Fiji ImageJ. TrakEM2 plugin

Hello,
Does anyone have or know how I can acquire ImageJ 1.50e for Mac computers. We are doing Serial Block-Face Scanning Electron Microscopy to get a 3D view of mitochondria in nerves. We want to trace these mitochondria throughout each slice to output a 3D reconstruction. In the most up to date version of Fiji we are not able to get the 3D viewer to work but in the past we have been able to get it in the 1.50e version. Please let me know if you have any suggestions on where I can find this version of Fiji for Mac computers.

1 Like

Hi @SamiJo,

Welcome to the forum.

You can get the 1.50 version with:
Help > Update ImageJ ... and selecting v1.50 dropdown.

Does that help? I fear there may be a deeper issue at play though.

Can you describe in detail what happens when you try using the 3d viewer with the latest Fiji?

John

Hello,

We are tracing mitochondria in the TrakEM2 plugin. Once I trace the mitochondria of interest, I right click to “view in 3D.” Once the 3D window pops up there is nothing, the window is just black. Someone else in a different lab has this issue. We do the exact same steps as when we used the 1.50e version but are able to see what we traced, in 3D.

Thank you!
Sam

Also, I am currently using ImageJ 1.50i but getting the blank 3D window. It seems only ImageJ 1.50e is the only one that can get us what we are looking for. Is there anyway to get the ImageJ 1.50e version?

Hello,

We are still having a lot of trouble with the newest version of Fiji. Do you know where I can find the 1.50e version. It is very important that it is version e.

Hi @SamiJo,

You can find the ij.1.50e.jar here:
http://maven.imagej.net/content/groups/public/net/imagej/ij/1.50e/

John

Great, thank you!

We have an older version of ImageJ (1.50e) we would like to add the Trak2EM plugin. We have found the TrakEM2 file on GitHub but are unsure of how to download and load it into the older ImageJ. Any help would be greatly appreciated.

Hi @SamiJo,

I strongly advise against trying to build / install TrakEM2 yourself (reasons below).

Instead, I recommend you try out older (“life line”) versions of Fiji available here. Hopefully, one of those will work in the way you want.

John

  • You will need to find a version of TrakEM2 that is compatible with the ImageJ version you chose.
  • You will need to build 3D viewer as well, again being careful to ensure you choose a version compatible both with the ImageJ version, and TrakEM2 version.
  • Managing everything is a huge pain, and saving people from this pain is the main reason that Fiji exists.