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:
- Raw image (3D image)
- Create segments with Open Source
- Export segments as labeled images
- 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
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
Image courtesy of Dr. Markus Neumann, Carl Zeiss Microscopy Munich
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.
Image courtesy of Dr. Markus Neumann, Carl Zeiss Microscopy Munich
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.
- An easy workflow integrating special functionality offered by other software packages
- Create high quality movie renderings, for publications from segmentation results
- Visualize results in synchronized 2D/3D split views
- Visualize results with feature-based color coding or interactive gating in scatter plots or time line graphs
- Explore and further edit your results with InViewR in Virtual Reality
- Analyze your 3D objects to measure, e.g. volumes or count vesicles within cells or arbitrary 3D ROIs
- Add further processing such as Tracking and Grouping with our flexible arivis Pipeline
- No need for programming skills of the users
