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Re: combine particles in ROI manager automatically

Posted by karo03 on Apr 20, 2009; 9:47am
URL: http://imagej.273.s1.nabble.com/combine-particles-in-ROI-manager-automatically-tp3692844p3692852.html

... with some programming you can avoid the enlargement and use the  
joined pattern to select the pieces for roi generation. Some "Create  
Selection" and roiManager("Update") could generate the roi of the  
(underlying) disconnected pieces.
Regards
Karsten

Am 20.04.2009 um 11:31 schrieb Karel Jansseune:

> 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 ROI’s found within a certain distance of each other.
>>> (let
>>> say, if the 2 ROI’s are less than 2mm apart, they should be  
>>> combined).
>>
>> Karsten
>> [hidden email]

Karsten
[hidden email]