Assessment Software

Assessment Software

Automatic detection and analysis:

1. Number of necrosis chlorosis, lesions, or other effects.
2. Single area of the effects
3. Total Area of leaves or needles
4. Color classification
5. Reanalyzing with new parameters
6. manual correction (delete, split, unify and add of objects) All done corrections are logged automatically.
7. Automatic deleting artifacts

Database:
Administration of the data by Database interface

Data export:
All data can be exported to known spreadsheets

The LemnaTec Scanalyzer is a complete system to classify needles and leaves using digital image processing.

LemnaTec Scanalyzer for assessment of damage

General Features

Researching phythopathogenes demands optical assessment of requires looking for leave areas and colour changes. These changes in colour - lesions, chlorosis or necrosis - derive either from direct pathogenic influence or become visible after treating the leave with staining reagents.
Up to now the assessment of damage was performed by hand and eye, so not very precise and with much effort. Only after hard training the human eye is able to perform reproducible and objective assessments, whereas automatic measurement with LemnaTec’s Scanalyzer makes exact, highly differentiated and reproducible assessment easily possible. Even the colour and the area of the objects is measured quantitatively.
For example, the LemnaTec Scanalyzer is used to analyze chlorotic and necrotic areas in a very large quantity of pine-needles, in each single needle separately with up to ten needles measured at one time. The Scanalyzer takes and evaluates the amount of affected area in leaves that underwent some gradual changes in colour, like they derive from fungi. The colours of the samples can be arranged into classes (dark-green, light-green, yellow, brown, etc.). These classes may represent different kinds of quality (healthy, chlorotic, necrotic, etc.), so that new quantitative aspects of the assessment of damage are reached with this method.
Besides taking images of several samples in one session and thus saving valuable time, morphological recognition in Imageprocessing supports the user with the assessment of damage. Rims of leaves can be omitted before measuring. Locally distributed lesions like from tobacco mosaic virus can be counted, the area measured and given in relation to their colour and sizes.
The LemnaTec Scanalyzer allows to take images with direct light and back light under stable, reproducible conditions. The image range may vary between 20 x 30 cm and 2 x 3 cm (please ask for special applications on smaller ranges). Applying a microscope is possible. The
Scanalyzer may very well be used in fieldwork, too.

Because of the digital documentation in a database all the images and results may be brought up, viewed and reanalyze with new parameters i.e. a different colour classification, at any time.
The results can be exported into known spreadsheet programs.

Features of the analytic software

To find an object

At first an image of the whole sample is taken. Then the program analyses the digital picture and recognizes all the leaves or needles as a whole. Area is measured and numbers are counted. This can be performed with a whole variety of shapes and samples, from tobacco-leaves to pine-needles every object can be found and analysed!
Besides, single mistakes of the analysis or special cases can be corrected manually using an easy drawing-tool. This tool allows to exclude, include, merge and separate objects. After the analysis a set of detailed data is collected, describing number, area, colour and shape of the duckweed.
Recognizing and measuring the affected spots and areas

The software for the analysis was developed cooperating with biologists. So the software is able to connect the colours and structures found in the image with the corresponding biological effects. Objects of no interest like folds of the leave or damages at the edges may be eliminated by image analysis. Of course, this assessment scheme can be altered by the user himself, so yet unknown effects may be found supporting scientific research.

Classification of colours

Visual assessment of damage is paralleled by the automatic analysis. The colours found in the object are put into colour classes the user has arranged by himself in an assessment scheme. The colours in question can be taken directly from the original image and the whole assessment scheme of colour-classes can be stored and saved for later use in other tests. When arranging the classes, the original image and and the false colour image are visible simultaneously. In this way visual assessment of damage is paralleled by automatic analysis. The assessment scheme may be changed or further optimised at any time
and reanalysis of all data guarantees homogeneous data sets.

Tobacco (Nicotiana spec.) shows characteristic lesions after infection with the TM virus.

The Scanalyzer is able to detect such changes and to quantify the effects. For a better depiction the analysed areas are marked. The shown leave has 268 lesions with a proportion of 8,2% of the total leave-area.
Sampling many objects

The Scanalyzer is able to find and separate many objects in the same picture. Then each object is analysed individually. This makes the testing of larger numbers of samples much faster and the objects may remain in their containers.

Infection of Pseudooeronospora cubensis on a cucumber leave. The surface was slightly damaged by rubbing with sandpaper. For a better assessment of the effects a picture in false colours shows the infected areas.

Managing a test-series

In general the LemnaTec Scanalyzer is used in a routine of larger scale series of tests. All steps of the whole test are supported by the LemnaTec Scanalyzer. A special software assistant suggests coded
names to all samples in a test. The images of the samples then can be taken without following a prescribed sequence. A barcode scanner can be applied to make identification of the samples even easier.
Preview diagrams are shown. The tabled results of each observation parameter are then ready to be printed and exported for further documentation and analysis.

The most convenient method for data calculation and report is BioStat This validated tool automatically performs all calculations and statistics (inhibition, EC-values, NOEC) necessary for a report, compliant to various standards and guidelines. BioStat is also available as stand-alone version without the Scanalyzer. Please ask for
further information.

Documentation

All images and data are stored and saved. So they can easily be traced, reconstructed and reanalysed at a later time. Highest control of quality according to GLP is guaranteed.

Perspectives

Quantifying shape, colour and area of biologic objects is a key issue in many widely used biological tests. Please ask for the actual state of development.