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Murphy Lab

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Typical Image eXtractor

Various Bits of Info

This page is the development page for TypIX. This service isn't officially "working" yet, so If you want to select a representative image from a group, use TypIC for now...

--Jim Gajnak

Status: This web page now checks the input it receives, and creates an upload directory, similar in style to TypIC. The directory created does not interact in any way with TypIC. Both systems, although using the same upload area, are completely independent.
There is also a page if someone should stumble on TypIX accidentally.

Currently, I am finishing the initial version of the web backend. I should be testing the system soon (hence the addition of this location to the lab "Internal" section).

How To Use This Service

Preparing Your Data

TypIX accepts various image file formats. (Finish this section later.)

To reduce upload times, you may upload your image collection in a compressed format. Two compression formats are currently accepted: zip (Zipv-Lempel compression) or tar.gz (tar archiving/gzip compression). For Windows-based comptuers, we recommend WinZip; to create zip files compression on MacOS (Macintosh) machines, ZipIt.

Step 1: Create an Upload Directory

Point the user to the form below, explain what options mean.

Step 2: Uploading Your Images

Should we give better instructions for each platform, or use the same instructions as TypIC had? Peronsally, I would like to redo them...I honestly thought they were a bit hard to understand.
You will need to use an FTP client to perform the upload, since browsers are not capable of uploading files. An FTP client is built into most flavors of UNIX (type 'man ftp' at the command prompt for details); for other operating systems, we recommend WS_FTP for Windows and Fetch for MacOS. Instructions on using FTP clients are provided after the creation of your directory. Since the directory created for you is hidden and not visible through normal ftp client browsing, please use the instructions below to find and upload to your directory.

for UNIX systems  

At your command prompt type: 'ftp murphylab.web.cmu.edu' and press enter. Your ftp client will then prompt you for a username and a password. Use the username 'anonymous' and your email address for your password. You will then find yourself at a prompt. Enter 'cd' and the directory name supplied above. For instance, if your directory name was 'Pat_Smith_12_34', you would type 'cd /upload/Pat_Smith_12_34' and press enter. Finally, use the 'put [filename]' command to place files in your ftp directory. Use the ' bye' command to close the FTP session when you are done submitting.

for Windows systems
Open up WS_FTP. First you will see a 'Session Profile' dialog box. Click on 'New' to make the form blank. In the hostname field, type in 'murphylab.web.cmu.edu'. Click on the check box marked 'Anonymous Login', and replace the password field with your email address. Click on 'Ok'. After a moment, the client will connect to the FTP server. Press the 'ChgDir' button in the top right or the program, enter in the directory name in the subsequent dialog box, and press 'Ok'. You are now in your submission director y. You may now upload files from your computer (shown on the left) using the '->' button. Press 'Close' when you are done.

for Macintosh systems
Open up Fetch. When it starts up, you will see a 'New Connection' dialog box. For Host, type in 'murphylab.web.cmu.edu', for userid, use 'anonymous' and for passoword, your email address. Press 'Ok' and Fetch will make the connection. Next, go to the menu bar and choose 'Directories' and then 'Change Direcotry...'. Type in the directory name listed above and press 'Ok'. When you are in that directory, use the 'Put File' button to place your files in the upload directory.

Step 3: Getting Your Results

When TypIX processes your data, it will compile the results into an email and send it off to you. Any problems encountered during the processing will also be noted in the email. If you have any comments or questions about either one of these, feel free to contact us.

In addition to recieving your results by email, you can also choose to have a web page generated. After your results have been compiled, a web page will be generated containing your results. The URL of the web page will be sent in the email containing your results.

The web page generated will contain the images you submitted. However, they will be in PNG format. This requires that you use a browser suporting that format. Two free browsers that can display this format are:

  Microsoft Internet Explorer, v4.01 or later
   Netscape Navigator, v4.04 or later

Please note that the web page created will be kept on our server for only a week after processing. After that time, the web page will be removed.

Upload Directory Creation Form

Filling out and submitting this form will result in the creation of a directory into which you can upload your images. All field are required unless specified otherwise

Part 1: Images Information

Type of Microscopy:


Cell Type(optional):

Source of fluorescence(optional):

Additional Info(optional):

Part 2: Processing Options

Submitted Image Format(s):
TIFF (8-bit)

Do Preprocessing?

Select Feature Sets
"Ad Hoc"

Feature Selection Method
Principal Components
       Use  % of variance.
       Use principal components. (-1 is equivalent to using them all)
       Use highest skewness values. (-1 is equivalent to using them all)

Distance Metrics

Part 3: Retrieval of Results


Email address:

Create web page with your results?


Last Updated: 01 Dec 2004

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