Questions about channelunmixing using Poisson NMF

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

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]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html