different versions of Image J behaving differently

[Gaurav Joshi]

Hello,

Are there any differences in the way images are processed in the  
different versions of Image J?
I have set of images particularly of fluorescent mitochondria within a  
cell. Intensity of fluorescence in each image is different depending  
on the physiological state of the mitochondria.

When I am using Image J 1.40g, I get the ability of selecting an image  
whose maximum is 4095 and at the same time threshold it to the same  
value. Now I can go back to another image in the same set and select a  
minimum value of my choice based on the fluorescent intensity and  
continue with my intensity measurements.

When I try to do the same thing in Image J 1.42q i.e. once I have  
selected the maximum of 4095 for an image, threshold it to that value  
and go back to another image in the same set and select a minimum  
value it also changes the maximum value to the highest pixel value in  
that particular image and not keeping it to 4095. Now a great deal of  
problem is it does not reset the max value for every subsequent image  
by itself but it needs to be done manually. Doing this for about 125  
images in number of image sets is painstaking.

I recently upgraded from 1.40g to 1.42q so I am not aware of similar  
changes happening or not happening in the other released versions.

Sincerely,
Gaurav.

Gaurav Joshi
Graduate student,
Dept of Molecular and Cell Biology
University of Connecticut,
91-N Eagleville Rd, U 3125
Storrs, CT-06269
[hidden email]

[Gabriel Landini]

On Saturday 13 June 2009, Gaurav Joshi wrote:

> When I am using Image J 1.40g, I get the ability of selecting an image
> whose maximum is 4095 and at the same time threshold it to the same
> value. Now I can go back to another image in the same set and select a
> minimum value of my choice based on the fluorescent intensity and
> continue with my intensity measurements.
>
> When I try to do the same thing in Image J 1.42q i.e. once I have
> selected the maximum of 4095 for an image, threshold it to that value
> and go back to another image in the same set and select a minimum
> value it also changes the maximum value to the highest pixel value in
> that particular image and not keeping it to 4095. Now a great deal of
> problem is it does not reset the max value for every subsequent image
> by itself but it needs to be done manually. Doing this for about 125
> images in number of image sets is painstaking.
>
> I recently upgraded from 1.40g to 1.42q so I am not aware of similar
> changes happening or not happening in the other released versions.

I do not know the technical bit of the answer to your question, but perhaps it
is better no to assume that threshold limits are the same for all images.

Threshold values should be properties of each image. From what you say, I
guess that IJ now does it that way (sets an automatic threshold if the
threshold has not been set).

Perhaps you can write a simple macro that sets these limits automatically
instead of by hand, which is

Cheers,
G.

[Gabriel Landini]

On Saturday 13 June 2009, I wrote:

> Perhaps you can write a simple macro that sets these limits automatically
> instead of by hand, which is

more secure.

Cheers
G.