http://imagej.273.s1.nabble.com/Help-requested-for-finding-3D-local-maxima-tp3691210p3691215.html
> Thomas,
>
> I tried jni3d_.class. It is much faster. I ran your script with a few mods
> as there were some name differences. Here it is
>
>
> xr=5; yr=5; zr=5;
> rename("stack");
> // this may have changed fro mthe version o nthe internet ;-)
> //run("3D Filters", "filter=Maximum radius_x=5 radius_y=5 radius_z=5");
> // Note space after jni3d
> run("jni3d ", "filter=Maximum radius_x=xr radius_y=yr radius_z=zr");
> imageCalculator("Difference create stack", "stack","3D Maximum");
> run("Invert", "stack");
> //run("Set 3D Measurements", " centroid mean_gray_value dots_size=16
> font_size=10
> store_results_within_a_table_named_after_the_image_(macro_friendly)
> redirect_to=stack");
> run("Set Measurements", " centroid mean_gray_value dots_size=16
> font_size=10
> store_results_within_a_table_named_after_the_image_(macro_friendly)
> redirect_to=stack");
> //run("3D Objects Counter...", "threshold=255 slice=13 min.=1 max.=1134972
> exclude_objects_on_edges statistics");
> run("3D object counter...", "threshold=255 slice=13 min.=1 max.=1134972
> exclude_objects_on_edges statistics");
> David Webster
>
> On Thu, Sep 10, 2009 at 7:14 AM, Thomas Boudier <
>
[hidden email]> wrote:
>
>> Hi,
>>
>> I know this plugin is not very fast, but you can use the maximum filter in
>> my fast JNI filter and compute the difference between the original and max
>> filtered image, a max local should then be at zero in this difference image.
>> Here a small macro that uses 3D object counter to detect the max local
>> pixels and display their coordinates :
>>
>> rename("stack");
>> // this may have changed fro mthe version o nthe internet ;-)
>> run("3D Filters", "filter=Maximum radius_x=5 radius_y=5 radius_z=5");
>> imageCalculator("Difference create stack", "stack","3D Maximum");
>> run("Invert", "stack");
>> run("Set 3D Measurements", " centroid mean_gray_value dots_size=16
>> font_size=10
>> store_results_within_a_table_named_after_the_image_(macro_friendly)
>> redirect_to=stack");
>> run("3D Objects Counter...", "threshold=255 slice=13 min.=1 max.=1134972
>> exclude_objects_on_edges statistics");
>>
>> The 3D filters in fiji are nice and fast, but it looks like they work on a
>> 3x3x3 cube, I personally prefer to work with spheres.
>>
>> best,
>>
>>
>> Thomas
>>
>>
>>
>> David Webster a écrit :
>>
>> All,
>>> These functions seem to be real slow. You might want to try Fiji's
>>> Plugins/Process/Maximum (3D), if a 3x3 local neighborhood for defining the
>>> local max is OK.
>>> Also, this seems to only filter an image, so does not return a list of
>>> points. You may need to write a macro or a plugin to do this if something
>>> doesn't exist already.
>>>
>>> David Webster
>>> On Mon, Sep 7, 2009 at 3:20 AM, Thomas Boudier <
>>>
[hidden email]> wrote:
>>>
>>> Hi,
>>>> You can have a look to these plugins :
>>>>
>>>>
>>>>
http://imagejdocu.tudor.lu/doku.php?id=plugin:morphology:3d_binary_morphological_filters:start>>>>
>>>> Best,
>>>>
>>>> Thomas
>>>>
>>>>
>>>> Brad Busse a écrit :
>>>>
>>>> Hey all,
>>>>> I'd like to give imagej (or a plugin therein) a volume and an ideal
>>>>> radius
>>>>> and have it spit out where the 3D local maxima are. The task is similar
>>>>> to
>>>>> what "Process->Filters->Maximum..." already does in 2D, except I'm only
>>>>> interested in the maxima locations (so single points or a point list
>>>>> would
>>>>> be ideal). I figure there must be a plugin that does exactly this, but
>>>>> I'm
>>>>> at a loss for finding it. Anyone have any ideas?
>>>>>
>>>>> Thanks!
>>>>> Brad
>>>>>
>>>>>
>>>>>
>>>>> --
>>>> /**********************************************************/
>>>> Thomas Boudier, MCU Université Pierre et Marie Curie,
>>>> IFR 83. Bat B 7ème étage, porte 709, Jussieu.
>>>> Tel : 01 44 27 20 11 Fax : 01 44 27 22 91
>>>> /*******************************************************/
>>>>
>>>>
>>>
>> --
>> /**********************************************************/
>> Thomas Boudier, MCU Université Pierre et Marie Curie,
>> IFR 83. Bat B 7ème étage, porte 709, Jussieu.
>> Tel : 01 44 27 20 11 Fax : 01 44 27 22 91
>> /*******************************************************/
>>
>
>
IFR 83. Bat B 7ème étage, porte 709, Jussieu.