Generate an image using imagej-ops

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Generate an image using imagej-ops

Jan Eglinger
Dear all,

I'd like to use ImageJ-Ops to create an image with "virtual beads" of a
given diameter with a given intensity.
I thought of using a 3D Gaussian to get the spatial intensities for each
bead (at a random subpixel position), and then summing up single bead
images to get a volume with randomly distributed spots.
Finally, I might want to convolve these ideal 3D Gaussian spots with a
given point-spread function (PSF).

I guess I'll need
   ij.op().image().equation()
   ij.op().math().add()
and finally
   ij.op().filter().convolve()

but I am unsure how to proceed.

Could anybody give me some hints how to start?

Thanks,
Jan

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Re: Generate an image using imagej-ops

Brian Northan
Hi Jan

I am not sure of the best to draw points that are at a sub-resolution position. 

Below is an example that shows how to use imglib2 (in a script) to draw points and then convolve them.   (note it works with imagej-ops-0.16.0 and above)

https://github.com/imagej/imagej-tutorials/blob/scripting/jython/CreateAndConvolvePoints.py

If you know the equation you want to use for a point at sub-resolution maybe you can implement it using the same imglib2 interfaces...



 

On Wed, Aug 19, 2015 at 7:32 AM, Jan Eglinger <[hidden email]> wrote:
Dear all,

I'd like to use ImageJ-Ops to create an image with "virtual beads" of a given diameter with a given intensity.
I thought of using a 3D Gaussian to get the spatial intensities for each bead (at a random subpixel position), and then summing up single bead images to get a volume with randomly distributed spots.
Finally, I might want to convolve these ideal 3D Gaussian spots with a given point-spread function (PSF).

I guess I'll need
  ij.op().image().equation()
  ij.op().math().add()
and finally
  ij.op().filter().convolve()

but I am unsure how to proceed.

Could anybody give me some hints how to start?

Thanks,
Jan

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Re: Generate an image using imagej-ops

Jan Eglinger
Hi Brian,

thanks a lot for the example script, that's a great starting point!

Cheers,
Jan



On 19.08.2015 15:52, Brian Northan wrote:

> Hi Jan
>
> I am not sure of the best to draw points that are at a sub-resolution
> position.
>
> Below is an example that shows how to use imglib2 (in a script) to draw
> points and then convolve them.   (note it works with imagej-ops-0.16.0
> and above)
>
> https://github.com/imagej/imagej-tutorials/blob/scripting/jython/CreateAndConvolvePoints.py
>
> If you know the equation you want to use for a point at sub-resolution
> maybe you can implement it using the same imglib2 interfaces...
>
>
>
>
>
> On Wed, Aug 19, 2015 at 7:32 AM, Jan Eglinger <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Dear all,
>
>     I'd like to use ImageJ-Ops to create an image with "virtual beads"
>     of a given diameter with a given intensity.
>     I thought of using a 3D Gaussian to get the spatial intensities for
>     each bead (at a random subpixel position), and then summing up
>     single bead images to get a volume with randomly distributed spots.
>     Finally, I might want to convolve these ideal 3D Gaussian spots with
>     a given point-spread function (PSF).
>
>     I guess I'll need
>        ij.op().image().equation()
>        ij.op().math().add()
>     and finally
>        ij.op().filter().convolve()
>
>     but I am unsure how to proceed.
>
>     Could anybody give me some hints how to start?
>
>     Thanks,
>     Jan
>

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Re: Generate an image using imagej-ops

Curtis Rueden
Hi all,

The link Brian sent was to a topic branch, which is now merged to master.

Here is a stable permalink for it:


Be aware that the tutorials repository will undergo heavy shuffling around and additions in the next couple of weeks, as we prepare the Scripting with Ops workshop.

Regards,
Curtis

On Wed, Aug 19, 2015 at 9:23 AM, Jan Eglinger <[hidden email]> wrote:
Hi Brian,

thanks a lot for the example script, that's a great starting point!

Cheers,
Jan



On 19.08.2015 15:52, Brian Northan wrote:
Hi Jan

I am not sure of the best to draw points that are at a sub-resolution
position.

Below is an example that shows how to use imglib2 (in a script) to draw
points and then convolve them.   (note it works with imagej-ops-0.16.0
and above)

https://github.com/imagej/imagej-tutorials/blob/scripting/jython/CreateAndConvolvePoints.py

If you know the equation you want to use for a point at sub-resolution
maybe you can implement it using the same imglib2 interfaces...





On Wed, Aug 19, 2015 at 7:32 AM, Jan Eglinger <[hidden email]
<mailto:[hidden email]>> wrote:

    Dear all,

    I'd like to use ImageJ-Ops to create an image with "virtual beads"
    of a given diameter with a given intensity.
    I thought of using a 3D Gaussian to get the spatial intensities for
    each bead (at a random subpixel position), and then summing up
    single bead images to get a volume with randomly distributed spots.
    Finally, I might want to convolve these ideal 3D Gaussian spots with
    a given point-spread function (PSF).

    I guess I'll need
       ij.op().image().equation()
       ij.op().math().add()
    and finally
       ij.op().filter().convolve()

    but I am unsure how to proceed.

    Could anybody give me some hints how to start?

    Thanks,
    Jan


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