Re: [Software Feedback] source code for "intensity macro for background subtraction"

[ctrueden]

Hi Bryne,

> I'm trying to use fiji to do background subtraction from an ROI for my
> image analysis. This particular macro doesn't do exactly what I want,
> but I'd like to see if I can modify it to do what I want.
> Unfortunately, I was having trouble finding the exact source code
> for this project and was hoping I could get some assistance from you
> in locating it.

* Press L to bring up the Command Finder.
* Type "subtract b" into the box. It should filter down to a single command
called "Subtract Background..."
* Click that item on the list.
* Click the "Source" button at the bottom of the dialog.

And voila! You will find yourself looking at the source code at:
http://imagej.nih.gov/ij/source/ij/plugin/filter/BackgroundSubtracter.java

Regards,
Curtis


On Fri, Dec 20, 2013 at 6:08 PM, <[hidden email]> wrote:

> Hi-
> I'm trying to use fiji to do background subtraction from an ROI for my
> image analysis. This particular macro doesn't do exactly what I want, but
> I'd like to see if I can modify it to do what I want. Unfortunately, I was
> having trouble finding the exact source code for this project and was
> hoping I could get some assistance from you in locating it. Thanks!
> -Bryne
>
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Bryne,

> I tried the method you outlined above to get the source code and got
> this error message "Unable to display source for this plugin".

Yeah, unfortunately, that method only works for core ImageJ routines.

> this:
> http://loci.wisc.edu/software/intensity-macro-background-subtraction
> sounds more like what I want to do
...
> I also tried looking on github using this link:
> https://github.com/uw-loci/misc-plugins and still wasn't able to find
> exactly what I'm looking for.

That is the right place. Source is at:
https://github.com/uw-loci/misc-plugins/blob/master/src/main/resources/IntensityMacro_Squirrell_Ogle.ijm

> basically what I'm trying to do is just do a background subtraction
> using an ROI with a 3-color hyperstack so if you know of an efficient
> way to do that, that would be useful.

From your description, I am not sure what you are trying to do. I am CCing
the ImageJ list in case others have more insight. Please note that after
today I am on vacation, and may not respond to private mails until after
the new year.

Regards,
Curtis


On Fri, Dec 20, 2013 at 7:21 PM, Bryne Ulmschneider <[hidden email]>wrote:

> Thanks, but that wasn't actually exactly what I was looking for. The
> rolling ball radius algorithm is the wrong thing to use for the type of
> image analysis that I'm using.
> this: http://loci.wisc.edu/software/intensity-macro-background-subtraction
> sounds more like what I want to do, but it doesn't work with
> non-brightfield images apparently. I tried the method you outlined above to
> get the source code and got this error message "Unable to display source
> for this plugin".
>
> I also tried looking on github using this link:
> https://github.com/uw-loci/misc-plugins and still wasn't able to find
> exactly what I'm looking for.
>
> Alternatively- basically what I'm trying to do is just do a background
> subtraction using an ROI with a 3-color hyperstack so if you know of an
> efficient way to do that, that would be useful.
> Thanks!
> -Bryne
>
> ------------------------------------------------------------
> Bryne Ulmschneider, PhD Candidate
> University of California, San Francisco
> Department of Anatomy, Nystul Laboratory
>
>
>
> On Fri, Dec 20, 2013 at 4:29 PM, Curtis Rueden <[hidden email]> wrote:
>
>> Hi Bryne,
>>
>> > I'm trying to use fiji to do background subtraction from an ROI for my
>> > image analysis. This particular macro doesn't do exactly what I want,
>> > but I'd like to see if I can modify it to do what I want.
>> > Unfortunately, I was having trouble finding the exact source code
>> > for this project and was hoping I could get some assistance from you
>> > in locating it.
>>
>> * Press L to bring up the Command Finder.
>> * Type "subtract b" into the box. It should filter down to a single
>> command called "Subtract Background..."
>> * Click that item on the list.
>> * Click the "Source" button at the bottom of the dialog.
>>
>> And voila! You will find yourself looking at the source code at:
>> http://imagej.nih.gov/ij/source/ij/plugin/filter/BackgroundSubtracter.java
>>
>> Regards,
>> Curtis
>>
>>
>> On Fri, Dec 20, 2013 at 6:08 PM, <[hidden email]> wrote:
>>
>>> Hi-
>>> I'm trying to use fiji to do background subtraction from an ROI for my
>>> image analysis. This particular macro doesn't do exactly what I want, but
>>> I'd like to see if I can modify it to do what I want. Unfortunately, I was
>>> having trouble finding the exact source code for this project and was
>>> hoping I could get some assistance from you in locating it. Thanks!
>>> -Bryne
>>>
>>>
>>
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Michael Schmid]

Hi Bryne,

If you have a roi with the background and the background varies rather
slowly, you can try to fit a polynomial:

http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:fit_polynomial:start

Michael

______________________________________________________________________

 On Fri, Dec 20, 2013 at 7:21 PM, Bryne Ulmschneider
 <[hidden email]>wrote:

> Thanks, but that wasn't actually exactly what I was looking for. The
> rolling ball radius algorithm is the wrong thing to use for the type of
> image analysis that I'm using.
> this:
> http://loci.wisc.edu/software/intensity-macro-background-subtraction
> sounds more like what I want to do, but it doesn't work with
> non-brightfield images apparently. I tried the method you outlined above
> to
> get the source code and got this error message "Unable to display source
> for this plugin".
>
> I also tried looking on github using this link:
> https://github.com/uw-loci/misc-plugins and still wasn't able to find
> exactly what I'm looking for.
>
> Alternatively- basically what I'm trying to do is just do a background
> subtraction using an ROI with a 3-color hyperstack so if you know of an
> efficient way to do that, that would be useful.
> Thanks!
> -Bryne
>
> ------------------------------------------------------------
> Bryne Ulmschneider, PhD Candidate
> University of California, San Francisco
> Department of Anatomy, Nystul Laboratory
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html