MaMut Export Plugin

Hello,
I exported my output from Tracking with Learning using the plugin csv, and it worked fine.
Next I wanted to export the MaMuT output file, but I receive an error no such file or directory, although it worked perfectly for CSV file

Appreicate the help
thanks

Hi Khaleel,

the MaMuT export is a bit more involved.

Have you checked the video we have for this: https://youtu.be/kjVqWSSdDmU (make sure to enable subtitles) and followed the instructions and still experience problems? Could you paste the full error (maybe from the logfile) here?

In short you need to first export your data to Bdv (big data viewer) XML/hdf5 format in Fiji:

  • import/load your image data (raw data)
  • Plugins -> BigDataViewer -> Export for BigDataViewer

You need to supply this xml file then in the plugin export in ilastik

Hello Dominik,
Thank you for the reply and sorry for getting back to you, i was a little under the weather.
anyways.
I have used the export feature before for MaMuT and did the steps by generating exported big data viewer and all.
In this case, the error was twofold: 1) Could not generate export file and 2) File was not found. (As a result of the first one)
Error is here:
ERROR 2020-03-31 23:09:52,949 log_exception 14672 9632 Failed to generate export file:
D:/Khaleel/Tracking_Fillipe/20191220/BrightnessAdjusted_Converted to H5 images/BrightnessAdjusted_H520200326/mtGFP slice3 roi2 zstack trial base n7-zm3DREG_Tracking with Learning_20200331/mtGFP slice3 roi2 zstack trial base n7-zm3DREG-data_Tracking-Result.h5/exported_data
[Errno 2] No such file or directory: ‘D:/Khaleel/Tracking_Fillipe/20191220/BrightnessAdjusted_Converted to H5 images/BrightnessAdjusted_H520200326/mtGFP slice3 roi2 zstack trial base n7-zm3DREG_Tracking with Learning_20200331/mtGFP slice3 roi2 zstack trial base n7-zm3DREG-data_Fiji-MaMuT_mamut.xml’
INFO 2020-04-02 22:04:44,266 ilastik_main 14636 11520 Starting ilastik from “C:\Program Files\ilastik-1.3.3post2”.