OPEN SCALABLE INTEGRATED

Importing labelled images from Open Source

The most flexible way to import & export imaging data & results

With arivis you can now integrate all tasks of image visualization and analysis of multidimensional microscopy imaging data 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 users prefer a commercial, robust and fully supported image analysis platform with a unified UI that covers all aspects of image processing, analysis and visualization of results via desktop workstation, cloud computing or Virtual Reality. Therefore an easy transition between open source/third party packages and our arivis Scientific Imaging Platform is essential.

With the Vision4D Exchange Objects with Open Source module 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 with open source packages such as Fiji, ImageJ, Ilastik, Python or with commercial solutions such as MATLAB or ZEN/APEER software by ZEISS Microscopy.

No programming knowledge needed - Vision4D adapts to your requirements and workflows!

arivis-open-source-exchange-module-info

Talk with an Expert

Importing Labelled Images Workflow

arivis-exchange-objects-workflow-imaging-data-vision4d

Acquire Acquire your raw microscopy data

Create

Perform segmentation with your preferred scientific open source or commercial package

Export Export segments as labeled images

Analyze Convert labeled images into 3D objects to create 3D movies and enable further analysis

Webinar

Use Machine Learning-based segmentation in whole mouse brain light sheet data

Constanze Depp from the Max Planck Institute of Experimental Medicine is presenting a whole brain quantification of amyloid plaque load using Machine Learning in arivis Vision4D.

Vision4D Video Tutorials

Import Objects from Open Source

Import from open source or other software into Vision4D and create impressive movies

Import resulting objects e.g. from Fiji or any other software in a single step into Vision4D and visualize the segmentation in 3D to create impressive movies with our arivis storyboard. This is a combined workflow using Ilastik autocontext, 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

Explore & edit resulting objects from open source and Vision4D in arivis VisionVR

Import resulting objects e.g. from Fiji or any other software in a single step into Vision4D, then explore and edit the results from open source in immersive Virtual Reality with VisionVR. This is a combined workflow using Ilastik auto context, 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

Full Integration in arivis Vision4D

The one-step import and export of objects allows to add more functionality from Open Source or other microscopy software packages to the proven 3D visualization and analysis functionality of your arivis Scientific Imaging Platform, making it the most flexible solution on the market. No specialized coding/programming skills required!

Your benefits:

An easy workflow integrating functionality offered by other software packages
Create high quality movie renderings for your publications
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 VisionVR 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

arivis Vision4D works for several different multi-dimensional images from many modalities in microscopy:

Fluorescence Microscopy
Superresolution Microscopy
Transmission Light or Label Free Microscopy
Confocal Microscopy
Light Sheet Microscopy
Electron Microscopy (2D and 3D)
X-ray Microscopy
CT and MRT images

CZI, TIFF, JPG, PNG, TXM and all Bio-Formats compatible images including third-party vendor-specific file formats enabled through SIS Converter.

The arivis Imaging Platform

The arivis Imaging Platform is a flexible computing universe for Imaging Science that scales, parallelizes, integrates and connects all imaging workflows, sparking organization-wide image data proficiency and efficiency at all levels. The integrated toolsets take care of everything from the file storage format to user and project-specific computations to reporting. The computational and management hubs that comprise the platform connect your datasets and take care of your central imaging databases and can expose data assets - including raw data and specified portions of raw data - to Machine Learning and AI routines.

VisionHub Your nucleus of computational activity and collaboration at scale. VisionHub enables design and execution of large-scale experiments that produce results from images, whether datasets are already stored or are actively being produced. Mass quantities of imaging datasets are onboarded and processed by a virtual team of computational workers. Smartly utilize processing cores in servers or workstations with the maximum speeds possible. Read More

Vision4D

Your modular software platform for extracting results from scientific images. Adjusts to your hardware for maximum power and smooth interactivity even with large image datasets of virtually unlimited size. Bring diverse tools into one environment and enable your users to connect them into productive workflows. Highly interactive for optimization and quality at every step. Extend Vision4D directly via Python and connect it to other applications via libraries.

VisionVR Display real image data in Virtual Reality by utilizing patent-pending direct volume rendering techniques with no need to convert data or create surface models. Directly use your hands to move, rotate, scale, and shape your digital image data. Interactively proofread, edit, track or segment multi-dimensional images from nearly any source instrument. Discuss your findings and results worldwide in a collaborative connected environment. Read More

OUR TEAM IS READY TO HELP

Use the form below to get in contact with our arivis experts. Please describe your query and our team will contact you.