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Dear Tim,

On Thu, 22 Sep 2011, Tim Feinstein wrote:

> [talking about ImageJ]
>
> * difficult to do nonlinear brightness modification (gamma, curves).  
>   Most users do not know that this is not an accepted image manipulation 
>   in many contexts and can get you in trouble with journals.  
>   Gamma/curve adjustment is trivially easy in other apps like Photoshop.

Note that it is not _that_ difficult to do in ImageJ. But I do agree with 
journals not accepting images manipulated in that way. See e.g. 
http://www.uab.edu/researchintegrityandimages/guidelines/list.html. It is 
not exhaustive but gives beginners an idea what to watch out for.

In general, however, I would like to see journals accepting only articles 
together with the raw data and the method used to process them. After all, 
we want to be able to reproduce the results.

> * Advanced techniques like deconvolution and 3D presentation or analysis 
>   are best done with proprietary software.

I would like to know the evidence and logic behind that claim.

> * Many microscope makers package pretty good presentation/analysis 
>   software with their system, e.g. Zen for Zeiss, Elements for Nikon.  
>   This is often much more user-friendly.

At least sometimes correctness beats user-friendliness: Just the other day 
I found a bug in a Wavelet implementation (instead of factors 1,4,6,4,1 it 
used 1,4,6,1,1, clearly a typo). Personally, I like it when I can 
investigate such a bug not having to ask whether it is possible that 
there is a bug and waiting for an answer but being able to point at the 
bug directly, and when the website has a corrected version the next day.

If you think that correctness in image processing is easy, have a look at 
this page, and weep: http://www.4p8.com/eric.brasseur/gamma.html (Note 
that I am not saying that this applies to images recorded by a confocal 
microscope, but maybe you want to question the way standard software 
displays those images after reading through that webpage).

Ciao,
Johannes