Stackreg and Turboreg

[Christian_Tischer]

Hello,

Could it be that Stack- and Turbo-reg are not included in Fiji anymore?
I also could not find a corresponding update site.

[imagejan (Jan Eglinger)]

Could it be that Stack- and Turbo-reg are not included in Fiji anymore?

These were moved to their own update site due to licensing issues. Please see this announcement:

EPFL BIG plugins moved to their own update site

The ImageJ plugins from EPFL’s Biomedical Imaging Group have been split to their own independent update site. The following plugins are included in this transition: Differentials Extended Depth of Field MosaicJ PointPicker Shepp-Logan Phantom Snakuscule StackReg TurboReg UnwarpJ And the following supporting libraries moved with them: imageware MIJ wavelets These plugins and libraries have no dependencies on anything besides ImageJ 1.x, so they should be usable with or without the Fiji upd…

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I warmly recommend to subscribe to the Announcements category on the forum, by choosing the respective option at the top right on that category page

[Madina (Madina Makhmutova)]

Hello everyone. I’m just transitioning to Fiji from regular ImageJ and I have troubles downloading Turbo-reg. From the thread above I can see that the Stack- and Turbo-reg were moved to a different update site and are not a part of the Fiji. Does that mean that I need to download them separately to Fiji? I have been trying to add Turbo-reg Jar to Fiji but that didn’t help. Is there another plugin in Fiji which is similar to Turbo-reg or how can I upload Turbo-reg?

[imagejan (Jan Eglinger)]

Does that mean that I need to download them separately to Fiji?

No, it simply means that you have to activate the respective update site (BIG-EPFL) in your installation.

[Madina (Madina Makhmutova)]

Thank you very much! I have tried to run the updater but I do not get an option to select update sites. If I go Help > Update the updater just starts running and then it gives an error message

[imagejan (Jan Eglinger)]

This error might have one of the following causes:

• you run Fiji from the opened disk image (.dmg) file without first copying Fiji.app to your local disk, or
• you run Fiji from a location where you don’t have full write permissions, e.g. the Applications folder on a Mac configured for multi-user access.

It should run fine if you copy Fiji.app e.g. to your Desktop and run it from there.

[Madina (Madina Makhmutova)]

Thank you very much! It seems to be working now!

[wq_s]

I run Stackreg， then show below! what is the matter? how can I use this Stackreg? Thank you very much!

StackReg_ not up-to-date because 1 source files are not up-to-date (C:\Users\ciomp\AppData\Local\Temp\java6031322077514304355\src\main\java\StackReg_.java)
Compiling 1 file in C:\Users\ciomp\AppData\Local\Temp\java6031322077514304355
[-classpath, C:\Users\ciomp\AppData\Local\Temp\java6031322077514304355\target\classes;C:\Users\ciomp\Desktop\Fiji.app\plugins\3D_Blob_Segmentation-
…
No javax.tools.JavaCompiler available. Checking for explicit javac.
No javac.jar found (looked in C:\Users\ciomp\Desktop\Fiji.app\jars)!
java.lang.ClassNotFoundException: com.sun.tools.javac.Main

[acrise]

Hello, I have the same problem wq, did you manage to solve it? Thank you!

[Christian_Tischer]

Hi!

In case of doubt I would always recommend to

1. download a new Fiji
2. enable the update site BIG-EPFL

Could you let us know if that helps?