3D using Stack Focusser?

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3D using Stack Focusser?

Joel Sheffield
Colleagues,

Here's an interesting challenge.  As I understand it, both the 3D Viewer or
the 3D rotation utility built into ImageJ work on some form of an algorithm
in which the relative positions of the slices in a stack are shifted
relative to each other, and then a Maximum projection is generated, creating
a new view through the shifted stack.  We have been looking at the DIC
stacks that are generated either with confocal or manual DIC systems, which
also have optical slices.  However, when we try a standard Max projection,
the resultant is a mess, since the criteria for inclusion are not intensity,
but contrast.  On the other hand, we have been able to use the Stack
Focuser  plugin to create "flattened" images of these stacks so that all
components remain in focus.  I am wondering if it is possible to use an
image shift algorithm similar to the one for transparent fluorescent objects
to generate a rotating, or at least a simple stereo view of such DIC
samples.

--


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
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Re: 3D using Stack Focusser?

Mikhail Umorin-2
Do you mean you want to use something like stack focuser on the rotated
stack?

Mikhail Umorin, Ph.D.

On Thu, Apr 21, 2011 at 7:28 PM, Mikhail Umorin <[hidden email]> wrote:

> Do you mean you want to use something like stack focuser on the rotated
> stack?
>
> Mikhail Umorin, Ph.D.
>
>
> On Thu, Apr 21, 2011 at 2:23 PM, JOEL B. SHEFFIELD <[hidden email]> wrote:
>
>> Colleagues,
>>
>> Here's an interesting challenge.  As I understand it, both the 3D Viewer
>> or
>> the 3D rotation utility built into ImageJ work on some form of an
>> algorithm
>> in which the relative positions of the slices in a stack are shifted
>> relative to each other, and then a Maximum projection is generated,
>> creating
>> a new view through the shifted stack.  We have been looking at the DIC
>> stacks that are generated either with confocal or manual DIC systems,
>> which
>> also have optical slices.  However, when we try a standard Max projection,
>> the resultant is a mess, since the criteria for inclusion are not
>> intensity,
>> but contrast.  On the other hand, we have been able to use the Stack
>> Focuser  plugin to create "flattened" images of these stacks so that all
>> components remain in focus.  I am wondering if it is possible to use an
>> image shift algorithm similar to the one for transparent fluorescent
>> objects
>> to generate a rotating, or at least a simple stereo view of such DIC
>> samples.
>>
>> --
>>
>>
>> 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
>>
>
>
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Re: 3D using Stack Focusser?

Joel Sheffield
No.  I want to create a rotating image from a DIC stack, so I can see some
depth.

On Thu, Apr 21, 2011 at 8:44 PM, Mikhail Umorin <[hidden email]> wrote:

> Do you mean you want to use something like stack focuser on the rotated
> stack?
>
> Mikhail Umorin, Ph.D.
>
> On Thu, Apr 21, 2011 at 7:28 PM, Mikhail Umorin <[hidden email]> wrote:
>
> > Do you mean you want to use something like stack focuser on the rotated
> > stack?
> >
> > Mikhail Umorin, Ph.D.
> >
> >
> > On Thu, Apr 21, 2011 at 2:23 PM, JOEL B. SHEFFIELD <[hidden email]>
> wrote:
> >
> >> Colleagues,
> >>
> >> Here's an interesting challenge.  As I understand it, both the 3D Viewer
> >> or
> >> the 3D rotation utility built into ImageJ work on some form of an
> >> algorithm
> >> in which the relative positions of the slices in a stack are shifted
> >> relative to each other, and then a Maximum projection is generated,
> >> creating
> >> a new view through the shifted stack.  We have been looking at the DIC
> >> stacks that are generated either with confocal or manual DIC systems,
> >> which
> >> also have optical slices.  However, when we try a standard Max
> projection,
> >> the resultant is a mess, since the criteria for inclusion are not
> >> intensity,
> >> but contrast.  On the other hand, we have been able to use the Stack
> >> Focuser  plugin to create "flattened" images of these stacks so that all
> >> components remain in focus.  I am wondering if it is possible to use an
> >> image shift algorithm similar to the one for transparent fluorescent
> >> objects
> >> to generate a rotating, or at least a simple stereo view of such DIC
> >> samples.
> >>
> >> --
> >>
> >>
> >> 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
> >>
> >
> >
>



--


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
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Re: 3D using Stack Focusser?

Gabriel Landini
On Friday 22 Apr 2011, JOEL B. SHEFFIELD wrote:
> No.  I want to create a rotating image from a DIC stack, so I can see some
> depth.

Joel,
Can you post a smallish stack as an example to work with?

Regards

Gabriel
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Re: 3D using Stack Focusser?

Daniel James White
In reply to this post by Joel Sheffield
Hi Joel,

On Apr 22, 2011, at 6:03 AM, IMAGEJ automatic digest system wrote:

> Date:    Thu, 21 Apr 2011 15:23:20 -0400
> From:    "JOEL B. SHEFFIELD" <[hidden email]>
> Subject: 3D using Stack Focusser?
>
> Colleagues,
>
> Here's an interesting challenge.  As I understand it, both the 3D Viewer or
> the 3D rotation utility built into ImageJ work on some form of an algorithm
> in which the relative positions of the slices in a stack are shifted
> relative to each other, and then a Maximum projection is generated,

3D viewer is not using a max projection i think.... its more like an average or sum projection
through the volume in a given direction/line... but maybe thats not so important here...

> creating
> a new view through the shifted stack.  We have been looking at the DIC
> stacks that are generated either with confocal or manual DIC systems, which
> also have optical slices.  However, when we try a standard Max projection,
> the resultant is a mess, since the criteria for inclusion are not intensity,
> but contrast.  

Yes, this is expected to be the case...
the intensity in a DIC image is a complicated function
of the local refractive index gradient, and the direction of that gradient
with respect to the angle the polarizers and prisms are set at.

I have seen no good way to convert this kind of image into
something that will give an intuitively sensible looking 3D volume rendered result...
but it would be neat.

> On the other hand, we have been able to use the Stack
> Focuser  plugin to create "flattened" images of these stacks so that all
> components remain in focus.  I am wondering if it is possible to use an
> image shift algorithm similar to the one for transparent fluorescent objects
> to generate a rotating, or at least a simple stereo view of such DIC
> samples.
>

the problem here is that, (unlike fluorescence) the same object looks very different in DIC depending on its orientation,
so when you move to a new view point in 3d space... well, things just dont add up or make sense...

Perhaps this might help:

Interesting features in DIC are usually where there is a steep intensity grdient in the image.
So, you can take a DIC image z stack, compute its gradient image per slice,
and use that for 3D rendering.

I dont have a DIC z stack handy... but i imagine the above trick might give something useful? Maybe?

?

D


> --
>
>
> 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

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Processing and Analysis
Light Microscopy Facility
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

+49 (0)15114966933 (German Mobile)
+49  (0)351 210 2627 (Work phone at MPI-CBG)
+49  (0)351 210 1078 (Fax MPI-CBG LMF)

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[hidden email]
( [hidden email] )