particle aggregate length measurement problem

[Steve83]

Hi all,

 

I have a particle aggregate analysis problem and I hope to find some help
here among all those ImageJ experts (for visualization of what I need to
realize pls look at the attached .png picture):

I am investigating particle aggregates - or to be more precise: I am
investigating how particle aggregates dispense when being exposed to a flow.
Therefore I have an optical monitoring and I take screenshots at different
times (e.g. t1 and t2). Then I take the raw pictures, and do the following
ImageJ operations:

run("8-bit");

run("Auto Threshold", "method=Minimum");

                run("Convert to Mask");

As a result I get images like the ones I marked in the attached example with
(1). Now, after setting a global scale, I need to measure the maximum
distance between the most peripheral black pixels. I do that by drawing a
horizontal line between the relevant pixels (in the example I indicated this
with a green line) (2). Finally I can measure the line length to get the
exact distance of particle dispersion (3).

Due to the fact that I have a lot of pictures I need to analyze, I need an
automatic batch process solution providing the following:

.         Recognizing the relevant peripheral pixels

.         Drawing a horizontal line between the pixels

.         Measuring the line length

.         Giving readout as a txt file that I can use for further
analysis/plotting etc.

 

Is it possible to realize that?  I hope someone is willing to help me and
generally I want to say thank you for taking your time reading my problem.

Best,

Steve

 



 


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[Avital Steinberg]

Hi Itzi,
You may find this link helpful:

http://fiji.sc/Batch_Processing

Good luck,
Avital

On Tue, Sep 8, 2015 at 11:33 PM, Itzi Bitzi <[hidden email]> wrote:

> Hi all,
>
>
>
> I have a particle aggregate analysis problem and I hope to find some help
> here among all those ImageJ experts (for visualization of what I need to
> realize pls look at the attached .png picture):
>
> I am investigating particle aggregates - or to be more precise: I am
> investigating how particle aggregates dispense when being exposed to a
> flow.
> Therefore I have an optical monitoring and I take screenshots at different
> times (e.g. t1 and t2). Then I take the raw pictures, and do the following
> ImageJ operations:
>
> run("8-bit");
>
> run("Auto Threshold", "method=Minimum");
>
>                 run("Convert to Mask");
>
> As a result I get images like the ones I marked in the attached example
> with
> (1). Now, after setting a global scale, I need to measure the maximum
> distance between the most peripheral black pixels. I do that by drawing a
> horizontal line between the relevant pixels (in the example I indicated
> this
> with a green line) (2). Finally I can measure the line length to get the
> exact distance of particle dispersion (3).
>
> Due to the fact that I have a lot of pictures I need to analyze, I need an
> automatic batch process solution providing the following:
>
> .         Recognizing the relevant peripheral pixels
>
> .         Drawing a horizontal line between the pixels
>
> .         Measuring the line length
>
> .         Giving readout as a txt file that I can use for further
> analysis/plotting etc.
>
>
>
> Is it possible to realize that?  I hope someone is willing to help me and
> generally I want to say thank you for taking your time reading my problem.
>
> Best,
>
> Steve
>
>
>
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Herbie]

Steve,

just a hint concerning the length measurement:

Have you considered to project the images in vertical direction. Then,
you get 1D-signals (arrays of numbers) that are easier to evaluate...

HTH

Herbie

::::::::::::::::::::::::::::::::::::::::
Am 08.09.15 um 22:33 schrieb Itzi Bitzi:

> Hi all,
>
>
>
> I have a particle aggregate analysis problem and I hope to find some help
> here among all those ImageJ experts (for visualization of what I need to
> realize pls look at the attached .png picture):
>
> I am investigating particle aggregates - or to be more precise: I am
> investigating how particle aggregates dispense when being exposed to a flow.
> Therefore I have an optical monitoring and I take screenshots at different
> times (e.g. t1 and t2). Then I take the raw pictures, and do the following
> ImageJ operations:
>
> run("8-bit");
>
> run("Auto Threshold", "method=Minimum");
>
>                  run("Convert to Mask");
>
> As a result I get images like the ones I marked in the attached example with
> (1). Now, after setting a global scale, I need to measure the maximum
> distance between the most peripheral black pixels. I do that by drawing a
> horizontal line between the relevant pixels (in the example I indicated this
> with a green line) (2). Finally I can measure the line length to get the
> exact distance of particle dispersion (3).
>
> Due to the fact that I have a lot of pictures I need to analyze, I need an
> automatic batch process solution providing the following:
>
> .         Recognizing the relevant peripheral pixels
>
> .         Drawing a horizontal line between the pixels
>
> .         Measuring the line length
>
> .         Giving readout as a txt file that I can use for further
> analysis/plotting etc.
>
>
>
> Is it possible to realize that?  I hope someone is willing to help me and
> generally I want to say thank you for taking your time reading my problem.
>
> Best,
>
> Steve

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

[jerie]

Itzi,

select'all' then plot a profile; get the first value above the threshold
counting from the end of the profile vector. I have recently done a number
of macros in that direction. If you provide the two unprocessed images I
can see if something works directly.

Kind regards, Jens

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[jerie]

Hi Steve,

IJmacro_itzi_ver0.ijm

seeing the actual image, I thought a different strategy fit better and used the color thresholder HSB. There set the hue to match the brown color of the precipitate, then the particle analyzers bounding rectangle width returns the length of the pecipitate. See linked file.

If you would like to use the batch processor as recommended by Avital, I suggest to remove the 'clear' from the run("Analyze Particles...", command, so that all the results should appear. Just make sure the results table is empty before you run the batch.

Good success with the next steps
Let me know if further help is needed,

cheers, Jens