Hi Ann,

as a workaround, you can use a one-line macro to prevent you from manually typing the numbers:

  setMinAndMax(0, 16384);

See also the macro functions documentation:
http://rsbweb.nih.gov/ij/developer/macro/functions.html#setMinAndMax

Hope that helps,
Jan

Dear Jan

Thanks for the quick response

End users don’t like macro languages in Cell biology imaging facilities. This isn’t a problem I personally have, it is a problem 200 of my end users have that I am raising on their behalf. 

Really we would like the 14 bit option implemented in the dropdown menu for 16 bit unsigned tiffs. Since I’m aware of several facilities worldwide which use Coolsnap HQ2 and other cameras that acquire in 14 bit I’m not sure why this isn’t implemented in the GUI. Particularly as 15 bit, which is a workaround for fixed pattern noise of Flash4 sCMOS cameras, is.

Regards

Ann
Dr Ann Wheeler
Head of Advanced Imaging Resource 
MRC Institute of Genetics and Molecular Medicine
University of Edinburgh
Western General Hospital
Crewe Road
Edinburgh EH4 2XU
E: ann.wheeler@igmm.ed.ac.uk
T: 0131 4678425
W: www.igmm.ac.uk

Hi Ann,

 If you're comfortable with macros, you may want to incorporate Jan's workaround into a plugin that you could then distribute[1] to your users. This could also be helpful if there are additional pre-processing steps that should always be taken when opening this data, and would allow you to shield your users from writing macro code on their own.

 Also, are you opening your data with File > Open? If you run "Edit > Options > ImageJ2" and check or un-check those boxes is there any difference in how your datasets open?

 Finally, if you use the Bio-Formats importer (File > Open > Bio-Formats) with the "Autoscale" box unchecked, does your data still need to be scaled?

Thanks,
Mark


[1] http://imagej.net/Distribution

Here is a way to permanently set the range to 14-bits:

  1. Open the Edit>Options>Startup dialog.
  2. Select "12-bit (0-4095) range" from the drop down menu.
  3. Change "12" to "14" in the code that was added to the text box.
  4. Click "OK"

Hi

Thanks everyone so such a prompt response. I think we have a new research group converted to quantitative image analysis at the IGMM!

Its great to have easy to use workarounds for newbies. The adjustment of startup code and bioformats import can be used on any computer too, whereas the macro I would more likely put on the 6 image analysis computers.

BTW if you know of anyone looking for an image informaticist job we're hiring.

>>> Dr Ann Wheeler
>>> Head of Advanced Imaging Resource
>>> MRC Institute of Genetics and Molecular Medicine University of 
>>> Edinburgh Western General Hospital Crewe Road Edinburgh EH4 2XU
>>> E: ann.wheeler@igmm.ed.ac.uk
>>> T: 0131 4678425
>>> W: www.igmm.ac.uk

It turns out that my proposed method for setting the display range to 14-bits by adding "call("ij.ImagePlus.setDefault16bitRange",14)" to the Edit>Options>Startup dialog did not work. For it to work, you will need to upgrade to the latest ImageJ daily build, which you can do by using the Help>Update ImageJ command and selecting "daily build" from the drop down menu. The daily build also fixes a bug the caused "14-bit (0-16383)" to be missing from the "16-bit range" drop down menus in Edit>Options>Appearance and in the "Set" dialog of the "B&C" window.

Hi Wayne

Many thanks for fixing the bug in the daily build so quickly, it works really well and the IGMM users I'm sure will be very pleased.

Ann