Difference between revisions of "Bleach Correction"

(Remove links to defunct MBF ImageJ website)
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| maintainer            = Kota Miura
| maintainer            = Kota Miura
| author                = Kota Miura, Jens Rietdorf
| author                = Kota Miura, Jens Rietdorf
| source                = [http://fiji.sc/cgi-bin/gitweb.cgi?p=fiji.git;a=blob;f=src-plugins/CorrectBleach_/ in GitWeb]
| source                = {{GitLink|jar=CorrectBleach}}
| released              = 18/04/2012
| released              = 18/04/2012
| latest version        = 18/04/2012
| latest version        = 18/04/2012

Revision as of 10:05, 2 August 2014

Bleach Correction (ImageJ)
Author Kota Miura, Jens Rietdorf
Maintainer Kota Miura
Source Template:GitLink
Initial release 18/04/2012
Latest version 18/04/2012
Development status stable
Category Category:Plugins
Website http://cmci.embl.de/downloads/bleach_corrector

Bleach Correction

The plugin was made available by Kota Miura and Jens Rietdorf and the full documentation is available at EMBL's site.

This plugin contains three different methods for correcting the intensity decay due to photobleaching. They all work with either 2D or 3D time series. In case of 3D time series, image properties should be appropriately set. If you are not sure, check your image header by [Image → Properties].

  • Simple Ratio Method:
  • Exponential Fitting Method:
    • Similar to the description on the T-functions page. Additionally, this plugin also works with 3D time series.
    • MBF ImageJ suggests to use “Exponential” equation for fitting, whereas this plugin uses “Exponential with Offset”
  • Histogram Matching Method:
    • A brand-new method for bleach correction.
    • This algorithm first samples the histogram of initial frame, and for the successive frames, histograms are matched to the first frame. This avoids the increase in noise in the latter part of the sequence which is a problem in the above two methods.
    • This method does much better restoration of bleaching sequence for segmentation but not appropriate for intensity quantification.
    • See the blog entry, a bit more detail on this issue