Recent changes to 17: Erronious activity on "Membrane Detection" classifier tool

#17 Erronious activity on "Membrane Detection" classifier tool

Ben Padman — Mon, 21 Jan 2019 23:16:14 -0000

Thank you for all your help!
Everything is now working as expected.

I will have a look at Ilastik as well.
All the best

#17 Erronious activity on "Membrane Detection" classifier tool

Ben Padman — Sun, 20 Jan 2019 01:18:58 -0000

I have identified a work around for the issue:
I was able to segment beyond image number 8 after isolating the data into a new folder, with its own RF_Temp directory. All images processed without an error. See attached screenshots.

I think its related to the unusual activity shown in Bug3b.png above, where membranes from an unrelated dataset were being segmented in the current dataset.

The issue is much less urgent now, but do you need any more information from me to determine why the membrane detection classifier was segmenting an unrelated image?

#17 Erronious activity on "Membrane Detection" classifier tool

Ben Padman — Sun, 20 Jan 2019 01:01:11 -0000

Thanks Ilya, I keep trying to post the files but Sourceforge keeps failing.
Sorry about the delay. I'll see if there is another way for me to send.

I want to send you:
The first 10 images from the stack
The classifier file generated after training
The successful FM output for slice 7 and the failed output for 8

I generated the training model in the middle of my stack, so I'll need to find a way to reduce the filesize to one slice.

Erronious activity on "Membrane Detection" classifier tool

Ben Padman — Sat, 19 Jan 2019 08:47:35 -0000

The Membrane Detection tool works as intended, but stalls on the 8th section if the "predict dataset" function is used on a stack. Sections 1 to 7 are processed successfully (they generate a selection that can be assigned to a material). Section 8 is never completed. (as discovered below, it also seems to segment unrelated files occasionally)

I tested this with 3 different datasets (ranging 10-250 slices with different pre-processing on each stack), and 3 different classifiers. It doesnt seem to matter if the classifier is new or loaded. Images attached to illustrate the issue.

The most recent attached example used a 250 section stack with preloaded classifier. Processor usage dropped to background levels on the 8th section at the expected time (~45s after previous section), but a selection was not generated and the process did not proceed.

I also attempted to "predict shown slice" on the 8th section after the process stalled, and nothing happened.

This is surprising....
shutting down and reloading MIB apparently didn't enable me to use "predict shown slice" on the 8th section, even without attempting the entire stack.
I also tried segmenting the file with the first 50 sections removed... it still stalled at the 8th section, but now it seems to be displaying membranes from an entirely unrelated image! see "bug3b.png"

Is the classifier file uniquely tethered to the dataset?
I dont understand how it could possibly be segmenting information from an unrelated file right now.
Strange.

I'm using MIB version is V2.40 31.08.2018 deployed version
Running it on a computer that is 5-10x more valuable than my car, all drivers are up to date.
Windows 10 home edition 64bit (10.0, build 17134)

Please let me know if you need more information. I love the work you're doing, and appreciate the youtube videos. I've only been using MIB for a week, and I already want to add it to my routine workflow.