Mailman 3 November 2012 - scikit-image

Re: Oversplitting by watershed
by Josh Warner 13 Nov '12

13 Nov '12

I can probably put something together. What should the goal be? Expand the featureset of one algorithm, such that the other can be collapsed into a wrapper function with no loss of backwards compatibility, or expand the featureset of one and eliminate the other (carefully changing all internal references to the old function)? The latter might be the best/ideal world solution, but even if all of the internal references were changed appropriately it could break 3rd party code. I would lean toward the former option, moving in the direction of `is_local_maximum`, though this does appear to be the slower algorithm at present. On Monday, November 12, 2012 9:43:27 PM UTC-6, Tony S Yu wrote: > > Thanks for the detailed response! > > On Mon, Nov 12, 2012 at 6:57 PM, Josh Warner <silvertr...(a)gmail.com<javascript:> > > wrote: > >> I've looked at these two algorithms, and the biggest difference seems to >> be in the output. `is_local_maximum` returns a Boolean array, while >> `peak_local_max` returns the indices of points corresponding to maxima (a >> la `np.sort` vs. `np.argsort`, though you cannot just pass the output of >> `peak_local_max` as indices). >> >> The other differences are more subtle, but significant. >> >> The API for `peak_local_max` could use some cleanup - the first threshold >> kwarg is set to 'deprecated'(!) and IMHO should be removed - but this >> algorithm allows finer control over thresholding and peak searching. >> > > > I think it's marked 'deprecated' so that it can be removed gracefully > (i.e. it gives people time to change their code). That said, it was marked > 'deprecated' a few releases back, so it's probably ripe for removal. > > > >> This would be good to avoid finding phantom peaks in noise if large dark >> regions were present. One significant drawback of this algorithm is the >> min_distance kwarg is set by default to 10, rather arbitrary, and ANY input >> (even the minimum value of 1) excludes both neighboring pixels AND the >> border. See example below. >> >> In contrast, `is_local_maximum` has a much simpler API. It doesn't have >> the finer thresholding / peak searching controls, but has a unique ability >> to search for peaks ONLY within arbitrary, connected, labeled regions. >> This has some interesting potentials for masking etc, though I believe >> within each label only one peak will be found. This algorithm also has the >> ability to search arbitrary local regions for peaks using something akin to >> a morphological structuring element, through the `footprint=` kwarg. The >> documentation for this could probably be clarified. >> >> The way `peak_local_max` excludes borders concerns me for general use, as >> does its default `min_distance=10`, and personally I would prefer to wok >> around the limitations in `is_local_maximum`. >> >> A best-of-both-worlds combination could probably be created without >> overly much effort... >> > > > This is a great summary of the API differences. I agree that excluding the > border region is a bit of a wart. (My guess is that this could be fixed by > changing the boundary condition on the maximum filter used in > `peak_local_max`.) Although I agree that defaulting to `min_distance=10` is > arbitrary, I'm not sure there's an obvious choice. I would normally assume > that peaks separated by 1 pixel are just noise. > > The footprint and mask parameter would definitely be a nice addition to > `peak_local_max`. > > If you have time, a pull request to address some or all of these issues > would be great. If not, maybe you could this as an issue on github? > > Thanks, > -Tony > > > >> >> >> Snippet showing border-excluding behavior of `peak_local_max`, which will >> only get worse with higher values of `min_distance`: >> >> import numpy as np >> import matplotlib.pyplot as plt >> from skimage.feature import peak_local_max >> from skimage.morphology import is_local_maximum >> >> # Generate standardized random data >> np.random.seed(seed=1234) >> testim = np.random.randint(0, 255, size=(20, 20)) >> >> # Find peaks using both methods >> ismax = is_local_maximum(testim) # Boolean image >> returned >> peakmax = peak_local_max(testim, min_distance=1) # (M, 2) indices >> returned >> >> # `peakmax` not plottable - placing values in 2d array >> Ipeakmax = np.zeros(testim.shape) >> Ipeakmax[peakmax[:, 0], peakmax[:, 1]] = 1 >> >> # Show the results >> fig, ax = plt.subplots(ncols=2, nrows=1) >> ax[0].imshow(ismax, cmap='gray') >> ax[0].set_title('Peaks found by `is_local_maximum`') >> ax[1].imshow(Ipeakmax, cmap='gray') >> ax[1].set_title('Peaks found by `peak_local_max`') >> >> plt.show() >> >> >> >> On Monday, November 12, 2012 3:57:28 PM UTC-6, Tony S Yu wrote: >> >>> >>> >>> On Mon, Nov 12, 2012 at 7:43 AM, Frank <pennek...(a)googlemail.com> wrote: >>> >>>> Dear group, >>>> >>>> I have some issues with the watershed algorithm implemented in scikits >>>> image. I use a global threshold to segment cells from background, but some >>>> cells touch and I want them to be split. Watershed seems the appropriate >>>> way to deal with my problem, however my particles are split in too many >>>> pieces. Is there a way to adjust the sensitivity of the watershed method? >>>> >>>> Many thanks for any suggestion! >>>> >>>> The code that I use looks like below. An example image that I want to >>>> process can be downloaded here: https://dl.dropbox.com/u/** >>>> 10373933/test.jpg <https://dl.dropbox.com/u/10373933/test.jpg> >>>> >>>> # packages needed to perform image processing and analysis >>>> import numpy as np >>>> import scipy as scp >>>> import matplotlib.pyplot as plt >>>> import matplotlib.image as mpimg >>>> import scipy.ndimage as nd >>>> import skimage >>>> from skimage import io >>>> from skimage.morphology import watershed, is_local_maximum >>>> from skimage.segmentation import find_boundaries, visualize_boundaries >>>> from skimage.color import gray2rgb >>>> >>>> #read files jpeg file >>>> image = mpimg.imread('c:\\test.jpg') >>>> image_thresh = image > 140 >>>> labels = nd.label(image_thresh)[0] >>>> distance = nd.distance_transform_edt(**image_thresh) >>>> local_maxi = is_local_maximum(distance, labels=labels, >>>> footprint=np.ones((9, 9))) >>>> markers = nd.label(local_maxi)[0] >>>> labelled_image = watershed(-distance, markers, mask=image_thresh) >>>> >>>> #find outline of objects for plotting >>>> boundaries = find_boundaries(labelled_**image) >>>> img_rgb = gray2rgb(image) >>>> overlay = np.flipud(visualize_**boundaries(img_rgb,boundaries)**) >>>> imshow(overlay) >>> >>> >>> Hi Frank, >>> >>> Actually, I don't think the issue is in the watershed segmentation. >>> Instead, I think the problem is in the marker specification: Using local >>> maxima creates too many marker points when a blob deviates greatly from a >>> circle. (BTW, does anyone know if there are any differences between >>> `is_local_maximum` and `peak_local_max`? Maybe the former should be >>> deprecated.) >>> >>> Using the centroids of blobs gives cleaner results. See >>> slightly-modified example below. >>> >>> Best, >>> -Tony >>> >>> # packages needed to perform image processing and analysis >>> import numpy as np >>> import matplotlib.pyplot as plt >>> import scipy.ndimage as nd >>> >>> from skimage import io >>> from skimage import measure >>> from skimage.morphology import watershed >>> from skimage.segmentation import find_boundaries, visualize_boundaries >>> from skimage.color import gray2rgb >>> >>> #read files jpeg file >>> image = io.imread('test.jpg') >>> >>> image_thresh = image > 140 >>> labels = nd.label(image_thresh)[0] >>> distance = nd.distance_transform_edt(**image_thresh) >>> >>> props = measure.regionprops(labels, ['Centroid']) >>> coords = np.array([np.round(p['**Centroid']) for p in props], dtype=int) >>> # Create marker image where blob centroids are marked True >>> markers = np.zeros(image.shape, dtype=bool) >>> markers[tuple(np.transpose(**coords))] = True >>> >>> labelled_image = watershed(-distance, markers, mask=image_thresh) >>> >>> #find outline of objects for plotting >>> boundaries = find_boundaries(labelled_**image) >>> img_rgb = gray2rgb(image) >>> overlay = visualize_boundaries(img_rgb, boundaries, color=(1, 0, 0)) >>> >>> plt.imshow(overlay) >>> plt.show() >>> >> -- >> >> >> > >

