Issue on plugin: Multi-Scale Oriented Flux Tubularity Measure - Fiji crashes

filaments
issue
simpleneuritetracer
fiji
Tags: #<Tag:0x00007fd546858e78> #<Tag:0x00007fd5468589a0> #<Tag:0x00007fd5468583d8> #<Tag:0x00007fd54686bf78>

#1

Hello everyone!

I am working with 3D images of filamentous structures, so I have been trying to use the OOFTubularityMeasure_Plugin without success. It is a filament enhancement method (like Frangi Vesselness) and it was proposed by LAW, M. W. K., CHUNG, A. C. S. - ECCV 2008 . The plugin itself was developed by CVLab with information here and GitHub repository available. I tried to contact the email delin at epfl.ch to report the issue a few months ago. Since I had no reply, I would like to throw the issue for discussion here. UPDATE: I have sent invitations to some suggested contacts at EPFL via the forum invite tool (Mr. Pascal Fua lead of the CVLab group at EPFL, Mr. Enging TĆ¼retken which participated in the project).

The OOF method is a pre-processing step required to run the ā€œTubular Geodesicsā€ option in Simple Neurite Tracer. This Tubular Geodesics approach proposed by CVLab seems to be very good, but without the enhanced images it is not possible to run their Tubular Geodesics implementation.

I am not sure if this is easy to solve or not. Unfortunately, I am still not an advanced programmer in C++ and Java to look thoroughly through the code to identify where the issue is. From the repository, it appears that the plugin for Fiji uses an ITK implementation of the OOF (optimally oriented flux).

I am using ImageJ Fiji 1.51n for Linux 64 bits and java 1.8.0_66. The image is 16bit but I also tried the same with 8bit images and the issue is the same.

The description of the issue follows:

  1. I open my .tif image of choice and go to Plugins>MultiScale Oriented-Flux Tubularity Measure
  2. Then I Set the number of scales and the min/max scales according to my filament size.
  3. The File saver pop-up appears with edited file name as filename.oof.nrrd

OOFIssuereport-snapshot1

  1. I finally change the file to filename.oof.tif since my file type is .tif and I wish to have a .tif as output from the plugin (which should supposedly work).

OOFIssuereport-snapshot2

  1. File saver pop-up closes and plugin starts processing the file - you can see from the status bar already something different: The file is being saved as ā€˜filename.oof.oof.nrrdā€™

  1. After a few seconds, ImageJ crashes and closes and there is no output file available.

So, I am not sure how to approach this issue. I will gladly help if someone can give hints on where the issue is.

Thanks!
Cheers,


Filter to enhance the vessel and restore connectivity
#2

To start tackling this issue, you could have a look at the troubleshooting section (If ImageJ crashes) on the wiki.