Posted by
Thomas Boudier on
URL: http://imagej.273.s1.nabble.com/Help-requested-for-finding-3D-local-maxima-tp3691210p3691213.html
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
/*******************************************************/