brightness change correction

Posted by Thorsten Mielke on Aug 27, 2014; 3:20pm
URL: http://imagej.273.s1.nabble.com/brightness-change-correction-tp5009385.html

Dear all,

I am using Fiji/Trakem2 to stitch TEM images (mrc-format, 32 bit real,
map mode 2) automatically recorded from thin sections using Leginon.
Since the sequential data collection from several positions typically
takes several hours (up to > 10 hours ), we sometimes observe intensity
changes, most likely due an intensity change of the LaB6 cathode or a
change in beam diameter over time. This results in a gray level gradient
within the montages. We tried to use "Histogram matching" under "Image
-> Adjust ->  Bleach Correction" to normalize the intensity. However, it
seems that this works only for 16 bit mrc-stacks, which we obtain using
programs such as IMOD or Eman2.

Is there an easy way to convert 32 bit mrc to 16 bit mrc files within
Fiji? Is it possible to run the bleach correction (or any better tool?)
within individual TrakEM2 layers comprising up to ~1000 images?

Thanks for comments and help,

Thorsten

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