====== Acinar Tree Extraction for Stepanizer ======
====== MeVisLab ======
Use one of the networks in P:\doc\MeVisLab-Networks\2010\AcinarTreeExtraction\ to shunt of acini in the lung with the "manhole covers", extract them with a RegionGrowing Modula and export the addition of all acini with a DicomTool Module as single DICOM slices.

Additionally, export a binned dataset with the tomographic slices as a DICOM stack using an ImageSave Module.
===== Overlay =====
Import both the original data and the stack of exported acini into [[http://pacific.mpi-cbg.de/|Fiji]] or ImageJ.

{{  :imageprocessing:mevislab:acinus_import.png?150|}}The exported stack with the colored acini can be opened with using "File" > "Import Image Sequence", the Stack of the original data can just be opened normally with "File" > "Open"

{{ :imageprocessing:mevislab:acinus_rgb.png?150|}}Once you have both stacks, you need to convert the Tomography stack to RGB using "Image" > "Type" as shown on the right.

{{ :imageprocessing:mevislab:acinus_imagecalculator.png?150|}}When both stacks are RGB, you can add them together using "Process" > "Image Calculator", as shown on the right.

{{:imageprocessing:mevislab:acinus_addimages.png|}}

When you've added both stacks to each other, you should get a new image looking like the one below. 

{{ :imageprocessing:mevislab:acinus_overlay.png?333 |}}

Now you only need to export this combined stack as .JPG slices for further processing.

{{:imageprocessing:mevislab:acinus_saveas.png|}}

After you've saved the stack somewhere, you should have a bunch of .jpg images in a directory of your choice.

===== Processing for STEPanizer =====
To use the [[http://www.stepanizer.com|STEPanizer]] with the stack of .jpgs exported above, we first need to rename the images sequentually to Image_Number_a.jpg and Image_Number_b.jpg.

To do this, it's probably easiest to use the [[http://www.ghisler.com/|TotalCommander]].

{{ :imageprocessing:mevislab:acinus_totalcommander_mark.png?150|}}Mark all even images (*0.jpg, *2.jpg, *4.jpg, *6.jpg, *8.jpg) as shown on the right, and use the Multirename Tool (CTRL+M) to rename them sequentally to Name_[C]_**a**, as shown below.

{{ :imageprocessing:mevislab:acinus_totalcommander_rename.png?333 |}}

Mark all odd images (*1.jpg, *3.jpg, *5jpg, *7.jpg, *9.jpg) as you've marked the even ones, and use the Multirename Tool (CTRL+M) to rename them sequentally to Name_[C]_**b**, as shown below.

{{ :imageprocessing:mevislab:acinus_totalcommander_renaming.png?333 |}}

Now you're good to go to use the STEPanizer!

===== STEPanizer =====