Selected Features, Use Cases and Modules for Advanced Image Analysis: ZEISS arivis Pro

Finding cell boundaries based on membrane-localized contrast is made many times easier by new algorithms that enhance membranes in 3D and an operator designed to segment cells in 3D. This workflow allows use of any image filters upstream of the Membrane-based Segmentation, which enables optimization of results and/or application to challenging images.

Users can select between Membrane Enhancement and Objectness Measure (sheets) filters depending on data quality and time constraints. Membrane Enhancement gives the highest quality but takes longer while Objectness Measure computes faster. The Membrane-based Segmentation is adjusted interactively to increase cell segmentation yield and “over splitting” is easily proof-edited with the Merge tool.

The Seeded Region Growing Operation of ZEISS arivis Pro uses two different channels to achieve more precise segmentation results. In a simple two-step approach, you can choose one channel for seeding and another one for growing. You can easily segment whole cell bodies based on positive nuclear staining to easily separate close cells. The Watershed Operation for easy detection of non-roundish cells splits objects of any shape.

Create great results using any segmenter for seeding, using these as a starting point for Region Growing. Also, objects added into the data set via the VR Toolkit can be used for Region Growing. Use the new Splitting Operation as a modifier of segmentation objects to automatically split them in a pipeline run.

Some samples may be too large to be imaged in a single field of view at the desired resolution. Mosaic tiling can commonly workaround this limitation and the arivis Pro Tile Sorter can conveniently stitch such images into a single large volume. In some cases mosaic tiling may not be sufficient and it may be necessary to move/turn the sample to image the complete volume which can prevent stitching methods that rely on translation alone. The arivis Pro Volume Fusion Module overcomes these limitations and allows to fuse volumes based on landmarks and/or the free movement, rotation and scaling of a surface representation.

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 ZEISS arivis Pro 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.

Import resulting objects e.g. from Fiji or any other software in a single step into ZEISS arivis Pro (formerly 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.

Tracking cells or subcellular particles in microscopic data can be challenging. The Tracking Module allows analysis of the movement of small (i.e. particle tracking) or large objects (e.g. nuclei, cells, organisms) over time in both 2D or 3D multichannel image sets of any size (100s of GBs or TBs). With ZEISS arivis Pro we offer an easy to use approach with full control and interactivity at all steps. The novel software architecture and algorithms deliver top performance on tracking analysis of complex biological data. Combined with our Machine Learning segmentation, tracking and lineage analysis of multidimensional data sets will become an easy task, without the need to be an expert in image analysis. ZEISS arivis Pro allows you to create expert results and meaningful output data for any kind of tracking or lineage data sets. A manual track tool creates a track or branch interactively in the viewer by placing spots (using markers or Magic Wand). Use the VR Toolkit to proofread and correct your automatically created results much more efficiently than ever before.