Exchange Objects with Open Source and other software

With arivis you can now integrate all tasks of image visualization and analysis of 3D images of any size in a single software package.

The Open Source community offers many special functionalities and regularly adds new ones to the research community. On the other hand many efficiencies are enjoyed via a commercial, robust image analysis platform with a unified UI which covers all aspects of image processing, analysis and visualization of results via desktop, web sharing or Virtual Reality. Therefore an easy transition between open source and arivis products is essential.

 

With the new arivis Vision4D Module Exchange Objects with Open Source we offer an integrated solution to imaging facilities and PIs to connect with open source workflows as well as with any other software which is capable of exporting/importing labelled images. Easily interface with your specific workflows whenever you are using segmentation functions in Open Source such as Fiji, ImageJ , Ilastik  and Python or in commercial solutions, e.g. MATLAB or Carl Zeiss ZEN Blue. No programming knowledge is needed.

Workflow steps:

  1. Raw image (3D image)
  2. Create segments with Open Source
  3. Export segments as labeled images
  4. Convert labeled images into 3D objects to create 3D movies and allow further analysis in arivis Vision4D and InViewR.

Data courtesy of Dr. Srigokul Upadhyayula (Assistant Professor of Pediatrics at Harvard Medical School).

 

Import objects from Open Source software

Just import your resulting objects e.g. from Fiji or any other software in a single step into Vision4D and visualize the segmentation in 3D, create impressive movies with our arivis storyboard, or explore and edit them with InViewR in Virtual Reality. Alternatively you can also integrate the results from open source in your arivis Analysis Pipeline and do further processing, Tracking, Classification with our flexible pipeline including batch processing.

Transfer from 2D/3D segmentation in Open Source

Combined workflow: Ilastik autocontext and 3D segmentation using ImageJ-Matlab.
Image courtesy of Dr. Carlo Beretta, Livia Asan, Dr. Johannes Knabbe and Prof. Dr. Thomas Kuner, Department of Functional Neuroanatomy, Heidelberg University

to arivis Vision4D

Image courtesy of Dr. Carlo Beretta, Bioquant BQ0004, Heidelberg

 

or to arivis InViewR

Image courtesy of Dr. Carlo Beretta, Bioquant BQ0004, Heidelberg

 

Export objects to other software

Exchange objects from arivis Vision4D back to Open Source or any other software to do a very specific analysis and also return the results easily into any product of the arivis platform. » arivis Vision4D » arivis InViewR

Transfer from arivis Vision4D

Image courtesy of Dr. Markus Neumann, Carl Zeiss Microscopy Munich

 

 

 

 

 

 

 

 

 

 

 

to Fiji

Image courtesy of Dr. Markus Neumann, Carl Zeiss Microscopy Munich

 

Import objects from other software packages

Third party software such as ZEISS ZEN (e.g. Intellesis module) can be used to create 3D objects plane by plane. These can be converted in a single step into Vision4D to visualize the segmentation in 3D, create impressive movies with our arivis storyboard and edit the result in Virtual Reality with arivis InViewR in Virtual Reality. Alternatively results from ZEISS ZEN  may be further processed in your arivis Analysis Pipeline, adding 3D tracking, or Classification with our flexible pipeline approach.

 

 

 

 

 

 

 

 

 

 

 

Transfer from ZEISS ZEN

Image courtesy of Dr. Markus Neumann, Carl Zeiss Microscopy Munich

to Vision4D

Image courtesy of Dr. Markus Neumann, Carl Zeiss Microscopy Munich

 

 

With arivis it is easier to combine different software packages.

 

Benefits:

The one step import and export of objects allows to add more functionality from Open Source or other software packages to the proven 3D visualization and analysis functionality to your arivis platform.