Posted by
Michael Schmid on
Apr 20, 2009; 9:48am
URL: http://imagej.273.s1.nabble.com/combine-particles-in-ROI-manager-automatically-tp3692844p3692849.html
Hi Karel:
two remarks:
(1) the Process>Binary>Dilate, Erode, Open, Close commands use square
kernels. If distance is really important, use Process>Math>Minimum or
Maximum instead, these have circular kernels.
If you have large distance, thresholding the EDM
(Process>Binary>Distance Map) of the inverted image will be faster
than the Math>Minimum or Maximum filters. With the current
implementation of the EDM in ImageJ it is not 100% accurate; we might
see an EDM with better accuracy soon.
(2) you can enlarge/shrink the ROIs: Edit>Selection>Enlarge
This uses a circular kernel for irregular rois as those from the
particle analyzer.
Michael
________________________________________________________________
On 20 Apr 2009, at 11:31, Karel Jansseune wrote:
> The binary step is no problem, the image is turned to binary anyhow.
>
> the process itself is fine, it neatly closes the gap, but it also
> expands
> the selected region. Also it requires some user input as the gaps
> aren't
> always the same distance, for our research, it is important to get the
> user input to a minimum (to minimize error)
>
> anyway, this might solve some of the issues that I'm encountering ,
>
> thank you for the help
>
>
> On Mon, 20 Apr 2009 11:04:40 +0200, Karsten Rodenacker
> <
[hidden email]> wrote:
>
>> One possibility is the application of a Process->Binary->Close-
>> operation with appropriate size. This would join objects with
>> distance
>> less than the given size. Unluckily this operation works on binary
>> images not on ROI's.
>> Regards
>> Karsten
>>
>> Am 20.04.2009 um 09:42 schrieb Karel Jansseune:
>>
>>> For our research we are making images of Arabidopsis plants
>>> growing in
>>> plates andwe try to measure the area of each plant automatically. In
>>> this
>>> way we try to obtain the growth rate of each plant in the plate
>>> We successfully made a macro to do the analysis of a folder of
>>> images and
>>> return the results in a text file, but now we sometimes have the
>>> problem
>>> that one plant is divided into two during automatic analysis.
>>>
>>> Now I was wondering if it is possible to write a macro to instruct
>>> ImageJ
>>> to combine the ROIs found within a certain distance of each other.
>>> (let
>>> say, if the 2 ROIs are less than 2mm apart, they should be
>>> combined).
>>
>> Karsten
>>
[hidden email]