The NIH/NIGMS
Center for Integrative Biomedical Computing

 All of our mailing lists are public and searchable through Google. For best search results, include the "iv3d-users" or "sympa" in your search terms.

Alternatively, you can browse the iv3d-users mailing list archive.

ImageVis3D Mailing Lists
Reporting Non-fatal Bugs
Reporting Fatal Bugs
Developer Communications

Joining the ImageVis3D Users Mailing List

  1. Compose an email to This email address is being protected from spambots. You need JavaScript enabled to view it. with the following in the body of message: subscribe iv3d-users
  2. Nothing needed in the Subject line. Just send.
  3. You will receive a response from the list manager requesting confirmation. Just send back a reply message to confirm your subscription (no added text needed).
  4. Finally, you will receive a welcome message confirming that you have been added to the mailing list.

Unsubscribing

  1. Compose an email to This email address is being protected from spambots. You need JavaScript enabled to view it. with the following in the body of message: unsubscribe iv3d-users
  2. Nothing needed in the Subject line. Just send.
  3. You will receive a response from the list manager notifying you that the command has succeeded and you have been removed from the list.


The same procedure should be used to subscribe to the iv3d-develop and tuvok-developers mailing list.

 

ImageVis3D has built-in support for reporting bugs. This is the preferred method for you to submit issues you come across. It can be accessed via the "Help" menu, using the "Report an Issue" menu item.

 

Iv3d-issue-report

 

Description

Please provide a description of what went wrong here. Good things to include here are:

Exact steps to reproduce the problem! Please be verbose. "Select File | Open and then navigate to a pre-existing UVF file" is a much better step description than "open a data set", for example.

If you close ImageVis3D completely, reopen it, and then repeat the above steps -- does the bug appear or not appear? Is there something that must be done beforehand which might be relevant?

What you were trying to do at the time the problem occurred.

Every bit of information you can provide will be helpful. However, the most important thing you can do is to reproduce the bug! ImageVis3D keeps internal logs of what it is doing, and those logs are sent to us when you send a bug report. So, make sure ImageVis3D has demonstrated the bug in the same session you are using this submission dialog.

 

Additional Information

Please leave the Submit Debug Log box checked! This gives us very valuable information. We provide the option to leave those logs out in case you were working in a highly sensitive environment. HIPAA-compliant agencies generally are not: there is not much information in these debug logs, and certainly not enough to violate HIPAA compliancy.

If you can, please use the "Add Files" button to attach the data set[s] you were having issues with to your report. If you can, attach the original data, not the UVF data, as this will allow us to see if the conversion process is broken. Please note that adding a data file can violate HIPAA; if you anonymized your DICOMs before loading them into ImageVis3D, however, then there are no issues.

 

Personal Information

If you feel comfortable, please provide an e-mail address. This information is stored on our servers in a manner that only SCI personnel and collaborators can access it; your email will not be posted publicly.

The vast majority of bug reports are actually support inquiries: users trying to do something in a particular way, and not understanding that it must be done slightly differently in ImageVis3D. If you do not provide us with an email, such reports are not very useful to us. However, we've had many fruitful interactions with users as we explain how to accomplish what they are looking to do.

 

If ImageVis3D crashes, it is of course difficult to use it's "Report an Issue" dialog!

The solution to this is to run ImageVis3D twice: the first time, turn on debug logs to make sure you get a record of what's happening. Then, run ImageVis3D a second time and use the "Add File" button to add the debug logs from the first run.

1. In ImageVis3D's "Settings" dialog (ctrl-S on Linux/Windows; command-, on Mac), at the bottom of the "Performance" tab, you will find a section for Debugging. Check the "Write LogFile" box and make sure the "Loglevel" slider is cranked all the way to the right. Now hit "OK" on the dialog.

2. Do whatever you needed to do to get ImageVis3D to crash.

3. Let the operating system kill ImageVis3D because of the crash.

4. Start up ImageVis3D again. Use "Help | Report an Issue" to get the issue dialog, and fill out the forms as described in the previous tag "Reporting Non-fatal Bugs."

5. Attach the "debugLog.txt" file which was generated via the previous run, using the "Add File" button in the issue reporting dialog.

 

The ImageVis3D developers communicate via a variety of mechanisms.


Mailing Lists

The developer mailing list is where development concerns should be voiced. If you plan on working on a particular feature, it is a good idea to post your ideas here before you get too far in, so that we can give advice on how best to proceed.


IRC

The lead developer hangs out on the Freenode IRC network as 'tfogal'. He also idles in an #imagevis3d channel.

Please free to join the channel and/or message 'tfogal' directly, but note that IRC is commonly asynchronous: it may take hours or days for a reply.


Lingo

The ImageVis3D developers have developed some terminology which are frequently used in the context of ImageVis3D-related discussion. A dictionary for these terms is:

"iv3d"/"IV3D"/"ImageVis"/"ImgVis": ImageVis3D
"Tuvok"/"TUVOK": The Ultimate VOlume (rendering) Kit -- the renderer that powers ImageVis3D.
"UVF": ImageVis3D's custom file format, which enables fast access to multiresolution data.
"scio"/"SCIO"/"the io layer/subsystem": An independent library handling conversion from various data formats to UVF.