Computer Setup Notes

name and address
apr 9, 2009

Using Imal in Windows

Summary

This document describes how to run the imal image analysis software in Windows.

Windows users - setup

Although Imal is a Linux application, it is easy to run it from your Windows PC. The display shows up on your Windows desktop, but all the number crunching is done on the server, which is faster and more powerful. All the software needed to set this up is free; however, you will need to dedicate one computer to running Linux.

We run Imal over the network routinely. If you have a fast server, the display updates are actually faster than if you run it locally, because image analysis is computationally intensive. We get excellent performance from OpenSUSE Linux on a HP Proliant DL380 G5. This model is extremely fast, but it should be kept in a wire closet because it's a bit noisy.

Seven steps (described in detail below) are needed to run imal:

  1. Set up a Linux server running Imal on your local network. Ideally, this server should be on the same subnet as your Windows PC. If not, the data will go through your router, which will slow things down slightly.
  2. Obtain an account on the Linux server.
  3. Download and install putty and the public domain releases of Xming (non-Mesa), and Xming fonts (optional).
  4. If your IT department uses a firewall to block connections between computers within your organization, you may need to contact them to make an exception. Alternatively, if you can find a port that IT doesn't block, you can use that port to connect to the Linux server. This step is only necessary in organizations where IT exercises totalitarian control over your network, such as at one of our remote branches. In extreme cases, you can do what we did, which is to run your own cables and create your own local network that is free from their control.
  5. If you are at the remote branch of our organization, get the port number from Tom.
  6. Start XLaunch.
  7. Start a putty SSH session.
  8. Start imal.

OS X and Linux users - setup and usage

Non-Windows users do not need to install putty or Xming. From the command line, type ssh -X 192.168.111.222 or ssh -p port_number -X 192.168.111.222, substituting the IP address of the Linux server for 192.168.111.222. Use the second command if you need to use a non-standard port to get around a firewall.

If you are at the remote branch of our organization, get the port number from Tom.

Windows users - usage

Start an Image Analysis session.

To begin an image analysis session, you first connect to the server using Xming and putty. Then start imal on the server. The display will appear on your Windows desktop, but the working directory will be your home directory on the server.

Step 1: Start Xming.

  1. Click on the Xlaunch icon.
  2. Select Multiple windows and Display number 0.
  3. Select "Start no client".
  4. For Parameter Settings, accept the defaults..
  5. Click Finish.
  6. A large black X should appear on your Taskbar. This indicates that Xming is running.

Step 2: Start Putty.

  1. Click on Putty.exe icon.
  2. Click on the [+] next to SSH at left to expand it.
  3. Click on X11.
  4. Check the box that says, "Enable X11 forwarding". Don't click Open yet.
  5. Click on Session in the left panel.
  6. Under Host Name, enter the IP address of the Linux server.
  7. If you have to use a non-standard port, change the port number from 22 to the desired port number. Leave the other settings the same.
  8. Click Open. A black ssh terminal window should appear, saying login as:
  9. Type your username and press the Enter key.
  10. Type your password and press the Enter key.
  11. It should say something like: your_server_hostname:/home/your_username$, for example: diarrhea:/home/joeshmoe$, or just /home/joeshmoe>. This means you are logged in on the server and can start a program.

Step 3: Start Imal.

  1. Type imal in the black ssh terminal window and press the Enter key. The image analysis program should start. You could also type imal&. This would free up the terminal in case you want to type some Unix commands.
  2. You can make the imal window larger or smaller by dragging on the lower right corner. In imal, images are shown in their original size. Up to 512 images can be displayed simultaneously.
  3. The manual is available online at http://brneurosci.org/imal-manual/index.html