Zen SuperResolution software

This software is supported on behalf of the Facility for Imaging by Light Microscopy (FILM). It is provided on four dedicated servers running Windows Server 2012, which can be accessed from within the Imperial firewall via a Remote Desktop connection. Each server has 96 GB RAM, 24 CPU cores and 2TB fast local storage available for analysis jobs.

Accessing the software

Registering to use the software

Requests to access the software should be made via the film-service@imperial.ac.uk

Connecting and transferring data

Data should be transferred to a file share which is accessable over a high-speed network from the Zen servers, and then copied to local storage on a zen server for analysis. Instructions on connecting to the servers and making data available on them can be found below:

Zen instructions

Connecting to a Zen server

Access to the software is available using a Windows Remote Desktop session to access the servers hosting the software. Clients are available for Windows, Mac and Linux operating systems

Windows Clients

  1. From the 'Start' menu, select 'Remote Desktop Connection'
  2. Enter the name of the server in the 'Computer' field of the 'Remote Desktop Connection' window. This should be 'zenXX.bioinformatics.ic.ac.uk' where the 'XX' is replaced with the specific server you are trying to login to i.e. zen02.bioinformatics.ic.ac.uk.
    1. Remote Desktop Connection

 






Various options are available which may improve the usability of the connection under the 'Options' menu. You can adjust the size of the remote desktop here by selecting the 'Display' tab.

RDP size

 

 

The connection can also be optimised to your connection speed. If you are on an Imperial campus, select the 'LAN' option. Remote connections via VPN connections will produce better results using either the 'High Speed Broadband' or 'Low Speed Broadband' options, depending upon the quality of your connection.

RDP Speed

Once you are happy with the settings, click the 'Connect' button

You will be asked to 'Enter Your Credentials'. Enter your normal College logon username and password, then click 'OK'.
You should now see a desktop session on the server on your local display.

If your login is interrupted due to network isses, and you reconnect within 15 minutes your session will still be active, and any running applications will continue. Failing to reconnect within 15 minutes will result in you being signed out of the server to make it available for other users.

RDP desktop

Transfer data to Zen file share

Each server has a 1.8 TB high-performance 'scratch' storage volume for use as working space while carrying out analysis. Data should be first be transferred to this volume by transferring it to a centralised file share using SFTP, then copying the data to the required server's local disk space.

The first time you connect to a Zen server with a Remote Desktop session, a folder should be automatically created for you both on the server's 'scratch' volume, and the Zen File Share. This will be named with your username. Please note that each server has it's own 'scratch' area, so files will need to be transferred to the specific server you will be carrying out your analysis on.

Please note that this is currently an interim solution and the data transfer process will be streamlined in due course.

SFTP Transfer to Zen File Share - Windows Clients

Filezilla start menu

Standard College Windows installations include the FileZilla FTP client which can be used to transfer data to the Zen file share. Filezilla can be found from the Start Menu in the 'FileZilla FTP Client' group. Click the 'FileZilla' icon to start the program.

FileZilla Configuration

Setting up the FileZilla configuration is only required the first time you use the software.

  1. The configuration required to connect to the Zen fileshare is available to download. Right-click on this link and click 'Save Target as...' (or 'Save Link as...'), which should save a file named 'FileZilla_Zen_Share.xml' to your computer. Note where this file is saved.
  2. Select the FileZilla 'File' menu, then click the 'Import...' menu item, which will open a window showing a file browser.
  3. Navigate to the 'FileZilla_Zen_Share.xml' file you saved in step 1, and click 'Open'
  4. The following dialog should be displayed. Click 'OK'. A further message should appear indicating the successful import of the configuration. Click 'OK' again.
Import confirmation

 

  

  1. Open the FileZilla 'Site Manager'  by selecting the left-most button on the toolbar, or selecting 'Site Manager' from the 'File' menu. The site manager should open as shown below.
  2. The configuration is complete apart from the password required to login to the zen share. This can be found in the 'ICL ZEN README' file which can be found on the Desktop of the Zen servers. If you do not have a session open, start a Remote Desktop session to a Zen server as described on the previous page, then double click the 'ICL ZEN README' file. The password can be found in the 'SFTP Credentials for Zen fileshare' section. Select the 'zen share' in the FileZilla Site Manager, then enter the password in the 'Password' field. NB: Now click 'OK', rather than the default 'Connect' option. This will save the password so you will not have to enter it again in future.
  3. FileZilla Site Manager

 

 

 

 

 

 

 

 

Connecting to the Zen File Share

Zen Share Connection 
    1. Once the FileZilla configuration is imported and the password saved in the configuration, connect to the file share by clicking the down arrow icon alongside the Site Manager icon on the toolbar, and select 'zen share'.
    2. The first time you connect, an additional dialog box will appear since FileZilla has not connected to the file share previously. Click the 'Always trust this host...' checkbox, then click 'OK'

 

Unknown host

 

 

 

 

 

  1. The FileZilla window should now show two panes divided down the middle, with the left hand pane showing the filesystems on your local machine, and the right-hand pane showing the Zen File Share.

Transferring Data to the File Share

  1. In the left-hand pane of the FileZilla window, nagivate to the location of your image files on your local machine
  2. In the right-hand pane, navigate to your username in the file share
  3. Drag and drop your files from the left-hand pane to the right-hand pane
  4. Your files should now be copied over to the file share

Transfering data to a Zen server


Once your data is available on the Zen File Share, it should be transferred to the Scratch (D:) volume of the server you are using. Please ensure you have followed the instructions for transferring files to the Zen File Share (above) first.

Please note that these scratch filesystems are only for temporary usage while analysis jobs are in process. Data should be removed from these volumes once jobs are completed. Files left on these filesystems may be removed without warning.

It is necessary to follow steps 1-7 below the first time you connect to each server. If saved correctly, the crendentials will be retained by the server so you will not need to enter them again if you return to the same server in future.

  1. Open a Remote Desktop session to the server you will be running your analysis on.
  2. Double click the 'ICL ZEN README' icon located on the Desktop. This file contains the credentials necessary to connect to the Zen file share from the Zen servers
  3. Double click the 'Zen Fileshare' shortcut
  4. Click 'Connect using different credentials'
  5. Enter the username (zen) and password from the 'ICL ZEN README' file.
  6. Click the 'Remember my credentials' checkbox
  7. Click 'OK'
  8. A File Explorer window should now open showing the contents of the Zen File share. There should be a folder with your username present - double click this to open it.
  9. Double-click the 'Scratch (D)' icon on the Desktop. The resulting File explorer window should also include a folder with your username. Double-click this to open it.
  10. You can then transfer your files are results back and forth between the local storage and Zen file share by dragging and dropping between the two windows.