Hello Raphael What error did you get ? Can you post the traceback or the output after blob detection ? 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.... 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!