Equivalent of watershed for cutting connected components of an image of particles?

[Juan Nunez-Iglesias]

Hey Adam,




"Closing" is a dilation followed by an erosion. If you have "gaps" that are smaller than the footprint (aka structuring element) of the operation, they will be "closed". =) (e.g. a C turning into an O if the distance between the tips of the C is small enough.)




See a small example here:


http://nbviewer.ipython.org/github/jni/skimage-tutorials/blob/master/scipy-2014/solved/3_morphological_operations.ipynb




Though come to think of it we should change the shape to be a C rather than an O with a thin bit.






Juan.

On Fri, Mar 13, 2015 at 4:09 AM, Adam Hughes <hughesadam87 at gmail.com>
wrote:

> Thomas,
> Unfortunately, the cells of interest are the sickle cells, so isolating 
> cells on their side and sickle cells is really important.  If anything, it 
> would be better to toss out the healthy cells.  When you say the 
> "segmentation has gone sideways", what do you mean exactly?
> Juan,
> What would binary closing do in particular?  I didn't understand what you 
> were saying
> On Wednesday, March 11, 2015 at 7:01:54 PM UTC-4, Thomas Caswell wrote:
>>
>> Jumping in from the peanut gallery, can you reliable identify when the 
>> segmentation has gone sideways? Looking at the second moment, area to 
>> bounding box area, or some other compactness measure?  
>>
>> If you can get away with it, you could just drop the offending cells. If 
>> not, then you can try eroding the joined cells until they split into 
>> multiple segments. 
>>
>> Tom
>>
>> On Wed, Mar 11, 2015, 17:15 Claiborne Morton <claiborn... at gmail.com 
>> <javascript:>> wrote:
>>
>>> Hey thanks for the help, here are a few other issues we are running into. 
>>> When a sickle cell is in contact with a regular cell, we cannot find a way 
>>> to separate the two. Also bottom-middle circle is of a healthy blood cell 
>>> that is on its side. The watershed function tends to break these cells into 
>>> two or more partitions when the should not be separated.
>>> Any idea on how to fix these problems?
>>>
>>>
>>> On Tue, Mar 10, 2015 at 2:12 PM, Claiborne Morton <claiborn... at gmail.com 
>>> <javascript:>> wrote:
>>>
>>>> Hey guys, Im following up on Adam's behalf, but this is an example of an 
>>>> image we are working with in trying to separate cells that are touching 
>>>> each other. 
>>>> Also you can see the top middle particle has a crescent shape, but is 
>>>> actually a healthy red blood cell that has been segmented incorrectly 
>>>> because of glare. Is that a way to connect the two tips of the shape so 
>>>> that I could then run "binary_fill_holes()" to correctly segment the cell. 
>>>> Thanks!
>>>>
>>>>
>>>> On Wednesday, February 18, 2015 at 7:04:10 PM UTC-5, Adam Hughes wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> In ImageJ, one can select watershedding to break up connected regions 
>>>>> of particles.  Are there any examples of using watershed in this capacity 
>>>>> in scikit image?   All of the examples I see seem to use watershedding to 
>>>>> do segmentation, not to break connected particles in an already-segmented 
>>>>> black and white image.  
>>>>>
>>>>> Also, is there a straightforward way to remove particles on a the edge 
>>>>> of an image?  Sorry, googling is failing me, but I know this is possible.
>>>>>
>>>>> Thanks
>>>>>
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