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Additional tools
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Merge two datasets
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:menuselection:`File --> Merge two files`: Used to merge two experiments. 

.. container:: caution

	Both experiments have to include identical channel and metadata information!

Multichannel demo-/kymographs
=============================

:menuselection:`Tools --> Create multichannel demo-/kymograph`: Create multicolor demo- or kymographs by combining up to three individual channels in one image. 
	1. Create a demo-/kymograph and save it as a Matlab :code:`fig`-file.
	2. Create a demo-/kymograph from the same cells for a different channel and save it as a Matlab :code:`fig`-file.
	3. (Repeat for a 3rd channel if appropriate)
	4. Call `Tools --> Create multichannel demo-/kymograph` and select the  :code:`fig`-files and colors for the individual channels.

.. container:: hint

	The combined demo- or kymograph might look nicer, if the colormap of the individual demo- or kymographs is adjusted. This needs to be done for each demo- or kymograph separately.
	
Export annotated images
=======================

:menuselection:`Tools --> Save screenshot`: Save current segmentation view as :code:`png`, :code:`jpeg` or :code:`eps` file (sequence).
Creates a new figure and copies all cells (+overlays) from the segmentation view to it. Afterwards the figure content can be modified.

Export annotated movie
======================

:menuselection:`Tools --> Save movie`: Create movie of your current segmentation view as image file sequence (:code:`png`, :code:`jpeg` or :code:`eps`) or movie file (:code:`avi` and :code:`mp4`). Time metadata can be added as label of customizable fontsize and the framerate and movie quality can be set.

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Custom Matlab scripts
=====================

The cell/stalk segmentation data can be accessed in the following way for customized processing.

Run

.. code:: matlab
	
	BacStalk_data = getUIData(gcf);
	
to retrieve the underlying data and 

.. code:: matlab
	
	setUIData(gcf, BacStalk_data);
	
to apply any changes and make them visible in the GUI.

The segmentation data is stored in the structure

.. code:: matlab
	
	BacStalk_data.frames
	
A detailled description of the raw data Matlab structures is shown in the following figure. The PDF-version can be downloaded `here <../images/raw_data_explanation_sheet.pdf>`_.

.. image:: ../images/raw_data_explanation.png
   :alt:   Raw data Matlab structures of BacStalk
   :width: 585
   :align: center