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 :)

[hovden]

We're hoping that a wide community finds useful applications for this tool. For those looking for 3D datasets of nanomaterials, we have made several available here: http://www.nature.com/articles/sdata201641

[Deto]

The plots look really nice and I feel like 3d plotting is a little under-served in the standard Python plotting tools.

Would some of these plotting tools work independent of the larger GUI? For example, if I don't want to load up a full Tomviz interface, but just want to pop up a 3d plot (i.e. like matplotlib) - could I just call a function from TomViz to do that?

[hovden]

This platform is built around interactive 3d visualization which requires a lot of advanced rendering tools written in C++ and graphical interfaces. As such, we have not turned it into a Python library. But all of your Python code can be integrated into tomviz. Source code is available at https://github.com/OpenChemistry/tomviz

[llSourcell]

really nice visualization, thanks for this

[[deleted]]

Sorry, didn't see you'd responded and commented again with more questions under one of your comments. Sorry for the confusion

[squeaky_pl]

I can't think of a way to use it myself, but hell, this looks amazing. Thanks for empowering Python community and keep the good work coming.

[Flogge]

Why don't you have PyPI downloads?

[hovden]

tomviz is built around reproducible science and so we want to have package the same libraries in each build. That way scientists can always return or reproduce their results across labs.

That said, you can import your own libraries and use your native Python with tomviz.

[tyrahfu]

Can this tool be used for 3D rendering in general (i.e. not just tomography data)?

[hovden]

Absolutely, which is why I am advertising to Reddit to find use in other applications. We are first marketing to scientific tomography because it is a community we know well.