Plane correction

Many microscopes record images due to their setup in a tilted manner. Before starting the analysis process the correction of the tilt is crucial. Otherwise large errors will occur in course of the analysis process. The area calculation for instance would accidentally assign data pixels to objects where simply the surrounding structures exhibit apparently similar heights as the objects. Therefore, dotCube supports the scientists with extensive options to correct tilted images precisely and fast.

Read on for getting to know in detail about:

• How to detect the plane
• Where to apply the correction
• How to determine the detection level
• Two complementary correction algorithms
• Shortcut keys

How to detect your plane

DotCube is able to process the plane detection in three different ways:

• The first option "Find plane in entire image" will start an automatic plane search.
• For strongly distorted and noisy images, the second option may functions more reliably. Therefore, mark manually one or more flat regions and choose the "All selected points lie in one area" option. Correction functions are calculated and applied to your image according to the marked data points. A minimum of 16 data points has to be marked.
• If the whole image features mainly one flat base level, the option "Apply global plane" will be the best choice.

Where to apply the plane correction

The plane correction may be applied to a previous marked area or to the whole image. Just select the respective option.

Determine the detection level

DotCube detects flat regions in scan data by calculating locally the second derivative. Data points which deceed the value specified by "Maximum slope factor" are allocated to a flat region - a plane. Increase or decrease this value to assign more or less data points to the plane.

For monitoring the detected plane, select the "Show identified plane" option.

Select the correction algorithm

After detecting a planar region, a three dimensional correction function is applied to the image data in order to remove the tilt. Select the polynomial order (linear, parabolic or cubic) of the tilt distortion to gain the best results.

The correction function can be calculated by two algorithms:

• Matrix inversion: This algorithm is the fastest, but works only for functions of linear or parabolic order. The results of linear correction functions calculated by matrix inversion are comparable with the statistical approach of the second algorithm. But the parabolic correction results may be more accurate calculated by the statistical approximation algorithm.
• Statistical approximation: This algorithm consumes more computing time, but gains more precise results for higher polynomial orders. Select the proportion between speed and quality which suits your data best with the slider.

Shortcut keys

The execution of the function may be started by pressing two different shortcut keys:

• Return: The function will be applied to all selected images.
• Shift+Return: The function will be applied to the next selected image only.

For more shortcut keys see our detailed list.