Preprocessing

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This section describes the preprocessing step of the TLM-Tracker workflow. Within this step, images are prepared for the segmentation process.

Contents

General

Preprocessing mode

The preprocessing mode is the first step of the image analysis workflow. At this point, it is assumed that images have been successfully loaded and assigned to the fluorescence and bright field channels. The operations in this mode cannot be undone within the program, but the original image data on the disk remains unchanged. Thus, if something went wrong, it is possible to reload the image data.

Tools Panel (1)

Cutting

This tool allows to cut all images at once to a certain dimension. This reduction is useful because all following image processing operations will run much faster on smaller images. Click on the button with the scissors symbol Scissors.png and draw a rectangle on screen 1 or 2 that contains all visible cells over all image frames and press the Cut Section button. To include all cells into the analysis, it is preferable to perform this step in the last frame of a time series, as cells will usually grow over time.

Adjust Brightness

Press the Adj. Brightness button to adjust the brightness of all bright field images to one average level. This operation is useful to equalize all images, so that the following segmentation process requires less adaptation of single images.

Remove images

Press the Remove Image(s) button to remove image frames in the given (from - to) range. This is useful if some images are not appropriate for further investigation (e.g. blurred).

Edit parameters

To perform the following image analysis steps, the parameter settings must be adjusted as described here.

Continue

Click the 'Next' button in the Workflow panel or select the segmentation entry in the Workflow menu to enter the Segmentation step.

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