Differences

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--- working_with_omero [18.12.2014 - 10:27] – tnowak
+++ working_with_omero [10.01.2020 - 09:39] (current) – bschmid
@@ Line 3: / Line 3: @@
 The OMERO server supports multiple front ends to add, download and analyse image data. Currently, there are two o ptions available for OICE users:
-  -- The web interface accessible through [[https://romulus.oice.uni-erlangen.de]]: No configuration is necessary in this case, the only requirement for the user is an existing account in the central user database and an HTML-5 compliant browser.
+  -- The web interface accessible through [[https://romulus.oice.uni-erlangen.de]]: No configuration is necessary. The web interface comes with OMERO.figure for conveniently creating high-quality figures, but cannot be used to import data into the OMERO.server
-  -- The Java-based OMERO client, available for Windows, Mac OS X and Linux at [[http://downloads.openmicroscopy.org/omero/5.0.3/]] with its main module, **OMERO.insight**. This client requires the installation of an up-to-date version of [[http://www.java.com/download|Oracle's Java Runtime Environment]]. Additionally, the client has to be configured on the first run to find the OICE OMERO server. This will be described in the next chapter.
+  -- OMERO.insight, a desktop application available for Windows, Mac OS X and Linux at [[https://github.com/ome/omero-insight/releases/latest]]. It needs to be configured on the first run to find the OICE OMERO server. This will be described in the next section.
-The web interface is most useful for quick access to image data on third-party computers where no client software is installed. However, certain features like mass downloads of single files or easy drag-and-drop operation are not yet available with the web client (or can not be made available due to inherent limitations of HTML and Javascript), so OMERO.insight would be the preferred option where available.
+===== Download, installation and starting of OMERO.insight =====
+  - Download OMERO.insight from [[https://github.com/ome/omero-insight/releases/latest]]. The .exe file will install it system-wide for all users (admin right required), The .msi file will install it only for the current user (no admin rights required). Mac OS X users should choose the .dmg file.
+  - If working on a microscope, OMERO.insight is available on the Tools (Y:) drive and can directly started by clicking on the .exe file located within the OMERO.insight folder: {{::omero.insight.1.jpg?nolink&600|}}
-===== Configuration of the OMERO client software =====
+===== Configuration of OMERO.insight =====
+{{:omero.insight.2.jpg?nolink&400|}}
-  - Make sure to first install Java before trying to run the OMERO.insight module.
+  -- If you are working from within the hospital network, click the lock symbol (2) to encrypt all data transfer
-  -- Unzip the software package to an arbitrary directory and run the OMERO.insight executable. You will be presented with a window such as the one below:
+  -- Click on the white wrench icon (1) to open the server preferences window. Click on the blue plus icon (1) and add the following server ''romulus.oice.uni-erlangen.de'', then click on Apply.
-  .. {{:omero-insight-login-screen.jpg?nolink&500|}}
+  .. {{:omero.insight.3.jpg?nolink&400|}}
-  -- Click on the white wrench icon to open the server preferences window:
-  .. {{:omero-insight-server-prefs.jpg?nolink|}}
-  -- Click on the blue plus icon and ad the following server ''romulus.oice.uni-erlangen.de''. Leave the port (number next to the server) at the default value of ''4064''.
-  - Select the server (by clicking on the name) and click on Apply.
   - Next time you open OMERO.insight, the server name left of the white wrench icon should reflect your changes, i.e. state the new server instead of localhost.
   - Login with your username and password as usual.
@@ Line 22: / Line 20: @@
 ===== Importing/uploading files to OMERO =====
-There are two ways to upload files to the OMERO server. If you are using one of the OICE's on-site microscopes the preferred way is to use the OMERO DropBox facility. Since the automatic upload has some limitations (files will always appear in the ''Orphaned Images'' folder of the last used group), another option is to manually upload your images to the OMERO server. This can be done with the OMERO.insight client, which can both be downloaded separately or called via the OMERO.web interface.
