A converter for visualising ilastik projects in the MaMuT plugin(Fiji/ImageJ).

Usage:

0. Export the tracking results from ilastik as H5 event Sequence from the Tracking applet. This provides you with a folder full of numbered *.h5 files.

1. Save the raw images as HDF/XML file

   1. open Fiji

   2. import your raw image data

       	- use the hdf5 plugin, when your data is in HDF5 format (Help -- Update Fiji -- HDF5) 
      

   3. open BigDataViewer Plugin -> Export current Image as XML/HDF5

       	- the freshly exported XML and HDF5 should be in the same folder
       	- the name and path of the XML are input-parameters for the script in 2 (input-xml, xml-dir)
      

2. Execute the hdf_to_xml.py script

   python hdf_to_xml.py --parameters

   parameters

   		--input-dir: path to the event sequence folder (as created in step 0)
   		--input-raw: filepath to the HDF5 raw file (Yes, you need the raw data as HDF5 file AND the HDF5 file that was exported before, and the two are different)
   		--raw-filepath: filepath in the HDF5 raw file
   		--output-dir: full folderpath where the file should be saved
   		--input-xml: filename of the input xml from 1 (without the path!)
   		--xml-dir: folderpath that contains the input-xml (needs to be seperated, no filename)
   		[--is-3D: 1 if the input is in 3D (default 0)]
   		[--axes-order-raw: the axes order of the raw input (default txyzc)]
   		[--axes-order-label: axes order of the label input (default xyzc, without t)]
   

   Example:

   python hdf_to_xml.py --input-dir <PATH> --input-raw <PATH> --raw-filepath <PATH> --input-xml <XML-NAME> --xml-dir <PATH> 

   A file called 'output.xml' will be saved to the <--output-dir Path>

3. Open the output.xml with the MaMuT-plugin (MaMuT -- load MaMuT File)

   1. When opening 2D Images in the MaMuT-Viewer:

   	Dont forget to scroll in z until its on 0 (Hotkey-information by clicking 'help')
   	Go to Settings and change the Brightness & Color