UsingOpenMicroscopyEnvironment - BioImage Wiki (internal)

Using Open Microscopy Environment

This page contains notes for starting, stopping and using the Open Microscopy Environment (OME) software installed on the Dell microscope image capture system in Zoology. The environment has been configured to allow selected values relevant to the DTGED project to be captured in a structured fashion.

Contents:

Starting up OME
Shutting down OME
Using OME
1. Capture and annotate an image
2. Retrieve an image and annotation
Creating a new OME user

1. Starting up OME

OME runs in a "virtual machine" within the normal Windows environment on the Dell microscope image capture workstation. This virtual machine appears as a separate computer, except that it does not have a separate physical existence, and runs a Scientific Linux operating system rather than Windows, because that is what OME needs. The virtual machine environment is provided by a Windows program called "VMWare Workstation", and this program must be running whenever OME is running.

To start up OME:

Log in to the Local Admin account on the Dell computer. A password is needed for this.
If VMWare Workstation is not running (check the taskbar at the bottom of the screen), double click on the desktop icon labelled "VMWare Workstation".
- If Zone Alarm asks if VMware should be allowed to access the Internet, click on "allow".
In the "VMWare Workstation" application window, select the tab labelled "HelenOME".
Click on the blue text "Start this virtual machine" (which is beside a small green arrow symbol).
- The window will turn black andmany scary-looking messages are displayed. Many will be associated with a green "OK" message. If a red "FAILED" message is displayed there may be a problem, but it's worth letting the startup complete as the problem may be benign. The black screen may alternate several times with a grey windows with the label "Scientific Linux". This whole process may take several minutes, especially if the OME system was not shut down cleanly when the computer was last turned off.
Eventually, a blue screen with a "Welcome" bos is displayed. OME should now be running.
- To test this, switch to the Windows desktop and run the FireFox browser. Click on the browser toolbar button "OME Main page" - an OME logon page should be displayed. Close the browser window.
Switch to the Windows system user "drosophila" (use Start -> Log Off then Switch User; do not logout from the Local Admin account, as this will force the VMWare Workstation software to be terminated, and OME with it).
Start the web browser and select "Open Microscopy Environment" from the browser toolbar,

or browse to http://helenome.zoo.ox.ac.uk.

2. Shutting down OME

To shut down OME, first shut down the Linux operating system on the Virtual Machine, then you can shut down the VMWare Workstation software, or shut down the whole computer system.

Switch to Windows user "Local Admin". A password is needed for this.
Open the VMWare Workstation window.
SElect tab "Helen OME", and click on the button labelled "Actions". (If this button is not visible, it may be that the system has already been shut down, or that a different console window has been selected. Try oressing keys CTRL+ALT+F6 (need to check the key combination) to switch to the Gnome window manager.
On clicking "Actions", a small window is displayed. From this window, select "Shut down the computer". (Note that selecting this shuts down the Virtual machine, not the whole Windows computer system.)
- A series of messages will be displayed on a black window. This may take a couple of minutes. Eventually, the window turns white, with options "Start thius virtual machine" and others displayed.

3. Using OME

3.1. Capture and annotate an image

Initially, images are captured using the KY-link software and saved in a part of the Windows file system, C:\Pictures from microscope, that is shared with the OME system. OME then imports images from the shared file system into its own database, where annotations and other information are added. When importing images that have been captured using KY-link into OME, the directory /mnt/hgfs/pics/ on the OME system is mapped to the Windows directory C:\Pictures from microscope.

OME is accessed and controlled using an ordinary web browser. You can use the FireFox browser on the Dell microscope image capture machine (this being most convenient for performing at-microscope annotations), or from any other computer on the local network (which might be uiseful for reviewing images and/or annotations.

Browse to http://helenome.zoo.ox.ac.uk. An OME logon screen should be displayed. Log in using your designated account details.
For capturing images, first create a new dataset, by clinkinmg on "Create" unbder "Dataset" in the left hand menu bar, filling in the dataset name and description, and then clicking the button labelled "Create dataset".
- For the DTGED project, we use a dataset to collect a seried of images from a single slide. The dataset name should be based on a slide identifier of the form gene-who-date, e.g. hale_in_rfx-eg-010805. The description would usefully include an expansion of these details, together with a general explanation of what is on the slide.
Use the KY-link to capture the image on Windows in the normal way, saving the image to an appropriate sub-directory of C:\Pictures from microscope. Note that images must be saved in TIFF, not BMP, format.
Switch to the OME browser window and select "Import" command under "Images" from the menu bar at the left of the screen. Browse to the desired image using the directory browser links. Check the tick boxe(s) beside the desired file(s), and then select "Add to queue".
Check the "Existing dataset" button, and the appropriate dataset fromthe drop-down list, then click on the "Imort files" link (under the top display panel, at the right hand side of the window).
The image importat procedure begins. To view progress click the browsers's refresh button. After a few seconds, the import process is complete.
Now click the "Datasets" command under "Search" in the menu bar at the left of the screen. Locate and select the dataset used for saving the image.
A list of thumbnail images withinthe dataset is shown. Click on the upper left corner of the thumbnail for the image to be annotated. A simple form is displayed.
From the drop-down list labelled "Select a semantic type", look for and select the entry "DTGEDImageAnnotation", which is probably at the bottom of the list. Then click on "Create a custom annotation".
Fill in values as appropriate, then click on the button labelled "Create DTGEDImageAnnotation". The new annotation is now saved.

