Overlay and Organize Images from Any Source.

Connect All Your Multimodal Data to Expand Correlative Microscopy

Often, to fully understand your sample, you will need to combine multiple microscopy technologies or contrasting techniques.
Say you are wanting to understand synaptic ultrastructure in context with their brain region. Or assessing whether inclusions in a material sample are metallic. Or determining which particles are critical when analyzing the technical cleanliness of your processes.
In these cases and many others, a single microscopy method is not always enough to answer all your questions.

You can address some of them with correlative light and electron microscopy (CLEM), a field which ZEISS Microscopy has pioneered in recent years. Correlative microscopy combines the flexibility and large fields of view of light microscopes with the analytical power and nanometer resolution of electron microscopes. Now, with ZEN Connect, you can take that next important step and bring all of your imaging technologies together – ZEISS or not – to answer your scientific questions. ZEN Connect lets you combine multiple perspectives of your sample across scales and imaging modalities.

Simply acquire an overview image of your large sample on any low magnification system, then move to your confocal or electron microscope and align. Just once. You’re now set to use ZEN Connect with the overview image for navigation and all subsequent images will automatically appear in context. Or you can simply use ZEN Connect to align and overlay images from any source.
Your multimodal data is saved in well-organized projects with intuitive image labels. ZEN Connect always shows your data in context – you get unique insights, gain efficiency and save time.


Overlay and Align All Your Images

Expanding classic correlative microscopy, ZEN Connect is open to all your images: you can load complex multidimensional images as easily as simple overview images from your mobile phone. It makes no difference whether your imaging technology is from ZEISS or from third parties. All image data can be aligned, overlayed and shown in context. So long as your external images adhere to the well-established Bio-Formats standard, ZEN Connect will even keep their metadata.

Acquire Overview Images for Easy Navigation

Image your sample with a ZEISS stereo microscope or any other low magnification system. Then move to your high-resolution system of choice. With ZEN Connect you only need to align it once, then use the overview image to navigate and find your ROIs. All subsequent high-resolution images will be shown in context as you zoom in and out across the borders of resolution domains and imaging technologies. A single click on the overview image brings your stage to the right position to examine or re-evaluate any of your ROIs with the full image overlay.

Smart Data Management

All the images you acquire with ZEN Connect are saved in well-structured database projects, complete with an intuitive label attached automatically to each image file. You'll always stay on top of things – during your experiments as well as months afterwards when analyzing your work. It's easy to find all your overlay images and their connected datasets. You can even search for microscope type and imaging parameters with the new filter function of ZEN Connect.

Application Examples


Axio Scan.Z1 to LSM 800

With ZEN Connect it's easy to image entire mouse brain sections. First, acquire a quick overview image with the automatic slide scanner Axio Scan.Z1. Then move the sample and data to your LSM 800 with Airyscan. Use ZEN Connect to align the LSM to the overview image. Now simply use the overview image to navigate around your sample, identifying and relocating ROIs as you go. As you acquire your Airyscan superresolution images, they will be displayed instantly on top of the overview image. This overlay view means you will always see your multimodal data in context.

Section of a Thy1-YFP mouse brain
Section of a Thy1-YFP mouse brain
Section of a Thy1-YFP mouse brain - single neuron

Section of a Thy1-YFP mouse brain. Thy-1 (green) is involved in the communication of cells in the nervous system. Overview image (A) acquired on ZEISS Axio Scan.Z1. Inset shows enlarged ROIs imaged on ZEISS LSM 800 with Airyscan (B, C) The neuronal network is clearly visible. The depth of the Z-stack is color-coded. (D) shows a single neuron.
Sample: courtesy of R. Hill, Yale University, New Haven, CT, USA.


Axio Observer 7 to GeminiSEM 300

Connectomics research aims to explain the `wiring' of brains and, ultimately, how brains work. One of the biggest challenges in this field is the sheer scope of the investigation. You need ultrastructural information to be able to resolve single synapses. On the other hand, brain samples are huge in microscopic terms and you'll need to image large regions of interest to observe the interaction between different parts of the brain and various types of neuronal cells involved.

ZEN Connect lets you analyze ultrastructural data in a wider context, connecting large fields of view imaged on a widefield light microscope. Now you can work with multimodal data, bringing together different imaging modalities and resolution domains - from low magnification widefield to nanometer resolution EM data.

Ultrathin mouse brain section
Ultrathin mouse brain section

Ultrathin mouse brain section. (A) Overview image acquired with ZEISS Axio Observer 7 and ZEN Connect. Synapsin-1 was labeled with Alexa Fluor 647 (green) targeting the pre-synaptic vesicles and Alexa Fluor 594 labeled Gephyrin (red), targeting a part of the postsynaptic protein network. Nuclei were stained with DAPI (blue). The overview image was used for navigation and ROI relocation. The insets (1-3) were acquired with ZEISS GeminiSEM 300 and show the ultrastructure of the ROIs. (B) shows a zoomed image of inset (3).
Sample: courtesy of M. Ocana, Harvard University, Boston, MA, USA.

Cell Biology

Celldiscoverer 7 to LSM 800

In live cell imaging, your samples are especially sensitive to light and environmental stress. ZEN Connect helps to keep light doses small. Simply acquire a quick overview image, then navigate freely around the petri dish or slide – without needing to illuminate your specimen further. In addition, you will often want to image the same sample a number of times over the hours or days of your experiment. With ZEN Connect, it's easy to relocate your ROIs after taking a sample out of the incubator for the next round of imaging.

Fox lung fibroblast cells
Fox lung fibroblast cells

Fox lung fibroblast cells expressing Actin GFP (green) were imaged overnight with ZEISS Celldiscoverer 7. After widefield live cell imaging, the sample was fixed and stained with CellMask plasma membrane stain (red).
(left) The movie shows a petri dish with single cells and a time series showing cellular dynamics and cell division. After fixation and staining, the cells were imaged with ZEISS LSM 800 and Airyscan.
(right) Overlay image of one time point of the time series with confocal and ZEISS Airyscan data.


Axio Scan.Z1 to Axio Imager.Z2 with Apotome.2

In histology, you study cells and tissue with light or electron microscopes. You often need to combine multiple contrasting techniques to understand the structure and function of your specimens. For an even deeper understanding, you may sometimes need to go from large tissue sections to subcellular ultrastructure. Frequently this also requires you to combine complementary imaging technologies.

Fox lung fibroblast cells

In this example, a 5 μm thick section of an embryonic rat knee was first imaged with ZEISS Axio Scan.Z1 and polarized transmitted light. The rapid tiling of this automated slide scanner allowed to acquire a large area of the sample in the shortest possible time. The specimen and data were then transferred to ZEISS Axio Imager.Z2 with Apotome.2 for fluorescence imaging of muscle and physeal growth plate (red: Sirius-red, green: autofluorescence). ZEISS Apotome.2 allowed the acquisition of Z-stacks of striated muscle (upper row) and chondrocytes in the growth plate (lower row) with a Z-resolution of 1.4 μm.

Data Storage and Access Wherever You Are

Data Storage and Access Wherever You Are

Need to share your ZEN Connect projects remotely with colleagues and collaborators? Why not try ZEN Data Storage and ZEN Data Explorer? ZEN Data Storage forms the central database that holds multidimensional ZEN Connect projects. ZEN Data Explorer creates and manages access to your stored ZEN Connect projects, and it handles large files efficiently. Running as a App on smartphones and tablets (both iOS and Android) as well as in a web browser, it will be your companion for sharing your findings at conferences and impressing prospective collaboration partners with your data.



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

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ZEN Data Storage and Data Explorer

Smart data management in life sciences

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