solution: analysis of protein spots

Application Research on Neurodegeneration Research Lab at the University of Rostock

Prof. Dr. Dr. Pahnke Head of Neurodegeneration Research Lab (NRL) Rostock, focuses on the determination of factors responsible for the development of sporadic Alzheimer's disease (AD), which accounts for > 99% of all Alzheimer’s diseases. For this kind of research, various transgenic and knockout mouse models are used.

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Application

In order to analyse and interpret his biological studies, Prof. Dr. Dr. Pahnke uses digital slides that are generated by the MIRAX SCAN (Carl Zeiss MicroImaging GmbH) and realized as high-resolution images, which explains the extreme size of the specimen images.

digital slide of a mouse brain
(image clipping)

digital slide of a mouse brain
(Fullscreen)

When it comes to super high resolution images (e.g. more than 10 Gbyte for a single image), the market-dominating software for digital microscope specimens might be able to visualize images, but not to analyze the data in detail. The images are taken with a resolution of 230nm per pixel. Conventional software requires a reduction of the resolution to manageable 1.2 µm.By this reduction not only the fine structures become invisible, but it is also made impossible to perform a high quality measurement or analysis. Thus, research-relevant information might get lost.

Problems

• high resolution and large size of single images (about 10Gbyte/slide) hinders processing and analysing of digitized specimens

• conventional software does not allow interactive or automatic measurement and analysis of super high resolution digital slides

• considerable loss of information required for the detection, analysis, quantification and classification of small structures by reducing the resolution

Tasks for arivis

The arivis team was challenged to develop a solution for an automated object recognition and detection, quantification, classification and analysis of differently colored proteins relevant in Alzheimer's disease (ß-Amyloid) and its resulting debris (plaques), even on super resolution images. For further data processing, the results need to be easily exportable.

Solution

In order to fit the needs of Prof. Dr. Dr. Jens Pahnke, we developed a workflow for the analysis of protein spots as a new plugin for the arivis browser.

arivis Browser - Plugin: Workflow for protein spot analysis-

• automatic and interactive detection of protein spots within a short time and in full resolution
  (< 2s for an image with 576 Megapixels)
• definition of parameters as a basis for automatic analysis and calculation
• manual definition of "region of interests"
• manual classification of the "region of interest" spots
• export of the results to Excel for further analysis and interpretation

Advantages and benefits

Improvement in the analysis of biological experiments

For the first time, super high resolution images can be used for the detection, measurement, classification and structural analysis of Alzheimer's plaques in brains of mice without any restrictions. It is possible to obtain all information about the digitized specimens, which can effectively be viewed and analyzed.

Time and cost savings

The automated workflow for the detection and analysis of protein spots enables the scientist to quickly and intuitively gain results that can be easily processed further on.
For the detection and labeling of spots in a histological section with 25,000 pixels x 25,000 pixels, the workflow for protein spot analysis takes less then 10s.

Application-specific customization

As a highly flexible and modular software, the arivis browser offers many ways to support complex applications in a simple manner.
The central aim of our development is to offer any scientist a powerful and reliable software based on a mature technology, which can be supplemented with individual plugins, workflows or scripts.
Additionally, we provide every user with a comprehensive, elaborated, proved and constantly improved application programmer's interface (API). This API is even used by the arivis team to develop most of the arivis Browser features.
In this way, new import or export formats can be quickly implemented, existing devices can be interfaced, special algorithms for analysis can be evaluated and different possibilities for visualization can be explored.

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Fundamental Research on Alzheimer's dementia

Some pathogenetic mechanisms that occur in Alzheimer's dementia, are known to scientists. The real causes of this most common of all neurodegenerative diseases and the ways of treatment, however, are still the subject of intense research.

In Alzheimer's dementia are deposited gradually proteins in the brain, allowing the nerve cells die off and the intellectual achievements of those affected continue to deteriorate.

The Research of Prof. Dr. Dr. Jens Pahnke, Neurodegeneration Research Lab (NRL) Rostock and a member of the German Center for Neurodegenerative Diseases (DZNE), is focused on the determination of factors for the development sporadic Alzheimer's disease (AD). He and his team of scientists conducting research for possibilities to solve the deposited proteins and to remove them from the brain. He found out that this possibilities might be performed by certain transport proteins.

The laboratory of Prof. Dr. Dr. Pahnke examined, modeled and checked the mechanisms of Alzheimer's disease with various methodological approaches in its basics. Therefor transgenic mouse strains be used which are established in an own Mouse House.
Alzheimer's disease-related proteins such as the ß-Amyloid and its resulting debris will studied in these animal models.
Prof. Dr. Dr. Pahnke uses for the analysis of his biological studies, digital, high-resolution images of specimens that have a tremendous image size. The visualization of the entire specimen as complete image and simultaneous analysis could not previously be met by any imaging software without restriction.

Further details on the research activities of the Neurodegeneration Research Lab of Prof. Dr. Dr. Jens Pahnke, please visit: www.nrl.uni-rostock.de

The images used on this page were kindly provided by Prof. Dr. Dr. Jens Pahnke, Head of Neurodegeneration Research Lab (NRL) Rostock.

Application

Solution