Tomography reconstruction algos disabled

[darkworks]

I Loaded my 60 tiff images capture via x ray scanner and then when i go to Tomography > Reconstruction section i noticed all algo are disabled there ? so am wondering how to enable them like tomopy as am interested in reconstructing 3d mesh from my tiff stack. I even tried Sample Data menu to generate random particles but still tomography algos are disabled.

To Reproduce Steps to reproduce the behavior:

1. Sample Data > Generate random particles
2. Tomography > Reconstruction
3. Try to click Tomopy method
4. Disabled unable to click..

Expected behavior should be able to use and try various tomography reconstruction methods by default after installing the APP , as shown in the demo video.

Screenshots

My Data set screen shot

Desktop (please complete the following information):

• Operating system: Windows 10
• Tomviz version: 2.0.0-rc3-23-gdd39cc4c

Hardware (please complete the following information):

• Device: MSI Laptop
• Graphics card: Nvidia GTX 1080

[ercius]

You need to mark your data as a Tilt series. Click Tomography -- Mark data as tilt series. Then those will be available.

[darkworks]

You need to mark your data as a Tilt series. Click Tomography -- Mark data as tilt series. Then those will be available.

thanks for the help , now am getting error that there is no tomopy module ? how to install it for tomviz or should install it via conda on system ?

[psavery]

Unfortunately, tomopy's only supported installation method is through conda-forge, so we could not include it in the default packaging.

If you want to try using the tomopy reconstruction algorithm, you'll need to first install tomviz from conda-forge (conda install -c conda-forge tomviz), and then install tomopy from conda-forge (conda install -c conda-forge tomopy).

[darkworks]

thanks for the support @psavery . i installed tomviz using conda and also tomopy , however the reconstruction result is not 3D. can u please guide me what am doing wrong , as am new to tomviz

current output using tomopy Gridrec reconstruction method

however i was expecting output something like this : https://youtu.be/Bvj2gFvwjpU?si=2Acpcw6oC2mdQ52i&t=59

thanks a lot.

[ercius]

I would try one of the non-tomopy reconstruction techniques to see if that is the issue. If you can share the data I might also be able to look into the issue.

[darkworks]

I would try one of the non-tomopy reconstruction techniques to see if that is the issue. If you can share the data I might also be able to look into the issue.

ok here is data sample : https://drive.google.com/file/d/1SC5RDziQ2qvWy6YClO52wby37WIQjm_C/view?usp=drive_link

thanks

[ercius]

Unfortunately, I do not think Tomviz can reconstruct your data. Tomviz expects the tilt axis to be perpendicular to the projection direction and does the reconstruction assuming rotation around only that one axis. You inclined your object perpendicular to the beam axis and then rotated it around the beam. Actually, the machine used to acquire the data (see your youtube video) rotates the source around the object. These are equivalent, but neither is compatible with Tomviz as far as Im aware.

If you can reconstruct using a different software and then export it as a 3D volume then you can analyze the reconstruction.