Software for Digital microscopy

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For pre- and clinical research and diagnostic purposes, it’s important that medical images are not just images, diagnosis reports are not just unstructured information, molecular data are not just separated from results of image analysis. Researchers would be supported best, if suspicious or malicious structures of tissue samples are identified at the early stages. In that case the researchers and doctors be able to apply their expert knowledge more efficiently and to focus on the illness itself.
This is exactly, what the HS Analysis GmbH from Karlsruhe (GER) does science 2015, when it comes to automated image analysis, structure reports and bring them with knowledge from molecular data. The integration of these approaches in the hardware and its infrastructure is one of the main skills of HS Analysis.
The company is working worldwide closely with different partners together, when digitization, digitalization and automation of medical data is going to be a part of daily routine in diagnosis and research with AI techniques.
With the help of modern AI, Deep Learning and Active Learning supported methods HS Analysis, believes to seriously inspire quantification and prediction in diagnosis, CDx and research areas such as the evaluation or early detection of e.g. cancer.



The most up-to-date artificial intelligence is one key technology of automatic interpretation of tissue samples in the software of HS Analysis. Technically speaking, virtual slides are analyzed with deep learning. Virtual slides are digital images, that are produced by microscope roboters called slide scanner. In this way you quickly get quantitative results about effects of drug candidates on tissue.

Specialists of HS Analysis use the appropriate technology depending on requirements of customers.
Two examples of most used technologies are listed below.

Digital microscopy is a promising method for quantitative automatization in pharmaceutical research. The key technology was the introduction of Whole-Slide Imaging (WSI) or well plates with digital slide Scanners or HCS. They allow virtualization of the whole slide or well plate with large tissue sections or cell cultures in high microscopic resolution. Combination of WSI or well plates with automatic detection and quantification software enables numerous new possibilities and methods to search for drugs against diseases. HS Analysis develops automatic WSI and well plates quantification solutions for efficient workflows in pharmaceutical research. Our solutions are compatible with all slide scanner or HCS file formats.
Recent evolution in artificial neural networks allows reliable recognition of structures with complex morphology traits, similar like the human brain does. HS Analysis specialized in neural network applications and Deep Learning to detect your Region of Interest in automatic manner. Avoid manual annotations for ROI definition to achieve high throughput with short analysis times.


Cell tracking and analysis in real time

HSA in-house developed deep learning

Tracking of cellular morphology changes and behavior in concert with surrounding cells. Cells with increasing area are marked blue, decreasing area red. Length of individual cell borders, circumference, area and percentile change, compared to previous frame (Δ area, Δ circum.), are tracked in real time.

Self developed AI networks:
  • + Cell border gaps in the original image are closed intelligently
  • + Automatic tracking of length of individual cell borders, cellular morphology changes and behavior in concert with surrounding cells
  • + Visual representation of selected morphology changes (Area, circularity, neighbor cell behavior etc.)
  • + Simple export of all statistical data into an Exel file


Standard Deep Learning U-Net

Simple intensity dependent annotation of cell borders vs original image

Old U-Net based AI network:
  • - Gaps in the original image are not closed, therefore subsequent statistical analysis is impaired
  • - Tracking of cellular parameters difficult or only possible by additional programs
  • - No visual representation of selected changes in cellular morphology

Counting and segmentation of
cells in chamber slides

Detection and segmentation of nuclei and cytoplasm in cultured cells in chamber slides.

Segmentation of Tumour
and Stroma cells

Segmentation of nuclei and cytoplasm in tumour cells and cytoplasmic regions in stroma cells. If nuclear staining is not present or unspecific, nuclei can be detected by nuclear “holes” in cytoplasmic staining.

Kidney Tool

Segmentation of glomeruli and tubuli by using a Deep Learning model for brightfield data.

Kidney Tool

Segmentation of glomeruli and their compartments by using a tensorflow model for brightfield data.

Intracellular Compartments in EM

Ultra-structural analysis of intracellular compartments using electron microscopy provides new insights into cellular fine structures and sub-cellular organelle interactions.

Endoplasmic Reticulum

The endoplasmic reticulum (ER) is a dynamic structure consisting of branched domains and tubular sections. Automatic segmentation opens up new possibilities for quantitative analysis and efficient representation of this membrane structure at the ultra-structural level.

Cell Counting

Segmentation and counting of cells.  


Analysis of insulin receptors inside and outside of cytoplasm and the change over time.

Scratch Assay

Analysis of samples with scratches and the change of cell area over time.


Real time detection on microscopy devices

You look through the microscope and see in real time markings of the objects relevant to you. Subsequently, an automatic quantification of the detected objects takes place.

Blood vessel analysis

Blood vessels can be marked with immunohistochemistry. This allows blood vessel counting and analysis of blood vessel distribution.  


Segmentation of cells over time to measure proliferation. The analysis is done on Label Free Data.

Colorectal cancer

Segmentation of brightfield data with colorectal cancer using a deep learning model.

Lung analysis

Automated classification of tumors in non-small cell lung cancer (NSCLC) and quantification of tumor/stroma.

Annotation Software to set region of interests (ROI)

Manual drawing of regions of interest (ROI) as well as automatic ROI detection. Image analysis can be restricted to ROIs or different analysis methods can be allocated to different ROI types within one image.

Screening with oncology markers

Tissue evaluation with cancer specific markers, for example PD-L1, Ki67, p21, p53, Stathmin, bTubulin, etc.

TMA Screening & Analysis

Analysis Software for Tissue MicroArrays (TMA) with variable number of cores. Semi automatic naming of TMA cores. Export of TMA core results together with cores names into excel files.


Image Analysis Online Service

Solutions for your assay:
Repetitive tasks in your workflow can take precious time necessary for breakthrough ideas to happen. HS Analysis offers online services for image analysis services designed to improve the results of your most time-consuming and challenging manual assay analyses.

Image analysis made easy:
Your images will be analyzed manually by our high professional image analysis experts in Germany. Simplify your quantitative image analysis process by short description of your task, uploading your data to our server and receive your results each day per email. Reproducible, robust quantification at your hand without the need of buying new hardware or software.

Results that make a difference:
Extracting objective, reliable data to push your research forward is our commitment. No matter how complex your system or the problem you want to tackle is, we develop a solution to enhance your work. You take the images, we do the rest.

Analyse your images anywhere, anytime:
Follow these simple steps to start enjoying it. It’s as easy as it sounds:

  1. Fill in the Form.
  2. Describe the task
  3. Select the images you want to upload for analysis.
  4. After processing your images, an email will notify you with the results and with invoice.

    20 images - 250€50 images - 350€100 images - 400€250 images - 450€500 images - 500€1000 images - 550€5000 images - 750€10000 images - 1000€



    Research experts in pharmacology, bioscience and in university medical centers are permanently expected to increase efficiency and reduce timeinvest and cost.

    HS Analysis delivers software solutions for precise image analysis. In that way the researcher is going to be supported to get qualitative and reproducible data.

    The system reduces human errors, which are possible in manual evaluation. It finally allows to get Big Data results in a short time and at the end to analyse, manage and present them. That allows researchers to fulfill continuously increasing expectations concerning efficiency and output of results.



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    26th of September 2019
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    September 11, 2018
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