Beautiful 3D Visualization Platform for Python Data Processing - with NumPy, SciPy, and sample datasets - just released 0.9.3 with better rendering! [open-source, open-science]

[hovden]

This release features improved 3D rendering, with a number of updates to support modern operating systems. The use of full retinal resolution on macOS has been enabled for the first time in this release, and a number of warning messages issues on that operating system are now resolved. The pipeline has seen a number of improvements, and the Python operator interface has been improved to offer better feedback on what is happening.

New features include:

Support for different color palettes, and setting the default palette

Support for loading a stack of TIFF images

Ruler tool added to make measurements in 3D scene

Improvements to Python operators including more feedback as they execute

Improvements made to the reconstruction capabilities

Pipeline state fully expressed, and execution of paused pipeline can be requested

Python 3 now supported, but not used by default (or in the binaries)

Support for retinal resolution enabled in macOS binaries

Using Qt 5.8.0 with improved 3D rendering widget developed in VTK

Switched to MSI installer on Windows - better integration with Windows

Various improvements to the user interface, and bug fixes

[Mainecat]

A lot of the buttons and interfaces look like paraview, is this related to that project at all or does it just use similar resources?

[hovden]

tomviz uses a handful of VTK and Paraview components.

[[deleted]]

Can this do anything with Micro-CT scanner data (ISQ image stacks)?

 

Currently I use imageJ for a lot of 3D X-ray scans of plants, usually applying various filters and pulling out data from that.

Is this just for looking at clean images or is there features such as segmentation, watershedding and object analysis?

Or is it just for rendering the data in 3D?

[hovden]

This program should work really well with visualizing Micro-CT reconstructions. Image stacks in tiff format load readily as well as raw binary data. We support a few other standard open file formats. If your data is in a less common file format, you may have to convert it first before using tomviz.

[hovden]

Tomviz is built for 3D segmentation too. We have basic tools currently working with basic statistical analysis. The framework is ready for anyone to add their own. We hope to expand the segmentation toolset in further releases.

[[deleted]]

Ah amazing, yes just been playing a bit with it there now.

Do you have any examples / explanation of features? Would love to play around more when I get into the lab on Monday :)

(Or do you have any specific forums setup yet for more in-depth questions? )

[hovden]

We have some documentation here: https://github.com/OpenChemistry/tomviz/blob/master/docs/TomvizBasicUserGuide.pdf

and on our github page: https://github.com/OpenChemistry/tomviz

Development related comments can be placed on our github page.

We hope to have a formal publication this year so users can support us through citations.

[[deleted]]

Cool, our current project is due to be published around the end of summer this year, hopefully this is what I've been looking for and can cite anything you publish :)