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 theTracking
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