Frequently Asked Questions
New Version
- Telometer recently went down. When will the new version of Telometer be released?
- Why was Telometer unavailable (until recently)?
- How can I get a username and password to login?
- How do I perform a backup of my data in Telometer?
- I have data from the *OLD* version of Telometer which was stored on a Johns Hopkins University server. Since the JHU server is unavailable, is there another way I can get access to the data?
- My harddrive crashed (or was stolen, or I accidentally deleted my telometer_data directory) and I'm unable to get my data for Telometer. Do you provide a backup?
General
- How can I get more information on the meaning of field names, such as "TelomereSum" or "Cy3Background"?
- What operating systems can Telometer be run on?
- Telometer doesn't start when I double-click the jar file.
- After I select a CY3 or DAPI image, I get the error: "selected file for Cy3 not okay: Image needs to be a 16-bit grayscale, but it is a color image"
- What does the error "The write format 1 is smaller than the supported format 2" mean?
- I get the error "java.lang.OutOfMemoryError: Java heap space"
- I have another question that isn't addressed here, or a comment. Who should I contact?
New Version
- Telometer recently went down. When will the new version of Telometer be released?
-
The new version (version 3) is available now (as of May 3rd 2020). See the Downloads page.
- Why was Telometer unavailable (until recently)?
-
With the old version, Telometer required the use of a server, which was hosted at Johns Hopkins University (JHU).
We were required by I.T. to put the server behind JHU's firewall and require users to connect to JHU's VPN
to access the server, which means that Telometer became unavailable to users outside JHU.
However, with the new version of Telometer, no server is required, so Telometer may be used by anyone.
- How can I get a username and password to login?
-
With the new version, you no longer need a username and password.
(All the data is stored on your own machine.)
- How do I perform a backup of my data in Telometer?
-
It is important to back up your telometer data since it is no longer stored on our server,
but rather on your own computer.
Click the About button to view the storage directory on your local computer, and then copy the directory to
a backup location (such as your own backup server or a DVD)
- I have data from the *OLD* version of Telometer which was stored on a Johns Hopkins University server. Since the JHU server is unavailable, is there another way I can get access to the data?
-
Yes, but you'll need to contact Alan Meeker at ameeker1@jhmi.edu.
Please provide us with your username(s) on the old version.
- My harddrive crashed (or was stolen, or I accidentally deleted my telometer_data directory) and I'm unable to get my data for Telometer. Do you provide a backup?
- No. Unlike the last version of Telometer, all data is stored on the user's computer. See the FAQ entry on doing backups.
General
- How can I get more information on the meaning of field names, such as "TelomereSum" or "Cy3Background"?
-
Click on the 'View' button, and then hover the mouse over any field name. A tool tip with a more detailed description will be displayed.
- What operating systems can Telometer be run on?
-
Telometer can be run on any operating system that can run the Java Runtime Environment (JRE). This includes Windows, MacOS, and Linux.
- Telometer doesn't start when I double-click the jar file.
-
Run the "java -jar ..." command from the command line, as described in the documentation page
- After I select a CY3 or DAPI image, I get the error: "selected file for Cy3 not okay: Image needs to be a 16-bit grayscale, but it is a color image"
-
An image needs to be 16-bit grayscale before Telometer will process it. Even though the image may appear to be grayscale, ImageJ may still be recognizing it as a color image, or an 8-bit grayscale. You need to convert your image to 16-bit grayscale, which you can do using ImageJ:
- Backup your image first so that you have an original copy
- Open Telometer, then click the "Score" button, then the "Next" button. An ImageJ window should come up.
- Go to the ImageJ menu then "File" then "Open...". Then select your image.
- Go to the ImageJ menu then "Image" then "Type", then select "16 bit"
- Go to the ImageJ menu then "File" then "Save". Click "replace" if prompted to overwrite your image. The image will now be a 16-bit grayscale image.
- What does the error "The write format 1 is smaller than the supported format 2" mean?
-
In Telometer version 3.1.0 we upgraded the internal h2 database to version 2. H2 version 2 cannot open database files created by H2 1.4.200 or older versions. Thus you'll need to upgrade your h2 database if you want to use the latest version of Telometer, or start with a new database. Follow these instructions if you want to upgrade: http://www.h2database.com/html/migration-to-v2.html
- I get the error "java.lang.OutOfMemoryError: Java heap space"
-
Either use smaller images, or try running Telometer with more memory: "java -Xmx16384m -jar telometer-3.1.0.jar"
- I have another question that isn't addressed here, or a comment. Who should I contact?
-
Please contact Alan Meeker at ameeker1@jhmi.edu. You can contact the developer Jim Morgan at jmorgan@jhmi.edu