Image Processing

ZEN lite2012 Manual 4-1

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Mainly there are two fields for image processing: correction and optimization of the acquired image data.

Often digital image processing functions have to be used to overcome technical limitations of the available systems. Probably in most cases the image processing functions have to compensate the negligence during the image acquisition.

You should therefore pay attention to use all your available options of your equipment technology before and during the image acquisition in an optimum way. This is the only time where you really have access to the original information. At no other time you will have the chance to influence more the image quality.

The specimen preparation is another often unattended topic. Especially here it is true that you cannot expect a good image from a bad specimen. So you should also check self-critically, if your preparation quality is suitable for optimum acquisition results.

For what reason ever you plan to apply image processing functions, you should mind not to overwrite your original data, if possible. You always should keep the option to return to the original image. This will enable you to determine if the completion of a function really resulted in an improvement, or if relevant information is no longer available in the image.

Image Processing

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In ZEN lite you will find two ways for image processing. They have different properties and are made for different application fields. On the one hand all functions may be applied via the Processing tab. On the other hand you may optimize the quality of the image display (brightness, contrast, gamma) on your monitor via the response curve on the Display tab.

In both cases ZEN lite ensures, that your original data initially will not be modified:

Using the functions on the Processing tab the results will as default be shown in a separate image document. You may decide later to save the result in a new file, or to overwrite the existing file.

When working with the Display tab the brightness and color information of the images will generally not be modified. Instead only the display of the saved values will be adjusted on the monitor. As long as you save your images in the ZEN format “CZI” you will save together with the original data the adaptations from the Display tab in the file.

After opening the file you initially will see the optimized presentation. At any time you now may return to the original presentation via the Display tab. If you export the image to a different format you may define in the settings of the Export function, if you want to export the original data, or if you want to keep the modifications of the Display tab prior to the storage. But in the latter case the grey and color values will be modified. In this case there is no way to recover the original data.

Tip: We recommend always to save the images in the CZI-format first, and

to export images into an external format only if required.

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Image Processing

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In the following section we will use image format not as the file format (CZI, ZVI, BMP; TIF etc.), but instead for the way to display brightness and color in an image.

Common TV-cameras may distinguish 256 grey levels. This number of grey levels will cover the complete spectrum from black to white. In order to separate 256 grey levels in a PC you will need 8 Bit. This is why these images are called 8-Bit-images.

You will need 3 of these grey level images to display color images: one each for red, green, and blue. Basically these images are grey level images. A color image internally exists of 3x8 bit images. They are therefore called 24-Bit-images. With this up to 16.8 million colors may be separated.

Recent digital cameras meanwhile are able to distinguish not only 256 grey levels, but up to 65536. In this case 8 bit are no longer sufficient to save the data, we now have to use 16 bit. But also 16-Bit-images are just grey level images. If we combine three of these images to one color image we call them 48-Bit-images.

Tip: Some file formats are not capable to save 16- or 48-Bit-images. We

therefore recommend that you first always save your images in the CZI-format and only export them into an external format if required.

Image Processing

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Annotations are additional graphic elements (scale bars, text, arrows, etc.), that you may add to an image. Actually "into" the image is not correct, as within ZEN annotations will be drawn into an additional layer on top of the image. By this the original image information will not be destroyed.

As long as you save your images in the ZEN format “CZI” the layer’s information will be conserved. So annotations will be saved separated from the real image information. After the opening of a file the annotations may be changed, deleted, hided, or new ones may be added.

Other than ZEN-CZI formats do not support this layer technique. So if you have to export the image into an external format you have to define with the Export function if you want to burn-in the annotations into the image or not. You will have the following choices:

If you burn-in the information to the image, the pixels underlaying the annotations will be overwritten and therefore cannot be recovered.

If you disclaim the burn-in process the annotations will be lost.

You save the image once in the original form and again with burn-in annotations.

Tip: As you will have relevant limitations with the storage in external formats

we will recommend to firstly always save the images in the CZI format and export the images additionally only if required.

Image Processing

ZEN lite2012 Manual 4-5

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Here we will explain the principal mode of operation for the image processing functions. All described steps are identical for all functions. Further descriptions for the effects of each single function and its parameters you will find in the online help under Menu – Image Processing.

You may train yourself with each single step in the following examples with example images you will find on the product DVD.

On the Processing tab you will find under Method different groups of image processing functions. For each selected function you will find the associated adjustment parameters in the section Method Parameters under Parameters.

In the segment Image Parameters you define the input image under Input.

Image Processing

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You may get a Preview on the result of the function under Output. You may check the settings prior to the execution.

For the Preview you may select between 4 different ways for the display:

Custom Size shows one segment inside the image showing the processing result.

Half Size shows one half of the image processed and the other half unprocessed (see figure on the right).

Full Size shows the processing result over the entire image.

Split Mode shows on the left the unprocessed image and on the right the processed one.

Image Processing

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Under Adjust you will find various methods to adjust the image due to brightness and contrast, as well as adapt the color, or correct for misalignments and shading.

The adjustment parameters for each function can be performed in the Method Parameters field.

The function will be finally performed by a click to the Apply button.

Result of the Shading Correction function as an example for the Adjust functions. Automatic uses the smoothened original image as shading reference.

Image Processing

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Under Geometric you will find various methods to align, rotate, or mirror the image.

The adjustment parameters for each function can be performed in the Method Parameters field.

The function will be finally performed by a click to the Apply button.

Result of the Rotation function by 30° as an example for the Geometric functions.

Image Processing

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Under Sharpen you will find various methods to enhance contours in the image.

The adjustment parameters for each function can be performed in the Method Parameters field.

The function will be finally performed by a click to the Apply button.

Result of the Unsharp Mask function as an example for the Sharpen functions.

Image Processing

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Under Smooth you will find various methods to decrease noise in the image. But this will also more or less remove sharp edges.

The adjustment parameters for each function can be performed in the Method Parameters field.

The function will be finally performed by a click to the Apply button.

Result of the Median function with Kernel size 15 as an example for the Smooth functions.

Image Processing

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Under Utilities you will find various methods to post-process your images. Here you may copy your images or annotations, you create image subsets, or you re-calculate your image using the Image Calculator.

As an example we show how to calculate the square root of an image. The result is expanded over the dynamic range of the image.

The adjustment parameters for each function can be performed in the Method Parameters field.

You enter the Formula in the formula field. Under Operators you will find a number of trigonometric functions.

For the square root select SQRT() from the list and enter the image for the calculation via Input 1 into the brackets. You may use up to 2 images for the calculation. You have to define these images under image parameters Input.

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The function will be finally performed by a click to the Apply button.

Result of the Image Calculator function using the square root formula as an example for the Utilities functions.

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Image Processing

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Via Export/Import you will find various methods to transfer your images into different formats. You may export images, image sequences, or movies with other formats, or you may import images from external formats into the cvi-format.

As an example you will find here the Movie-Export as the direct selection from the Processing tab. This example you will also find explained in chapter 3.5 under Movie-Recorder.

If needed, you only have to adapt your specific settings under Parameters.

Finally click the Apply button to execute the function.