Detecting dark rod shaped cells

[verified.human]

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[Joel Sheffield]

HI Tom,

Part of the problem is that as good as the image may be, there is still a
bit of a background gradient in it.  I removed that by running the
FFT>bandpass routine, with an upper limit of 100 and a lower limit of 0,
without rescaling.

I then did a classic threshold setting, and used the Process>analyze
particles routine to count the particles.  I set the routine to count only
those particles that were greater than 50 pixels (that removed the small
objects), I tried playing around with the circularity settings as well to
select only elongated objects.

Joel


On Tue, Feb 14, 2012 at 2:15 PM, Tom Runia <[hidden email]> wrote:

> Hi all,
>
> I am trying to detect dark rod-shaped cells, see the two images below:
>
> http://tweakers.net/ext/f/4aFgguwN90w3v9VWSlYmSUZY/full.png
> http://tweakers.net/ext/f/VKs68WJOaoqk4wzPdVIzBSmj/full.png
>
> I have tried a couple of things, but I can't get a robust solution for this
> problem.
> Does anyone have some clever idea's about this problem?
>
> The first thing to do is the remove the small particles (bacteria) from the
> background and then sharpen the boundaries of the cells, I suppose?
>
> Thanks in advance!
>
> Best,
>
> Tom
>

--


Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  http://astro.temple.edu/~jbs

[Francis Burton-3]

Hi all,

I'm looping through some analyses in a plugin which produce
results in the form of a plot and a line in a ResultsTable.
It would be helpful to let the user have feedback  about the
analysis as it is happening by showing the data accumulating
and plots being updated. However, what happens at the moment
is that the windows go blank until all the analyses complete
and the plugin returns to the message handling loop. Is there
any way I can force the windows to update on each iteration,
or put the plugin into a mode akin to BatchMode(false) in
macros?

Thanks,

Francis

[Alistair MacDougall]

I have had similar issues with controlling the updating of the Results Table in a plugin and would also like to know what the suggested solution is.

Left to myself I was thinking of trying to store my calculated results initially in an array, to buffer and manage delivery to the results table for display. Another approach could be to choose not to call show("Results") so the system provided results table is not displayed, and to have a second results table that is displayed, with for example show("Results in Progress"), and to periodically update this with partial data during calculation.


Alistair MacDougall

-------------------------------------------------------------------------------

>Hi all,

>I'm looping through some analyses in a plugin which produce
>results in the form of a plot and a line in a ResultsTable.
>It would be helpful to let the user have feedback  about the
>analysis as it is happening by showing the data accumulating
>and plots being updated. However, what happens at the moment
>is that the windows go blank until all the analyses complete
>and the plugin returns to the message handling loop. Is there
>any way I can force the windows to update on each iteration,
>or put the plugin into a mode akin to BatchMode(false) in
>macros?

>Thanks,

>Francis