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Oversplitting by watershed
by Frank 13 Nov '12

13 Nov '12

Dear group, I have some issues with the watershed algorithm implemented in scikits image. I use a global threshold to segment cells from background, but some cells touch and I want them to be split. Watershed seems the appropriate way to deal with my problem, however my particles are split in too many pieces. Is there a way to adjust the sensitivity of the watershed method? Many thanks for any suggestion! The code that I use looks like below. An example image that I want to process can be downloaded here: https://dl.dropbox.com/u/10373933/test.jpg # packages needed to perform image processing and analysis import numpy as np import scipy as scp import matplotlib.pyplot as plt import matplotlib.image as mpimg import scipy.ndimage as nd import skimage from skimage import io from skimage.morphology import watershed, is_local_maximum from skimage.segmentation import find_boundaries, visualize_boundaries from skimage.color import gray2rgb #read files jpeg file image = mpimg.imread('c:\\test.jpg') image_thresh = image > 140 labels = nd.label(image_thresh)[0] distance = nd.distance_transform_edt(image_thresh) local_maxi = is_local_maximum(distance, labels=labels, footprint=np.ones((9, 9))) markers = nd.label(local_maxi)[0] labelled_image = watershed(-distance, markers, mask=image_thresh) #find outline of objects for plotting boundaries = find_boundaries(labelled_image) img_rgb = gray2rgb(image) overlay = np.flipud(visualize_boundaries(img_rgb,boundaries)) imshow(overlay)

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Re: Produce overlay between original image and labelled objects
by Frank 09 Nov '12

09 Nov '12

Hi Tony and Johannes, in fact visualize_boundaries works fine and fulfills all I want, so I will stick with it. The bounding box approach seems fine too! Thanks to both of you for the quick response and the helpful hints! Cheers, Frank On Thursday, November 8, 2012 6:38:56 PM UTC+1, Tony S Yu wrote: > > > > On Thu, Nov 8, 2012 at 4:30 AM, Frank <pennek...(a)googlemail.com<javascript:> > > wrote: > >> Hi, >> >> I want to use Python and scikit image for detection, counting and >> measuring cells from digital pictures. So far most of the things I want to >> do work fine: I just use a global threshold which separates my cells well >> from the background. After labelling the thresholded objects the >> regionprops function provides many of the features I am interested in >> (area, centroid *etc*). >> To be completely satisfied, I would like to produce an overlay between >> the original image and the identified objects after thresholding for error >> checking. I searched a while to find the proper function to do so and then >> encountered the mark_boundaries function. However, that one is not working, >> because the function is not found after importing the skimage.segmentation >> module (ImportError: cannot import name mark_boundaries). Do you have any >> suggestions, why it is not working? Or maybe you know a better way to >> achieve my goal? >> >> Many thanks, >> >> Frank > > > Hi Frank, > > Are you using the latest release (0.7) or the development version on > github? It's a bit unfortunate, but the documentation link on the website > goes directly to the dev docs instead of the latest release. > > I believe `mark_boundaries` is only in the development version of > scikit-image, but really that was just a slight modification of > `visualize_boundaries`, which should be available in 0.7. Note: > `visualize_boundaries` doesn't work with grayscale images, so you may need > to call `skimage.color.gray2rgb`. > > Hope that helps. > > -Tony >

