groovy\.

8. Edit the following parameters: dataset_id, USERNAME, PASSWORD.
#. Edit the following parameters: dataset_id, USERNAME, PASSWORD.

..
..
|image0|

9. The script will process all the Images in the specified Dataset,
#. The script will process all the Images in the specified Dataset,
applying threshold, analyzing particles and saving ROIs back in
OMERO i.e. we reproduce in a script the manual steps recorded.
Further, it will create a CSV and OMERO.table to be attached to
that Dataset in OMERO. Both are not necessary when analysing
data, this is mainly to show how it we

10. Click *Run*.
#. Click *Run*.

11. Return to OMERO.web and open an Image from this Dataset in
OMERO.iviewer.
#. Return to OMERO.web and open an Image from this Dataset in OMERO.iviewer.

12. Click the *ROIs* tab to see the added ROIs. Note that the ROIs have
been assigned a Channel index to indicate which Channel they were
derived from.
#. Click the *ROIs* tab to see the added ROIs. Note that the ROIs have been assigned a Channel index to indicate which Channel they were derived from.

13. In the *Settings* tab, turning channels on/off will also show/hide
ROIs assigned to those channels.
#. In the *Settings* tab, turning channels on/off will also show/hide
ROIs assigned to those channels.

14. Open the image in OMERO.figure for a quick publication by going to
Info tab in iviewer and clicking on OMERO.figure in the Open with
line.\ |image1|
#. Open the image in OMERO.figure for a quick publication by going to
Info tab in iviewer and clicking on OMERO.figure in the Open with
line.\ |image1|

15. This script was used previously to run on the whole **idr0021** Project
and produce the resulting CSV file. We can now download this file
from OMERO and open it in Microsoft Excel.
#. This script was used previously to run on the whole **idr0021** Project
and produce the resulting CSV file. We can now download this file
from OMERO and open it in Microsoft Excel.

16. In Excel, select the Dataset column and the column bounding_box and
then click on *Insert > X Y Scatter > Scatter*\ |image2|\.
Depending on the version of Excel you are using, this option
might not be available.
#. In Excel, select the Dataset column and the column bounding_box and
then click on *Insert > X Y Scatter > Scatter*\ |image2|\.
Depending on the version of Excel you are using, this option
might not be available.

..
..
|image3|

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