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Connect Toolkit - Seamless Correlative Imaging Experience in Life Science Research
ZEN SOFTWARE TOOLKITS

Connect Toolkit​ The Correlative Imaging Experience in Life Science

Ideal for versatile correlative imaging, the Connect Toolkit enables multi-modal acquisition on ZEISS imaging systems, providing intuitive alignment and registration tools. Stay focused on the big picture.

  • Effortless sample navigation
  • Smart data organization
  • Multi-scale perspective for new insights

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Discover ZEN Connect Toolkit

See how it revolutionizes correlative life science workflows in less than 60s.
Plunge-frozen adenocarcinoma cells grown on sapphire discs. All regions of interest are shown in context in ZEN Connect.

Plunge-frozen adenocarcinoma cells grown on sapphire discs. All regions of interest are shown in context in ZEN Connect.

Plunge-frozen adenocarcinoma cells grown on sapphire discs. All regions of interest are shown in context in ZEN Connect.

Multi-scale Perspective for New Insights

Unlock New Insights with Multimodal Perspectives at Different Scales

Correlative microscopy gives unparalleled insights into your specimen. Leveraging light, and electron microscopes, the Connect Toolkit facilitates such experiments with pre-defined configurations for standard sample holders, precise calibration procedures to align stages, and the capability to display imaging data of various scales. Elevate your imaging experience and gain a comprehensive understanding of your samples with the Connect Toolkit.

Correlative cryo dataset in ZEISS ZEN Connect

Correlative cryo dataset in ZEISS ZEN Connect

Correlative cryo dataset in ZEISS ZEN Connect

Effortless Sample Navigation

Keep a Good Overview of the Bigger Image During Acquisition

Maintaining a broad perspective during imaging experiments is always beneficial. The correlative viewer offers guided navigation by displaying the overview images of all relevant parts of your sample. During detailed acquisition, use the viewer to easily and promptly move the stage to all sample parts of interest. 

Automated slide scanning and detailed studies on other ZEISS microscope systems combined in a ZEN Connect project

Automated slide scanning and detailed studies on other ZEISS microscope systems combined in a ZEN Connect project

Automated slide scanning and detailed studies on other ZEISS microscope systems combined in a ZEN Connect project

Smart Data Organisation

Put All Your Eggs in One Basket 

The Connect Toolkit helps you organize your data in a clever way. Why make your work unnecessarily complicated with a large set of imaging files that sit in a folder? Forget about manual data organization and difficulty accessing these files. With the Connect Toolkit keep all your images in context in an overarching data container. Thanks to easy navigation, every single image is only one click away directly within the Connect Toolkit.

Calibration and Alignment Methods in Connect Toolkit

Correlative microscopy involves multiple modalities, each typically requiring stage calibration or alignment. The Connect Toolkit provides several methods for the positioning of a sample before and after acquisition, which contributes to the optimal imaging results. The next section provides an overview of the available methods.

2D Alignment

  • Align

    Align

    Basic alignment: Move, rotate, scale, or shear image sets in correlative viewer. Visually align a high onto a low-resolution overview image.

  • Manual Alignment Wizard

    Manual Alignment Wizard

    Like basic alignment but with a dedicated wizard. Enter translation, rotation, scaling, and shearing values numerically.

  • Point Alignment Wizard

    Point Alignment Wizard

    Using split view for reference points to define positions. Translate, rotate or scale an image with at least 3 distinct corresponding points.

3D Alignment

  • 3D Alignment

    3D Alignment

    An add-on to enable 3D rotation for a 3D data set in misaligned correlative imaging, addressing issues in camera perspective.

  • Point Alignment 3D Wizard

    Point Alignment 3D Wizard

    Draw reference points on any position within a 3D data set. The algorithm performs translations and x-y rotations.

  • Align Two Images in 3D

    Align Two Images in 3D

    Tomo3D viewer enables translating two 3D stacks in any 3D plane. The 3D Toolkit is required.

Stage Calibration

  • Align System

    Align System

    Unlike standard alignment, this method also recalibrates the stage, and uses custom reference points for system calibration.

  • Shuttle & Find

    Shuttle & Find

    Use with sample holders with fixed reference points. These help calibrate the stage in position, scale, and camera angle.

Connect base vs. Connect toolkit

Some basic correlative functions are already available in the base ZEN installation. The Connect toolkit, on the other hand, provides all existing correlative functions. This table serves as a reference of the features in Connect Base vs. Connect Toolkit.
Connect base
Connect toolkit

Correlative viewer / project

x

x

Align / Align system

x

x

Auto-registration with calibrated stage

x

x

CZI image acquisition / import

x

x

Stage control from viewer

x

x

Align two images in 3D

requires 3D toolkit

requires 3D toolkit

Measurements in correlative viewer

x

Regions definition and retrieval (on second system)

x

Shuttle & Find

x

Alignment Wizards / 3D (z-dimension) alignment

x

Bioformats & FIB stack image import

x

Extended image / movie export (project view, SerialEM)

x

Connect Toolkit Point Alignment

Effortlessly Align Points in the Sample

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Downloads​

  • Preview image of ZEISS ZEN Connect

    ZEISS ZEN Connect

    Overlay and Organize Images From Any Source to Connect Your Multimodal Data
    2 MB
    Download

Visit the ZEISS Download Center for available translations and further manuals.

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