Hallucinations about n2v HOT 3 CLOSED

Hi Volker,

happy to hear that trying N2V is by now an easy task. We indeed invested quite some time to make it so simple.

The image.sc forum is an ideal place to discuss such matters, but maybe you decide after reading the rest of this response.

I say that, because I think N2V just showed you something you did not look careful enough for. The hallucination you point out is, in fact, data. I have tried to show these intensities the good old way, using only Fiji (max-projection (only planes 29 to 35), a tiny bit of gauss (sigma=1.0), and the fire LUT).

The big halo around the dead pixel on the top right is bugging me a bit more, but since throughout the entire stack this pixel is super bright and just inside the darkest background area I would also not call this an hallucination.

What I often do is to download the final 3D prediction, open it in Fiji, and make a two channel image together with the original, noisy input data. In this way it is very fast to browse through the stack and switch quickly back and forth between reconstruction and raw data. Usually that convinces me about the sanity of our reconstructions even in places that seem surprising at first.

I hope this answer is helpful for you,
Best,
Florian

PS: in case you want to continue this discussion, please re-open this issue any time!

from n2v.

Hi Florian,

thanks for taking the time to reply.
Indeed, it appears that I was fooled by my own assumptions here (assuming that there should be no structures outside the wing) in combination with the fact that I was running the notebook on a remote server and therefore only looked at the projections.

I now see some of the structure in the raw data (although I still wonder why it is there, maybe residual material in the medium or reflections somewhere in the lightpath ?).
The dead pixel is indeed more difficult. However, there is at least one such dead pixel (looks like a needle in 3D) in the wing that ends in a bright structure. So maybe the network learnded something from that occurence.

Thanks for taking the time to answer and prompting me to have another look. It has restored enough confidence to now apply this to some of my own data.

from n2v.

Cool! Let me know about your experiences! Enjoy! :)

from n2v.