blob detection and dust removal
Raphael Okoye
raphael at aims.ac.za
Mon May 2 15:34:42 EDT 2016
hi Vighnesh
I plan to use this guy
http://scikit-image.org/docs/dev/auto_examples/plot_regionprops.html. The
documentation on regionprops (
http://scikit-image.org/docs/dev/api/skimage.measure.html#regionprops) says
I can get parameters such as co-ordinate positions, equivalent diameter etc
But first I need to think of a way to exclude the dust particles, that is
the main challenge.
Thanks
Raphael
On 2 May 2016 at 02:30, Vighnesh Birodkar <vighneshbirodkar at gmail.com>
wrote:
> 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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