Help needed using pymorph

[Thouis (Ray) Jones]

(Note, I'm responding to both pythonvision and scikits-image.  Sorry
to those people only subscribed to one list.)

I think more information might be helpful.

- How many images do you have that you need to analze?
- Are they movies, or completely separate frames?
- What is common in the images (background, lighting, camera pose?)

I wouldn't worry about efficient multi-template matching until you
know if multi-template matching works at all.  If template matching
can get 60% of the beads, though, I expect multiple templates should
be able to get almost all of them, possibly using a voting scheme
where you require a bead to match multiple different templates before
reporting it as a "hit".

You might look at ilastik (http://www.ilastik.org/) as another approach.

Thouis Jones



On Tue, Apr 12, 2011 at 06:24, Alex Liberzon <alex.liberzon at gmail.com> wrote:
> Thanks for the feedback.
>
> There are both effects, the beads are different sizes and also as you
> noticed at different depths. but the variation is not very large, i.e.
> within a difference of 10 - 15 pixels I'd say. I have no idea how to
> use multiple templates efficiently. Of course I can repeat normalized
> cross correlation attempt few times.
>
> I can modify the experiment, so the next time will be hopefully
> better. Meanwhile, this data is important to extract from the images
> as is.
>
> Regards,
> Alex
>
> On Apr 11, 10:56 pm, "Thouis (Ray) Jones" <tho... at gmail.com> wrote:
>> Are the beads actually different sizes, or just at different depths in
>> the image.  And how fixed is your camera system relative to the scene?
>>  I ask, because it seems like you could use multiple templates,
>> parameterized by image position, to adjust for the size and blur
>> variation.
>>
>> Also, do you have the option of modifying the scene illumination?  Can
>> you use color, or multiple exposures, or are the images "as-is" and
>> there's no option for making the beads more visible?
>>
>> Best,
>> Ray Jones
>>
>>
>>
>> On Mon, Apr 11, 2011 at 19:49, Alex Liberzon <alex.liber... at gmail.com> wrote:
>> > Dear pymorph members,
>>
>> > I have some difficulty to identify specific objects from the grayscale
>> > image. For example, in this image
>> >https://picasaweb.google.com/lh/photo/FYZ1_F4OAoe920iYj8bk7A?feat=dir...
>> > one can see about 15 glass beads on the floor illuminated from the
>> > left side. Human eye identifies them easily, but I cannot find the
>> > efficient way to identify them in such an image. Using Matlab the
>> > approach was 1) crop out one of the beads as is from the given image,
>> > and then 2)using normalized cross-correlation (normxcorr2) of the
>> > cropped bead with the image to identify the 50 - 60% of beads. The
>> > problems are due to uneven background illumination, different size of
>> > the beads and different light pattern due to their angle in respect to
>> > the light source.
>> > I could define the the problem of looking a feature that has two not-
>> > connected bright regions, separated by some distance that could be
>> > known within some reasonable limits.
>>
>> > Any suggestion is gratefully appreciated. If possible, the pseudo-code
>> > would be helpful. Note that I also posted this question on skikits-
>> > image mailing list so if you receive it double, I apologize for that.
>>
>> > Thanks,
>> > Alex