: Re: Stack Focusser

[Goldsmith, Noel]

NeLaS,
Hi,
We have tried the stack focusser as well and find it pretty good. Especially
for RGB images. And there are some others out there as well.
Some tips.
1. Your images do need to be in a precise Z stack, no translations. (or line
them up manually or use one of the stack aligners out there)

2. Your exposures for each image should be the same.

3. The exposure for each image should be such that there is no saturation,
except maybe for a very few white and black points.

4. Try numbers between 5 and 15 for the filter size. This has the effect of
smoothing the image before the sharpness is estimated.

5. Try some smoothing first, using median filters. But this should not be
necessary with the stack focusser.


6. Try putting the range or depth image into the 3-D visualization plug-in,
which with smoothing will make a really noisy depth image look reasonable.

7. Investigate less contrast in the imaging system, try to take smooth noise
free images.

If there are too many slices it seems to grind to a halt.

Hope this helps some
Noel

--
Noel Goldsmith
Air Vehicles Division
DSTO
506 Lorimer Street
Port Melbourne
Vic 3207
AUSTRALIA
Phone [phone]
Fax [phone]

>   4. Stack Focuser (2)
>  ..
>
> ----------------------------------------------------------------------

> Date:    Tue, 17 Oct 2006 07:34:49 -0700
> From:    NeLaS <[hidden email]>
> Subject: Stack Focuser
>
> Hello,
>
> I have a series of light microscopy photos with different focal planes,
> taken under DIC. I was trying to create a focused composition image of this
> photos, but I'm not getting very good images.
>
> I'm creating a stack with the pictures and using the Stack Focuser plugin.
> If I use a small n (for the n x n kernel) like 3, I get the image in focus
> but with lots of blurring. If I use a bigger n (like 100) I get a better
> definition of the focused parts but the squares of the filter are very
> obvious, and some of them are not in focus at all!
>
> I know this images have a lot of unfocused noise which might be the
> responsible for the low quality result, but any suggestions in how to get
> focused stacks are very welcome!
>
> Is there any other tool/plugin I can use to do this?
>
> Thanks in advance!
>
> Bruno
>
> --=20
> Centro de Biologia Marinha (CEBIMar)
> Universidade de S=E3o Paulo
> Av. Manoel H. do Rego km 131,5
> 11600-000 S=E3o Sebasti=E3o, SP, Brasil
>
> www.myspace.com/nelas
>
>

[NeLaS]

Thanks Noel and Christophe for the suggestions!!!

I've been testing the Extended Depth of Field, Stack Focuser and Z
Projections and the results are getting better each time I try something
different! It seems that what you need to do really depends on the original
photos properties... so each set is a new challenge... Next time I'll take
better photos :-)!

I have one question about file format and one about taking photos for
focusing and 3D reconstruction.

1- I wanted to compare the results of focusing a JPG stack and a TIFF stack,
but I don't have any TIFF stack right now. Could the noise and abnormalities
present in my focused picture be a consequence of the jpg compression?

I know this sounds a bit obvious but maybe a high quality JPG does not
differ too much (or at least not visually) when compared to a focused TIFF
stack.

2- The minimum number of photos for a building a focused stack should be the
Z axis object size / Depth of field. This assures that every part of the
study object has an "in focus" section. Is that correct?

Now my question is: to get better results during Focusing stacks should I
take the minimum number of pictures or should I take more and overlap the
"in focus" areas of the object study??? don't know if I was clear enough...!

Cheers!!!

Bruno (NeLaS)



On 10/18/06, Goldsmith, Noel <[hidden email]> wrote:

>
> NeLaS,
> Hi,
> We have tried the stack focusser as well and find it pretty good.
> Especially
> for RGB images. And there are some others out there as well.
> Some tips.
> 1. Your images do need to be in a precise Z stack, no translations. (or
> line
> them up manually or use one of the stack aligners out there)
>
> 2. Your exposures for each image should be the same.
>
> 3. The exposure for each image should be such that there is no saturation,
> except maybe for a very few white and black points.
>
> 4. Try numbers between 5 and 15 for the filter size. This has the effect
> of
> smoothing the image before the sharpness is estimated.
>
> 5. Try some smoothing first, using median filters. But this should not be
> necessary with the stack focusser.
>
>
> 6. Try putting the range or depth image into the 3-D visualization
> plug-in,
> which with smoothing will make a really noisy depth image look reasonable.
>
> 7. Investigate less contrast in the imaging system, try to take smooth
> noise
> free images.
>
> If there are too many slices it seems to grind to a halt.
>
> Hope this helps some
> Noel
>
> --
> Noel Goldsmith
> Air Vehicles Division
> DSTO
> 506 Lorimer Street
> Port Melbourne
> Vic 3207
> AUSTRALIA
> Phone [phone]
> Fax [phone]
>
> >   4. Stack Focuser (2)
> >  ..
> >
> > ----------------------------------------------------------------------
>
> > Date:    Tue, 17 Oct 2006 07:34:49 -0700
> > From:    NeLaS <[hidden email]>
> > Subject: Stack Focuser
> >
> > Hello,
> >
> > I have a series of light microscopy photos with different focal planes,
> > taken under DIC. I was trying to create a focused composition image of
> this
> > photos, but I'm not getting very good images.
> >
> > I'm creating a stack with the pictures and using the Stack Focuser
> plugin.
> > If I use a small n (for the n x n kernel) like 3, I get the image in
> focus
> > but with lots of blurring. If I use a bigger n (like 100) I get a better
> > definition of the focused parts but the squares of the filter are very
> > obvious, and some of them are not in focus at all!
> >
> > I know this images have a lot of unfocused noise which might be the
> > responsible for the low quality result, but any suggestions in how to
> get
> > focused stacks are very welcome!
> >
> > Is there any other tool/plugin I can use to do this?
> >
> > Thanks in advance!
> >
> > Bruno
> >
> > --=20
> > Centro de Biologia Marinha (CEBIMar)
> > Universidade de S=E3o Paulo
> > Av. Manoel H. do Rego km 131,5
> > 11600-000 S=E3o Sebasti=E3o, SP, Brasil
> >
> > www.myspace.com/nelas
> >
> >
>

--
Centro de Biologia Marinha (CEBIMar)
Universidade de São Paulo
Av. Manoel H. do Rego km 131,5
11600-000 São Sebastião, SP, Brasil

www.myspace.com/nelas