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> As they say in Hungary (or so I was told), every good action gets its  
> punishment. I think that people with a PhD, or about to get one,  
> should know the difference between enhancing an image for display or  
> publication, and misrepresentation (or fraud). If they are in doubt,  
> they should also be smart enough to ask for advice. 

I agree here, as long as whomever they ask knows...

By trying to  
> protect everybody against themselves, I am somewhat worried that out  
> of all this, NIH or other agency will come up with a 1,500-page  
> manual full with regulations and guidelines that will only make our  
> lives just a little bit more complicated, probably with little impact  
> on the amount of misconduct or cluelessness...

Which is why MSA is trying (or at least I am, anyway) to come up with
guidelines that are easy to implement and make sense, to stave off further
complicated regulations. Input invited.

> I am currently analyzing cells labeled by FISH, and counting those  
> that have nuclear and/or cytoplasmic staining. Nuclear spots are  
> maybe 20-40 times brighter than the diffuse cytoplasmic signal. My  
> eyes, camera, and computer monitor, all have different dynamic ranges  
> and response curves. To see on the monitor what I see at the  
> microscope, or to be able to print it, I need a pretty severe gamma  
> adjustment to enhance the low intensities, otherwise I just will miss  
> a lot of cells. This procedure however will change pixel intensities  
> non-linearly, will not preserve intensity ratios between different  
> regions of the image, and is pretty irreversible once applied. But  
> that's OK... I know what I am doing and why I am doing it (and  
> keeping the original data). On the other hand, without this gamma  
> adjustment, the pictures I get on the screen (or paper) will just not  
> match what I see at the microscope. We certainly don't want  
> regulators telling us that non-linear contrast adjustment is no  
> longer allowed.

Same here, which is why I still think that our guidelines of being able to
adjust contrast, brightness, and levels/gamma makes sense.

Recap: The Microscopy Society of America's whitepaper says you can adjust
brightness and contrast, and levels/gamma over the entire image. Anything
else should be reported as manipulation or enhancement. And you need to
store the "original" as uncompressed TIFF on archival media. We haven't
lately looked at other formats, like RAW, so the latter may change. Again,
if anyone wants to make an argument for another format, just dive in.

Aloha, Tina

> 
> --
> Julio Vazquez, PhD
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.,  mailstop DE-512
> Seattle, WA 98109-1024
> 
> 
> http://www.fhcrc.org/
> 
> 

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* Tina (Weatherby) Carvalho               * [log in to unmask]           * 
* Biological Electron Microscope Facility * (808) 956-6251                 *
* University of Hawaii at Manoa           * http://www.pbrc.hawaii.edu/bemf* 
****************************************************************************