ZEISS ZEN Intellesis for Image Segmentation in Microscopy

Use the Power of Deep Learning to Easily Segment Your Images


As enjoyable as microscopic images are - their real value is in the data they provide. Image segmentation is currently one of the biggest challenges in microscopy and the foundation for all subsequent image analysis steps. ZEN Intellesis uses established machine-learning techniques powered by Python, such as pixel classification and deep learning to easily create robust and reproducible segmentation results, even for non-experts. You can now train the software once and then ZEN Intellesis can segment a batch of hundreds of images automatically. You save time and minimize user bias.
For additional information and technical details please use Open Application Development - Machine Learning *1


Use Deep Learning to Segment Your Images

To get reliable data from images, you often need to segment different classes of objects in multiple images. With ZEN Intellesis you can now use your expertise to train the software on a few images. All time-consuming segmentation steps on the hundreds of similar images will then be done by the powerful machine learning algorithms (including Deep Learning) of the software module ZEN Intellesis. The Python-powered tools offers pixel classification with real multichannel feature extraction and segmentation by pre-trained networks *2, even complex multidimensional, multi-modal data can be analyzed, regardless of their origin. The software even allows to import and use your own deep learning models *3

Enjoy Smooth Workflow Integration

The software module ZEN Intellesis makes machine learning easy to use: You simply load your image, define your classes, label pixels, train your model and perform the image segmentation. For common tasks like Nucleus Segmentation one can even import a pretrained model, which can be used to segment and analyze full datasets. Moreover, it is even possible to train your own network and import into ZEN. (The creation of customized pre-trained networks is also available as a paid service). Intellesis is fully integrated into the Image Analysis Framework in ZEN Blue and ZEN core Imaging Software and support scripting. This integration ensures that all valuable Metadata stay connected and are available for further processing steps.

Analyze Multi-Modal Images from Many Sources, in Many Formats

With the software module ZEN Intellesis you can easily segment multidimensional images from a wealth of different imaging sources, as diverse as

  • Widefield Microscopy
  • Superresolution Microscopy
  • Fluorescence Microscopy
  • Label Free Microscopy
  • Confocal Microscopy
  • Light Sheet Microscopy
  • Electron Microscopy
  • X-ray Microscopy

Together with ZEN Connect one can combine images from different microscopes from the same sample and use those results to extract even more valuable information by using ZEN Intellesis. The software will by use image features from all modalities at once to segment the structures of interest. By importing OME-TIFF or TXM images directly or when using the 3rd party import function ZEN Intellesis can also be used to segment all Bio-Formats compatible images.

Application Example Life Sciences

1. Scratch Assay

Single frame of recorded time-lapse movie. Segmentation result of ZEN Intellesis
Single frame of recorded time-lapse movie.
Segmentation result of ZEN Intellesis - scratch area (turquoise), cell layer (orange) and mitotic cells (red).
scratch area measured over time
Based on ZEN Intellesis segmentation results, the size of the scratch area was measured over time using the ZEN Image Analysis module.

2. Spines and Dendrites

spines on a dendrite
Dendrite of a neuron expressing Green Fluorescent Protein. Image acquired with structured illumination on an Elyra PS.1 showing spines on a dendrite.
Segmentation with ZEN Intellesis results in a clear separation
Segmentation with ZEN Intellesis results in a clear separation of spines (green) from dendrite (red) and background (blue)

3. Drosophila

X-Ray micrograph of a Drosophila melanogaster.
X-Ray micrograph of a Drosophila melanogaster. 1400 slide z-stack of the whole fruit fly acquired with ZEISS 520 Versa.
X-Ray micrograph of a Drosophila melanogaster.
Segmentation result obtained with ZEN Intellesis – exoskeleton (red), inner structures (blue and yellow), background (green)
X-Ray micrograph of a Drosophila melanogaster.
Rendered 3D model based on exoskeleton class.

Application Example Materials Analysis

XRM Sandstone – Original
XRM Sandstone – Original
XRM Sandstone – Labeled
XRM Sandstone – Labeled
XRM Sandstone – Trained & Segmented
XRM Sandstone – Trained & Segmented
XRM Sandstone – IP Function Output
XRM Sandstone – IP Function Output

How to Segment Your Images


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ZEISS ZEN Intellesis Machine Learning Software

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ZEISS ZEN Intellesis for Life Science

Image Segmentation for 2D and 3D Datasets

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ZEISS ZEN Intellesis for Materials Science

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Advanced Segmentation for Industrial Materials

Learn about machine learning – a solution to the segmentation problem with ZEISS ZEN Intellesis for initial data generation or analysis and processing of a segmented image.

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ZEISS ZEN Intellesis

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