Saving LIF to TIF with altered brightness/contrast

[Rich Stanton]

I have an 8 bit image, opened from a LIF file (via the LOCI plugin).  I have
altered the brightness/contrast via image/adjust/bc, and hit apply.  If I
now save as tif, the resulting TIF doesn't have my brightness/contrast
alterations.  How do I save the TIF with my brightness/contrast alteration?

 

Thanks!

 

[Michael Schmid]

Hi Rich,

B&C 'Apply' is for 8-bit images only. See
  http://rsb.info.nih.gov/ij/docs/menus/image.html#adjust

For 16-bit images, you could write a short macro that uses getMinAndMax,
and the Process>Math>... functions to subtract min and multiply by
65535/(max-min).

Michael
__________________________________________________________________________

On Sat, March 20, 2010 12:44, Rich Stanton wrote:

> I have an 8 bit image, opened from a LIF file (via the LOCI plugin).  I
> have
> altered the brightness/contrast via image/adjust/bc, and hit apply.  If I
> now save as tif, the resulting TIF doesn't have my brightness/contrast
> alterations.  How do I save the TIF with my brightness/contrast
> alteration?
>
>
>
> Thanks!
>
>
>

[ctrueden]

Hi Rich,

This appears to be a strange bug in Bio-Formats. I was able to reproduce the
problem with one of our 8-bit LIF datasets. The problem is that the "Apply"
button does not actually do anything (no pixel values are altered). We will
investigate and keep you posted on our progress.

-Curtis

On Sat, Mar 20, 2010 at 12:44 PM, Rich Stanton <[hidden email]> wrote:

> I have an 8 bit image, opened from a LIF file (via the LOCI plugin).  I
> have
> altered the brightness/contrast via image/adjust/bc, and hit apply.  If I
> now save as tif, the resulting TIF doesn't have my brightness/contrast
> alterations.  How do I save the TIF with my brightness/contrast alteration?
>
>
>
> Thanks!
>
>
>

[ctrueden]

Hi Rich,

Turns out this problem seems to be an issue with hyperstacks and/or
composite images. Bio-Formats uses these extensively to provide 5D
visualization with more flexible colors. For now, you can switch to a
"normal" stack with "Image > Hyperstacks > Hyperstack to Stack" and then
apply your brightness/contrast.

-Curtis

On Mon, Mar 22, 2010 at 12:50 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Rich,
>
> This appears to be a strange bug in Bio-Formats. I was able to reproduce
> the problem with one of our 8-bit LIF datasets. The problem is that the
> "Apply" button does not actually do anything (no pixel values are altered).
> We will investigate and keep you posted on our progress.
>
> -Curtis
>
>
> On Sat, Mar 20, 2010 at 12:44 PM, Rich Stanton <[hidden email]> wrote:
>
>> I have an 8 bit image, opened from a LIF file (via the LOCI plugin).  I
>> have
>> altered the brightness/contrast via image/adjust/bc, and hit apply.  If I
>> now save as tif, the resulting TIF doesn't have my brightness/contrast
>> alterations.  How do I save the TIF with my brightness/contrast
>> alteration?
>>
>>
>>
>> Thanks!
>>
>>
>>
>

[andas]

Hi,
Have you not solved this problem yet? It is almost 5 years since the original post.