blob detection and dust removal

Mon May 2 05:30:37 EDT 2016

How do you plan to find the position of the real crystals ? Maybe the
function you will use to find the original crystals will take a mask
argument ?

On Mon, May 2, 2016 at 1:07 AM, Raphael Okoye <raphael at aims.ac.za> wrote:

> hi Vighnesh,
>
>  Further processing involves getting the size and positions of real
> crystals (I want to use the positions to estimate the pair correlation
> function and then using the pair correlation function to estimate the
> structure factor) The image comes from a sequence of time lapse images.
> There are dust particles of various sizes in the images so if they are not
> eliminated, a false structure factor will be determined.  The median filter
> took care of the very little ones but didn’t work for the bigger ones.
>
> Thanks a lot.
>
> Raphael
>
> On 1 May 2016 at 21:27, Vighnesh Birodkar <vighneshbirodkar at gmail.com>
> wrote:
>
>> Hi
>>
>> That really depends on your application. What's your motivation for
>> removing these dust particles ? How are these images going to be processed
>> further ?
>>
>> Thanks
>> Vighnesh
>>
>> On Monday, May 2, 2016 at 12:13:27 AM UTC-4, Raphael wrote:
>>>
>>> hi Vighnesh,
>>>
>>>  Thanks a bunch!! I see my error now.
>>>
>>> Actually that blob you detected a dust particle. Which  operation would
>>> you suggest to erase it? I tried morphological erosion but it doesn't take
>>> it away.
>>>
>>> Thanks
>>> Raphael
>>>
>>> On 1 May 2016 at 18:27, Vighnesh Birodkar <vighnesh... at gmail.com> wrote:
>>>
>>>> Hello Raphael
>>>>
>>>> The error here is because the output of blob_doh in a numpy array of
>>>> blobs, it is not an image meant for display. If you notice the example the
>>>> blobs are being drawn separately inside the for loop. If no blobs are being
>>>> detected, you can adjust the threshold. Lowering the threshold will make
>>>> the function detect more blobs. It is clarified futher in the documentation
>>>>
>>>> http://scikit-image.org/docs/dev/api/skimage.feature.html#skimage.feature.blob_doh
>>>>
>>>> I was able to detect one blob in your image with the default threshold
>>>> value. See:
>>>>
>>>> https://gist.github.com/vighneshbirodkar/c16515126e648cf92f08d3319d3a023e
>>>>
>>>> Find the result attached.
>>>>
>>>> Thanks
>>>> Vighnesh
>>>>
>>>> On Saturday, April 30, 2016 at 2:02:51 AM UTC-4, Raphael wrote:
>>>>
>>>>> hi folks,
>>>>>
>>>>>   Got a problem removing dust and identifying blobs/crytals. Kindly
>>>>> see my code below
>>>>>
>>>>>
>>>>> from __future__ import division, print_function
>>>>> import matplotlib.pyplot as plt
>>>>> import numpy as np
>>>>> from skimage import io, feature, color, measure, draw, img_as_float,
>>>>> exposure
>>>>> from skimage.filters.rank import median
>>>>> from skimage.feature import blob_dog, blob_log, blob_doh
>>>>> from skimage.morphology import disk
>>>>>
>>>>> #raw image
>>>>> image_raw =
>>>>> img_as_float((io.imread('/home/raphael/Documents/ScikitImage/Run
>>>>> 4-2_00061cropped.tif'))) (RawImage.tif attached)
>>>>> plt.imshow(image_raw)
>>>>>
>>>>> #converted to grayscale
>>>>>
>>>>> img_gray =
>>>>> color.rgb2gray(io.imread('/home/raphael/Documents/ScikitImage/Run
>>>>> 4-2_00061cropped.tif'))
>>>>> plt.imshow(image_gray)
>>>>>
>>>>>
>>>>> #applied median filter to take out small dust particles. But the big
>>>>> dust particle on the top right corner still persists (see median1.png
>>>>> attached)
>>>>> img_filtered=median(img_gray,disk(10))
>>>>> plt.imshow(img_filtered)
>>>>>
>>>>>
>>>>> #applied  adapthist to make image more clearer (see adaptive.png)
>>>>>
>>>>> img_equalized=exposure.equalize_adapthist(img_filtered)
>>>>> plt.imshow(img_equalized)
>>>>>
>>>>> #trying to detect the crystals/blobs. I followed the example here
>>>>> http://scikit-image.org/docs/dev/auto_examples/features_detection/plot_blob.html
>>>>> But this gave an error. matplotlib was not happy with the data type
>>>>> blobs_doh = blob_doh(img_equalized,  max_sigma=30, threshold=.1)
>>>>> plt.imshow(blobs_doh)
>>>>>
>>>>> My problems are:
>>>>>
>>>>> 1. I could not get the dust particle out especially the really big one
>>>>> on the top right. How can I get it out?
>>>>>
>>>>> 2. I could not detect the crystals/blobs in the image using blob_doh
>>>>>
>>>>> Any ideas/suggestions is highly appreciated.  Thank you!
>>>>>
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