Separating Objects

[Luc_Paul]

Hi,

Relatively new to FIJI/ImageJ, but I need to separate the objects in these images and the resulting size is irrelevant to me.  The problem is that erosion or using a euclidean map leaves the particles connected, but watershed will divide some of the longer particles in half, i will attach two images of each of these issues along with an original.  Maybe this goes without saying, but a generic, repeatable approach would be best because I need to apply the same process to hundreds of images.  Any ideas are greatly appreciated.

[Luc_Paul]

One thing I forgot to mention, I have a greyscale versions of the original image that are not 'filled' so if your ideas need grayscale images I might be able to make it work.

With Much Appreciation,

Luc

[Michael Schmid]

Hi Luc,

it would make sense if you post a sample grayscale image.
Maybe some filtering (Gaussian Blur, Thresholded blur[]) plus 'Find
Maxima' would do the job?

You may also have a look at the Adjustable Watershed [2]

Michael

[1]
http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:thresholded_blur:start
[2]
http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:adjustable_watershed:start
________________________________________________________________

On 12/07/2017 20:15, Luc_Paul wrote:
> One thing I forgot to mention, I have a greyscale versions of the original
> image that are not 'filled' so if your ideas need grayscale images I might
> be able to make it work.
>
> With Much Appreciation,
>
> Luc

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

[Luc_Paul]

Michael,

Adjustable watershed was the answer to my problems, thank you very much!

-Luc

On Thu, Jul 13, 2017 at 1:49 AM, Michael Schmid-3 [via ImageJ] <[hidden email]> wrote:

Hi Luc,

it would make sense if you post a sample grayscale image.
Maybe some filtering (Gaussian Blur, Thresholded blur[]) plus 'Find
Maxima' would do the job?

You may also have a look at the Adjustable Watershed [2]

Michael

[1]
http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:thresholded_blur:start
[2]
http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:adjustable_watershed:start
________________________________________________________________

On 12/07/2017 20:15, Luc_Paul wrote:
> One thing I forgot to mention, I have a greyscale versions of the original
> image that are not 'filled' so if your ideas need grayscale images I might
> be able to make it work.
>
> With Much Appreciation,
>
> Luc

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

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