Help migration

FAQ.md

@@ -0,0 +1,89 @@
+Finding the log file
+--------------------
+
+Go to ``Help > Show Log File``.
+This will show you the location of the log file - ``omeroinsight.log``.
+If there are other log files with ``_1`` or ``_2`` appended to the name, ignore them.
+Alternatively you can find the log file in your user folder:
+ - Windows: ``C:\Users\you\omero\log\omeroinsight.log``
+ - Mac/Linux: ``/yourhomedir/omero/log/omeroinsight.log``
+
+Submitting files
+----------------
+
+If an error occurred during import you can upload the files using the submission dialog.
+Automatic uploading of files to OME QA will not work if the file size is greater than 2GB.
+Submission of smaller file sizes can also not work if you are uploading over a slow or
+unreliable network. If the file upload to OME QA fails, please contact the team using our
+[support page](https://www.openmicroscopy.org/support/) to discuss alternative mechanism to submit the files.
+
+Adding third parties JARS
+-------------------------
+
+OMERO.insight comes bundled with a number of standard Java Archives (JARs).
+However, functionality can be extended by adding JARs to OMERO.insight.
+An example of this is where some proprietary file formats require additional
+readers to enable OMERO to open and read the files. These readers can be provided
+by the owners of the formats as JARs, which need to be added to enable the functionality.
+
+If third-party JARs are related to the Bio-Formats import reader,
+they will also need to be added to the OMERO.server by your OMERO systems administrator.
+There is no need to do this if they are simply OMERO.insight update JARs.
+
+**Mac**:
+
+ - Right-click or control-click on on the omero.insight app.
+ - Choose ``Show Package Contents`` from the contextual menu.
+ - Navigate to the ``Contents`` folder.
+ - Select ``Java > lib``.
+ - Drag and drop, or copy, the third-party ``.jar`` file into the ``lib`` folder.
+ - Start the application.
+
+**Windows**:
+
+ - Select the executable in Explorer.
+ - Select the ``lib`` folder.
+ - Drag and drop, or copy, the third-party ``.jar`` file into the ``lib`` folder.
+  - Start the application.
+
+**Linux**:
+
+ - Unzip the app.
+ - Go to the ``lib`` directory.
+ - Drag and drop, or copy, the third-party ``.jar`` file into the ``lib`` folder.
+ - Start the application.
+
+
+Choose Show Package Contents from the contextual menu.
+
+Increasing Memory Allocation
+----------------------------
+
+By default, the Desktop client allocates a certain amount of memory
+during the start-up process which should be sufficient for most uses.
+The default values are ``-Xms256m, -Xmx1024m``.
+
+However, you may encounter out of memory exceptions while trying to import
+or display very large images. In these situations, it is beneficial to increase
+the memory allocation to the clients as outlined below.
+
+**Mac**:
+
+ - Right-click or control-click on on the omero.insight app.
+ - Choose ``Show Package Contents`` from the contextual menu.
+ - Navigate to the ``Contents`` folder.
+ - Open the file  ``Java > OMERO.insight.cfg``.
+ - Edit the ``[JVMOptions]``section.
+
+**Windows**:
+
+You must add an optional parameter file to the same folder as the application.
+Create a file called ``OMERO.insight.vmoptions`` in the same directory as your OMERO.insight.exe file and
+add the new JVM options.
+
+
+**Linux**:
+
+ - Unzip the app.
+ - Open the file ``bin/omero-insight`` in a text editor.
+ - Change the value of ``DEFAULT_JVM_OPTS``.

README.md

@@ -24,7 +24,7 @@
   ----------------------
 
   The compilation, testing, launch, and delivery of the application are
-  automated by means of a Gradle (https://gradle.org/) build file.
+  automated by means of a [Gradle](https://gradle.org/) build file.
   In order to perform a build, all you need is
   a JDK -- version 1.8 or later. From the command line, enter:
 
@@ -142,6 +142,11 @@
   ```
 
 
+  FAQ
+  ---
+
+  See [FAQ.md](FAQ.md)
+
   Licensing
   ---------