Digital pathology imaging



CRImage a package to classify cells and calculate tumour cellularity

CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity.

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AssayScope is an intuitive application dedicated to large scale image processing and data analysis. It is meant for histology, cell culture (2D, 3D, 2D+t) and phenotypic analysis. 

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A deep-learning solution for stain color normalization in digital histology images

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ZEN Intellesis Trainable Segmentation


Perform Advanced Image Segmentation and Processing across Microscopy Methods

Overcome the bottleneck of segmenting your Materials Science images and use ZEISS ZEN Intellesis, a module of the digital imaging software ZEISS ZEN.
Independent of the microscope you used to acquire your image data, the algorithm of ZEN Intellesis will provide you with a model for automated segmentation after training. Reuse the model on the same kind of data and beneft from consistent and repeatable segmentation, not influenced by the operator. 
ZEN Intellesis offers a straightforward, ease-to-use workflow that enables every microscope user to perform advanced segmentation tasks rapidly.


  • Simple User Interface for Labelling and Training
  • Integration into ZEN Measurement Framework
  • Support for Multi-dimensional Datasets
  • Use powerful machine learning algorithms for pixel-based classifcation
  • Real Multi-Channel Feature Extraction
  • Engineered Feature Set and Deep Feature Extraction on GPU
  • IP-Function for creating masks an OAD-enabled for advanced automation
  • Powered by ZEN and Python3 using Anaconda Python Distribution
  • Just label objects, train your model and segment your images – there is no need for expert image analysis skills
  • Segment any kind of image data in 2D or 3D. Use data from light, electron, ion or x-ray microscopy, or your mobile phone
  • Speed up your segmentation task by built-in parallelization and GPU (graphics processing unit) acceleration
  • Increase tolerance to low signal-to-noise and artifact-ridden data
  • Seamless integration in ZEN framework and image analysis wizard
  • Data agnostic
  • Compatibility with 2D, 3D and up to 6D datasets
  • Export of multi-channel or labeled images
  • Exchange and sharing of models
  • GPU computing
  • Large data handling
  • Common and well-established machine learning algorithms
  • SW Trial License available



Orbit Image Analysis is a free open source software with the focus to quantify big images like whole slide scans.

It can connect to image servers, e.g. Omero.
Analysis can be done on your local computer or via scaleout functionality in a distrubuted computing environment like a Spark cluster.

Sophisticated image analysis algorithms incl. tissue quantification using machine learning, object segmentation and classification are build in. In addition a versatile API allows you to enhance Orbit and to run your own scripts.


Skin Tools


The skin tools measure the thickness of the epidermis and the interdigitation index.

The input images are masks that represent the epidermis and that have been created from images of stained histological sections. The mask must touch the left and right border of the image. The dermal-epidermal border must be on the lower site of the image. The interdigitation index can be measured for one or more segments per image. As a measure of the thickness of the epidermis the lengths of a number of random line segments are measured. The line segments start at the lower border, are perpendicular to the lower border and end at the opposite border of the mask.

See installation Instructions on the website.

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Measure thickness from a mask

Adipocyte quantification ImageJ by Baecker


The Adipocytes Tools help to analyze fat cells in images from histological section. This is a rather general cell segmentation approach. It can be adapted to different situations via the parameters. This means that you have to find the right parameters for your application.

Sample Image: [0178_x5_3.tif](

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Adipocyte quantification MATLAB


Analysis of adipocyte number and size. The original code and example images supposed to be discovered at but currently the webpage is missing the code and sample images.

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NET - Network Extraction Tool


The ultimate goal of the NET framework is to make images of networks processable by computers. Therefore we want to have a pixel based image as input, as output we want a representation of the network visible in the image that retains as much information about the original network as possible. NET achives this by first segmenting the image and then vectorizing the network and then extracting information. The information we extract is

  • First and foremost the graph of the network. We find the crossings (nodes) and connections between crossings (edges) and therefore extract information about the neighborhood relations, the topology of the network.
  • We also extract the coordinates of all nodes which enables us to embed them into space. We therefore extract information about the geometry of the network.
  • Last but not least we track the radii of the edges in the extraction process. Therefore every edge has a radius which can be identified with its conductivity.

In the following we will first provide detailed instructions on how to install NET on several platforms. Then we describe the functionality and options of each of the four scripts that make up the NET framework.

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Kappa is a Fiji plugin for Curvature Analysis.

It allows a user to measure curvature in images in a convenient way. You can trace an initial shape with a B-Spline curve in just a few clicks and then fit that curve to image data with a minimization algorithm. It’s fast and robust.

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Kappa user interface