+  -- To start the importer, either select ''File>Import...'' from the menu or click on the importer icon in the tool bar: {{::omero.insight.4.jpg?nolink&700|}}
+  -- On the left side, select the files that you want to upload (1) and click the right arrow icon (2): {{::omero.insight.5.jpg?nolink&700|}}
+  -- Select a project (1) and a dataset (2) (or choose no project/no dataset, in which case the image will end up under ''Orphaned Images'') and click on ''Add to the queue''. You can repeat step 2 and 3 multiple times. {{::omero.insight.6.jpg?nolink&700|}}
+  -- After clicking ''Import'', you'll see the progress of the import. You can close the window once the upload is finished. Back in the OMERO.insight main window, you'll need to click the ''Refresh'' button to make the new images visible. {{::omero.insight.7.jpg?nolink&700|}}
-==== Automatic import via OMERO.DropBox ====
-This is the most comfortable way to upload image files to OMERO. Users at in-house OICE devices (in the future, this will be extended to off-site devices) will be provided with two network shares.
-  - H:\ which is the home share and has the same name as the user (e.g. mmustermann). Files which are saved here will be accessible on any device but will not be automatically uploaded to OMERO
-  - X:\ which is the OMERO-DropBox share. If you save any image files on this share, be it on the root level or in any folders or subfolders, those image files will be automatically uploaded to OMERO if the format is recognized (which is the case for over 100 proprietory and open image formats)
-Files on the OMERO-DropBox share will not be deleted after upload. Deleting those files is safe and will currently not lead to any action on the OMERO-Server, so your on the server will not be touched once uploaded. The same is true for deleting automatically uploaded files on the server, which will not trigger any action regarding files on your DropBox share. Moving files between folders on the OMERO-Share will not trigger a re-upload, only new files will be uploaded.
-<div important>**Do not save a file on the DropBox folder before you are finished working with it!** If you are planing to add more images to the same file, e.g. by taking more images without starting a new experiment and then pressing //Save...//, you have to keep your working file **outside** of the DropBox folder until you have finished your experiment and then copy it over manually. Should you save the same file multiple times inside the DropBox folder, every save-action will trigger a re-upload of the file and you will end up with a lot of identical images. In the worst case, the re-upload will be triggered before the old upload is finished, which can corrupt part of your data.</div>
-As soon as the upload is finished (depending on file size, this should not take longer than 5 minutes), users can find the uploaded images **in the "Orphaned Images" folder of the last-used group**. There is currently no way to indicate the Project or Dataset that automatically uploaded images should end up in, so you have to move those images using the web interface or OMERO.insight.
-OMERO.DropBox is a relatively new feature for the OME-Suite, so problems with the automatic upload can still occur. If you find that this feature is not working for you, you can try the manual upload or you can contact the [[Tristan.Nowak@fau.de|OICE administrator]]
-==== Manual import via OMERO.insight ====
-Manual import is currently only supported by the Desktop client OMERO.insight. Support for the web interface is planned and will be realized by the OME developers in the near future. Currently, you have to use OMERO.insight, select your target group (in case you are a member of more than one) by using the provided drop-down list and click on the Importer Icon in the top bar to upload your files. A dialog will pop up which allows you to select files, a target Project and a target Dataset.
 ===== Downloading files from OMERO =====
@@ Line 74: / Line 58: @@
 Both ImageJ and Fiji can be connected to the OMERO server with the same plugin, which allows for a straightforward and easy transfer of acquired microscopy images into these analysis platforms. In the following there will be a short description for new users of how to get both environments running.
+For users who want to work with the native MSR format of our STED microscope, it is currently still required to install a beta version of the Bioformats plugin for ImageJ (Fiji will not work with this version, unfortunately). The required daily build can be downloaded here: [[http://ci.openmicroscopy.org/job/BIOFORMATS-5.0-daily/lastSuccessfulBuild/artifact/artifacts/bioformats_package.jar]]. It has to be extracted into the ''plugins\'' subdirectory of ImageJ.
 ==== Installing ImageJ ====
@@ Line 87: / Line 73: @@
 ==== Installing the ImageJ/Fiji plugin ====
-Go to [[http://downloads.openmicroscopy.org/omero/5.0.6]] and download the ImageJ/Fiji plugin listed under **OMERO plugin downloads**. As stated above, this plugin works for both ImageJ and Fiji.
+Go to [[https://downloads.openmicroscopy.org/latest/omero5/]] and download the ImageJ/Fiji plugin listed under **OMERO plugin downloads**. As stated above, this plugin works for both ImageJ and Fiji.
 To install the plugin, you have to unzip the zip file including all folders to the ''plugins'' subdirectory of your ImageJ or Fiji installation directory. For example, if you have installed Fiji in ''C:\Programs\Fiji'', you have to unzip the plugin into ''C:\Programs\Fiji\plugins''. This will lead to a new directory called ''C:\Programs\Fiji\plugins\OMERO.insight-ij-(version)''