Java3D Issue: BoneJ with latest Fiji version - Problem solved

bonej
Tags: #<Tag:0x00007fd53ede17d0>

#42

Please stick with us & have a go with BoneJ2 experimental as @rimadoma suggests, and let us know how you get on.

I personally need something strong before doing anything with Apple products; happy to give you my Martini recipe off-forum.


#43

LOL, if only I drank martinis (don’t hate me).

We are using the Volume Fraction component.

The truly frustrating thing about this is that I had it BoneJ and the 3D libraries working two weeks ago. Then the iMac crashed (new BTW) and got wiped by the Apple Store folks.

Thank you for the instructions. I will try this soonest and get back.

-Dave


#44

@ctreuden:

Thank you for the detailed reply. Unfortunately, I only understood about half of what you said. My forté is Windows.

As far as “sticking with an older version of macOS”, that may not be an option. This is a brand new iMac. I will give it some thought.

Do you think a Linux VM would be easier than getting this to work on Sierra?


#45

It would be worth a try. The performance of Java 3D in a VM may suffer (or may not—try and see). But hopefully it will at least still function.

Alternately, you could Boot Camp to Windows or Linux, which should retain good 3D performance.


#46

@ctreuden

Update:

In an attempt to get this working anywhere, I have now downloaded Fiji w/Java 6 and Fiji w/Java 8 onto my Win10 PC.

Our best case scenario right now (on both Mac and PC) goes like this…

  1. File -> Import -> Image Sequence -> select folder containing images -> wait while images are imported
  2. Plugins -> 3D Viewer (3D viewer launches fine with no errors) -> we can see and manipulate the compiled image in the 3D Viewer.
  3. Plugins -> BoneJ -> Volume Fraction -> Immediately get message: “Java 3D libraries are not installed. Please install and run the ImageJ 3D Viewer…etc…”

Does this help?

Thank you again for your time and attention.

Dave


#47

@Dave_Maag

It’s possible that even if the 3D viewer works for viewing, the libraries it uses under the hood have changed, so BoneJ doesn’t recognise them. @rimadoma suggested making BoneJ’s environment check more specific so that it only complains about missing 3D libraries at the point in the code when they’re really needed. I’m a bit short on bandwidth right now to do this for BoneJ1; the alternative is to have a go with BoneJ2.


#48

Sounds great. Which version did you use for testing in your following report? Java 6? Or Java 8?


#49

Maybe it’d be best to only complain about missing 3D libs where possible, i.e. “You wanted me to display surfaces, but I can’t. Here’s your other results though.” instead of “I won’t run because there are no 3D libs”. With Volume Fraction having the libs for creating a mesh is essential, and the surface based version cannot run without them. But the voxel based can.


#50

I used both.

I will try BoneJ2. Thank you.


#52

OK, good news. I was able to get this working by using BoneJ2. Thank you for the suggestion @mdoube

Next, I will go try this on the iMac.

Once more unto the breach, dear friends, once more…


#53

@mdoube Just a side note: at the moment BoneJ2 can create meshes with marching cubes and calculate their properties in Volume fraction and Isosurface, but it doesn’t know how to visualize them yet.


#54

Hi @Dave_Maag,

@ctrueden (big thanks!) and I have been trying to reproduce your problem on Windows 10, but in our environments BoneJ works fine. Here are the steps we took to get BoneJ up and running:

  1. Download and install Java 6 lifeline version of Fiji
  2. Download BoneJ and drop it to the Fiji.app/plugins/ folder as per normal.
  3. Launch Fiji and start using the plugins.

We’ve tested that these steps work on both Win 8.1 64-bit and Win 10 64-bit.

Best regards,
Richard