watershed algorithm for segmentation

[Juan Nunez-Iglesias]

Amit,

The confusion here is just semantics. A gradient is an image. In our
context, any two-dimensional boolean or numeric array is an image. The
watershed algorithm works by flooding a landscape from the bottom up, so
you want your input to be an image where your regions will have low
intensity and the boundaries between them will have high intensity. In the
example, the distance transformed image satisfies this property, while the
original does not. In other cases, your input image may satisfy the
property without requiring a transform (for example, electron microscopy
data).

Juan.


On Fri, Apr 4, 2014 at 3:09 PM, amit bhatkal <amitbhatkal12 at gmail.com>wrote:

> Thank you Tony and Ronnie for your timely inputs.
> I was going through the link provided by Tony
> "http://scikit-image.org/docs/dev/auto_examples/plot_marked_watershed.html<http://scikit-image.org/docs/dev/auto_examples/plot_marked_watershed.html>" . Here in line 16 of the code
>
> # process the watershedlabels = watershed(gradient, markers)
>
> Also I came across this code : http://scikit-image.org/docs/dev/auto_examples/plot_watershed.html
>
> Which uses distance map in the place of image.
>
>
> The actual sytax is :
> watershed(*image*, *markers*, *connectivity=None*, *offset=None*, *mask=None*)
>
> The "image" parameter of the watershed function is fed with "gradient" instead of actual image. This is the point of confusion. So thats what I wanted to clarify. Should I be providing the actual image data or some edge detected or gradient image for the watershed.
>
>
> Thank you
>
> Amit
>
>
>
> On Thu, Apr 3, 2014 at 8:04 PM, Tony Yu <tsyu80 at gmail.com> wrote:
>
>>
>>
>>
>> On Thu, Apr 3, 2014 at 4:46 AM, <amitbhatkal12 at gmail.com> wrote:
>>
>>> Hi everyone,
>>> I was trying to segment a greyscale 8 bit image using the watershed
>>> algorithm present in skimage.morphology but I am confused as to what should
>>> I provide as inputs to the watershed().
>>> Can anyone please help me in this regard.
>>> This is what I gathered from the documentation.
>>>
>>> *image: ndarray (2-D, 3-D, ...) of integers* :
>>>
>>> Data array where the lowest value points are labeled first.
>>>
>>> *markers: ndarray of the same shape as `image`* :
>>>
>>> An array marking the basins with the values to be assigned in the label
>>> matrix. Zero means not a marker. This array should be of an integer type.
>>>
>>> Here "image" refers to original image or something else?
>>> How do I obtain the markers ?
>>>
>>>
>> Hi, you should take a look at the gallery examples. Here's a particularly
>> relevant one:
>>
>> http://scikit-image.org/docs/dev/auto_examples/plot_marked_watershed.html
>>
>>
>> Cheers,
>> -Tony
>>
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