3.2. Retrieve an image and annotation

Browse to http://helenome.zoo.ox.ac.uk. An OME logon screen should be displayed. Log in using your designated account details.
Some (recently created?) datasets may appear immediately following log on. If the desired image is in one of these, then click directly on the link provided. Otherwise, use the search datasets command to find and display the required dataset.
With the appropriate dataset displayed, select the required image from the list of thumbnails. Click on the upper left corner of a thumbnail to see a summary description of the image. Also displayed is a list of "modulke executions", some of whixh are described as "Annotation" with a date and time.
Click on an "Annotation" link to see details of the corresponding annotation, which are displayed under the (somewhat crypic) heading "Untyped outputs".

4. Creating a new OME user

OME records information about the user who imports or annotates an image. Thus, it is good to be logged in as yourself, rather than some arbitrary account.

Creating a new OME user involves logging in to the Linux system that hosts OME, and running an OME administration utility:

Log in to Windows User Local Admin on the Dell microscope image capture computer.
If it is not already running, start up the OME system (see above).
Select the "HelemOME" tab in the "VMWare Workstation" window. A "Welcome" panel should be displayed; use this to log in to account omeadmin. A second panel will ask for a password. (Please protect this password as it could be used by a malicious user to access the system from outside the university and wreak considrable damage to the OME system and saved OME data.)
Once logged in to OMEadmin, activate a new "terminal" (click the "Terminal command line" icon in the taskbar at the top of the window, which looks like an image of a blue window in a grey frame).

A list of current users can be listed by issuing the command:

ome admin users list

The system may ask for a username and password; use "omeadmin" and the same password as was used previously (step 3). (It is possible to use other accounts here, but I have set up the system to use omeadmin and the same password. Please protect this password as it could be used by a malicious user to access the system from outside the university and wreak considrable damage to the OME system and saved OME data.)

Example:

[omeadmin@helenome ~]$ ome admin users list
Cannot login via previous session.
Please login to OME:
Username? omeadmin
Password? 
Great, you're in.

ID  GID Username Name                 Email                Data Directory      
--- --- -------- -------------------- -------------------- --------------------
5   4   omeadmin OME admin                                 /mnt/hgfs           
1   4   graham   Graham Klyne         graham.klyne@zoo.ox. /home/graham        
6   4   ometest  OME test                                  /mnt/hgfs           
[omeadmin@helenome ~]$

To add a new OME user, use the command

ome admin users add

and follow the prompts, as in this example:

[omeadmin@helenome ~]$ ome admin users add
Username? [undefined]: liz
First Name? [undefined]: Liz
Last Name? [undefined]: Benson
Email Address? [undefined]: elizabeth.benson@zoo.ox.ac.uk
Data Directory? []: /mnt/hgfs/pics/
Group ID? [undefined]: 4
Password?
Verify: 

Confirm New User's Properties:
      Username: liz
    First Name: Liz
     Last Name: Benson
 Email Address: elizabeth.benson@zoo.ox.ac.uk
Data Directory: /mnt/hgfs/pics
      Group ID: 4
Are these values correct ? [y/n]: 
Created user #50.
[omeadmin@helenome ~]$

Note that the password must be at least 6 characters long. The group id of "4" is a mystery to me, but it seems to work. I think that in a larger OME environment with more workgroups, different numbers would allow them to prevent the possibility of interference, which I am assuming is not a concern for the DTGED propject. The directory /mnt/hgfs/pics/ on the Linux system is mapped to the Windows system directory C:\Pictures from microscope.

Repeat the above step for each new user to be added.
When finished, log out from the Linux omeadmin account (use Actions -> log out on the taskbar at the top of the window).
To continue using the system, switch to the Windows system user "drosophila" (use Start -> Log Off then Switch User; do not logout from the Local Admin account, as this will force the VMWare Workstation software to be terminated, and OME with it).

The new users added should now be able to use OME via the web interface, presenting their username and password at the OME login page ( http://helenome.zoo.ox.ac.uk/).

-- GrahamKlyne 2008-11-19 06:08:20