Questions about channelunmixing using Poisson NMF

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Questions about channelunmixing using Poisson NMF

Stoyan Pavlov
Dear community,
Recently I started experimenting with channel unmixing and more precisely
my interest was caught by the plugin "Poisson NMF" as it allows to do
blind  as well as unmixing  with known spectra , and even allows for mixed
approach (using known spectra as starting point for the deconvolution or
keeping known spectra constant and extracting unknown ). My first
impressions from the plugin are very good - there is minimum user
interaction and thus minimal bias, it's reasonably fast and produces images
of high quality.
I decided to try and extract autofluoresence from the images by adding it
as unknown source of fluorescence in addition to all the known spectra I
have. The idea was to create e.g. 4-channel image from a 3-channel set (the
fourth beeing the autofluorescent portions of the image): I add the known
spectra of the dyes as the first three sources and the autofluorescence as
the fourth source. Then I specify the channel wavelength boundaries of the
three initial channels. However the plugin returned an image with 4
channels but consisting of NaNs.
While experimenting to see what went wrong I figured out that this happens
all the time when the sources do not match the number of the initial
channels. It doesn't matter how I will specify the sources spectra
(manually, spectral library, ROI or Gaussian) nor if I keep some or all of
the known spectra constant.
Have any of you encountered this behavior? Is this a bug or am i doing
something wrong?

Best day,
Stoyan
---
Assoc.Prof. Stoyan P. Pavlov, MD, PhD
Departament of Anatomy, Histology and Embryology
Medical University "Prof. Dr. Paraskev Stoyanov", Varna
Prof. Marin Drinov Str.55
9002 Varna
 Bulgaria
Tel: +359 (0) 52 - 677 - 052
e-mail: [hidden email]
           [hidden email]

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Re: Questions about channelunmixing using Poisson NMF

Jan Kovac
Dear Stoyan
This is quite older post but I have a similar problem with the same plugin
"Poisson NMF". Did you recently solved the described problem? Or you have
some solution? In my opinion, the problem is hidden in java code and is not
easy for me to modify it. If I choose as a source stack some e.g. Leica
lambda stack it is working, but if I am using Olympus .oif files without
saved wavelenght in metadata, it is immposible to unmix spectra in real
wavelenght. Also NaN "values" appears. I am just asking if you find some
solution.

Jan



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Re: Questions about channelunmixing using Poisson NMF

Stoyan Pavlov
Hi Jan,
Unfortunately I didn't receive any answer in this otherwise very active and
helpful community.
I just couldn't continue wasting time with this at the moment,and let it
go. However the problem still stands and if you find a solution or someone
on the ImageJ list is kind enough to offer help on this issue I would much
appreciate it.
Stoyan


На вт, 29 ян. 2019 г., 18:55 Jan Kovac <[hidden email] написа:

> Dear Stoyan
> This is quite older post but I have a similar problem with the same plugin
> "Poisson NMF". Did you recently solved the described problem? Or you have
> some solution? In my opinion, the problem is hidden in java code and is not
> easy for me to modify it. If I choose as a source stack some e.g. Leica
> lambda stack it is working, but if I am using Olympus .oif files without
> saved wavelenght in metadata, it is immposible to unmix spectra in real
> wavelenght. Also NaN "values" appears. I am just asking if you find some
> solution.
>
> Jan
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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