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Re: graph.route_through_array, a route is "outside"
by Jean-Patrick Pommier 09 Nov '12

09 Nov '12

I could simplify my script<http://dip4fish.blogspot.fr/2012/11/using-geodesic-distance-to-resolve.html>but Zachary's message make me understand I can't directly use an idea from binary image to greyscale image. Thanks JP Le jeudi 8 novembre 2012 18:57:51 UTC+1, Stefan van der Walt a écrit : > > Hi JP > > On Thu, Nov 8, 2012 at 8:59 AM, jip <jeanpatri...(a)gmail.com <javascript:>> > wrote: > > How to get a minimal cost route "inside" a particle (<>255)? > > Could you upload a minimal snippet to illustrate this behavior to > gist.github.com? > > Thanks > Stéfan >

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graph.route_through_array, a route is "outside"
by jip 09 Nov '12

09 Nov '12

Hello, A contour is extracted from a greyscale image ("walls") where the background is set to 255. Several points near the contour are used to compute a path with graph.route_through_array: mincost = graph.route_through_array(walls ,p1,p2,fully_connected=True) One found path is not completely inside the array. When fully_connected=False is used all the paths are inside the chromosomes (i.e. they do not cross regions where grey level=255). How to get a minimal cost route "inside" a particle (<>255)? Thank you Jean-Patrick <https://lh6.googleusercontent.com/-YBi4a6avWfw/UJvgFAyisjI/AAAAAAAAA98/A5AD…>

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Re: Produce overlay between original image and labelled objects
by Schönberger Johannes 09 Nov '12

09 Nov '12

Hi, you could also have a look at the following example: http://scikit-image.org/docs/dev/auto_examples/plot_label.html Johannes Schönberger Am 08.11.2012 um 10:30 schrieb Frank <pennekampster(a)googlemail.com>: > Hi, > > I want to use Python and scikit image for detection, counting and measuring cells from digital pictures. So far most of the things I want to do work fine: I just use a global threshold which separates my cells well from the background. After labelling the thresholded objects the regionprops function provides many of the features I am interested in (area, centroid etc). > To be completely satisfied, I would like to produce an overlay between the original image and the identified objects after thresholding for error checking. I searched a while to find the proper function to do so and then encountered the mark_boundaries function. However, that one is not working, because the function is not found after importing the skimage.segmentation module (ImportError: cannot import name mark_boundaries). Do you have any suggestions, why it is not working? Or maybe you know a better way to achieve my goal? > > Many thanks, > > Frank > > -- > >

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Re: Produce overlay between original image and labelled objects
by Tony Yu 09 Nov '12

09 Nov '12

On Thu, Nov 8, 2012 at 4:30 AM, Frank <pennekampster(a)googlemail.com> wrote: > Hi, > > I want to use Python and scikit image for detection, counting and > measuring cells from digital pictures. So far most of the things I want to > do work fine: I just use a global threshold which separates my cells well > from the background. After labelling the thresholded objects the > regionprops function provides many of the features I am interested in > (area, centroid *etc*). > To be completely satisfied, I would like to produce an overlay between the > original image and the identified objects after thresholding for error > checking. I searched a while to find the proper function to do so and then > encountered the mark_boundaries function. However, that one is not working, > because the function is not found after importing the skimage.segmentation > module (ImportError: cannot import name mark_boundaries). Do you have any > suggestions, why it is not working? Or maybe you know a better way to > achieve my goal? > > Many thanks, > > Frank Hi Frank, Are you using the latest release (0.7) or the development version on github? It's a bit unfortunate, but the documentation link on the website goes directly to the dev docs instead of the latest release. I believe `mark_boundaries` is only in the development version of scikit-image, but really that was just a slight modification of `visualize_boundaries`, which should be available in 0.7. Note: `visualize_boundaries` doesn't work with grayscale images, so you may need to call `skimage.color.gray2rgb`. Hope that helps. -Tony

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