MaMuT Converter

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

Usage:

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.

Save the raw images as HDF/XML file

open Fiji

import your raw image data

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

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)

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>

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

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

ilastik/MaMutConverter

MaMuT Converter