Mailman 3 March 2015 - scikit-image

Water-shedding non-circular particles
by Claiborne Morton 19 Mar '15

19 Mar '15

Hey guys, Im still having trouble finding ways to separate touching particles if the are not both circular. Further when dealing with elliptical shapes, a single particle tends to incorrectly get cut in half. Any ideas how I could change parameters in the water-shedding function to correct for this? Attached are a few problem cases so you can see examples. Thanks, Clay [image: Inline image 1]

1 0

GSOC introduction: Dynamic time warping
by Michael Mueller 17 Mar '15

17 Mar '15

Hello everyone, My name is Michael Mueller and I am a first-year math and computer science major at the University of Massachusetts, Amherst. Last year, I participated in GSOC with AstroPy <http://www.astropy.org/>, an open-source astronomy library in Python. My project involved writing a C/Cython text file reader (and writer) to increase the speed of ASCII capabilities in `astropy.io.ascii`. My blog from the summer is viewable here <http://muellergsoc.blogspot.com/>. This year, having used scikit-image recently for image processing as part of a research project, I'm interested in submitting a proposal to work with scikit-image on the dynamic time warping project. While I have no previous knowledge of dynamic time warping, I found a nice introduction <http://www.springer.com/cda/content/document/cda_downloaddocument/978354074…> to the subject and am excited to read more about it. Any other references I should take a look at? I also noticed that the GSOC page <https://github.com/scikit-image/scikit-image/wiki/GSoC-2015> mentions that students should have a solid PR merged, which I plan to start. Are there any particular issues that might be good to tackle, or any good entry points to get used to the scikit-image code base? Cheers, Michael

2 1

Re: GSoC: Rewriting scipy.ndimage in Cython
by Ralf Gommers 15 Mar '15

15 Mar '15

On Tue, Mar 10, 2015 at 7:21 AM, Stéfan van der Walt <stefanv(a)berkeley.edu> wrote: > Hi Aman > > On Mon, Mar 9, 2015 at 9:52 AM, AMAN singh <ug201310004(a)iitj.ac.in> wrote: > > Please tell me whether I am on right track or not. If you can suggest me > > some resources which will be helpful to me in understanding the project, > I > > would be highly obliged. Also, I would like to know that how much part of > > ndimage is to be ported under this project since it is a big module. > > Kindly provide me some suggestions and guide me through this. > Hi Aman, the idea is to port the whole module. I think you should make a plan for that. We are aware that it's a large job, and whether or not it's feasible to complete all of ndimage within one GSoC depends on how fast you will go. Compared to porting scipy.cluster last year I'd guess that ndimage is >2x more work. However, Richard last year implemented new features in addition to completing the port, so for a fast student I expect it to be possible to complete the whole module. I would expect the main challenge to be to make the Cython version (close to) as fast as the current C code. > Thanks for your interest in GSoC 2015! Please have a look at the > issues for scikit-image, and try and submit a few PRs so that we can > work together and get to know you a bit better. > @all: it's maybe good to know that Aman has already submitted 5 PRs to Scipy (4 small ones merged, 1 larger one for which the bottleneck is on our side): https://github.com/scipy/scipy/pulls?q=is%3Apr+author%3Abewithaman+is%3Aclo… @Aman: the majority of expertise and mentoring power will likely come from the scikit-image devs, so it would be good to submit a few scikit-image PRs as Stefan says. Feel free to ping me - I read the scikit-image mailing list but not Github activity. Cheers, Ralf

1 0

COSFIRE Filters feature
by Ahmed Osman 14 Mar '15

14 Mar '15

Hi All, I am planning to implement the COSFIRE feature. I am new to contributing to scikit-image, so any form of mentorship is really valuable. Can some one let me know what I need to do for a smooth pull request merge? thanks

2 1

Re: SciPy 2015 Conference: Call for proposals
by Josh Warner 13 Mar '15

13 Mar '15

I can toss it around this weekend. Do we have a starting point, or should we work from scratch? Josh On Thursday, March 12, 2015 at 3:24:06 AM UTC-5, stefanv wrote: > > On Wed, Mar 11, 2015 at 4:39 PM, Josh Warner wrote: > > I'm definitely in this year! Blocked off the entire week for SciPy. > > Excellent, Josh! > > http://scipy2015.scipy.org/ehome/115969/259288/?& > > It's a 4 hour tutorial, which is quite lengthy and will mean having to > add some extra material. > > Do you have any bandwidth to work on an abstract? The deadline is the > 16th, I think. > > Stéfan >

2 2

Apply segmentation to a large binary image
by Yuta Sato 13 Mar '15

13 Mar '15

Dear SKIMAGE Developers and Users: I want to use the following algorithm in a large binary image that does not fit into my PC memory. So, I am thinking to split my large image into tiles and apply algorithm one by one. However, the original border definition change when I do it in parts. I need the result as applied in original full image. How can I do it efficiently? skimage.segmentation.clear_border(image, buffer_size=0, bgval=0) Thanks for your ideas.

1 0

Re: Equivalent of watershed for cutting connected components of an image of particles?
by Adam Hughes 12 Mar '15

12 Mar '15

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...(a)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...(a)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 >>>> >>> -- >>> You received this message because you are subscribed to a topic in the >>> Google Groups "scikit-image" group. >>> To unsubscribe from this topic, visit >>> https://groups.google.com/d/topic/scikit-image/VL6SZTWvAz8/unsubscribe. >>> To unsubscribe from this group and all its topics, send an email to >>> scikit-image...(a)googlegroups.com <javascript:>. >> >> >>> For more options, visit https://groups.google.com/d/optout. >>> >> -- >> You received this message because you are subscribed to the Google Groups >> "scikit-image" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to scikit-image...(a)googlegroups.com <javascript:>. >> For more options, visit https://groups.google.com/d/optout. >> >

3 2

peak_local_max() Question.
by Claiborne Morton 12 Mar '15

12 Mar '15

Hey guys, I am currently using this function for water-shedding in a project of mine. I am a bit curious as to what the parameter, threshold_abs is actually doing. The website here: http://scikit-image.org/docs/dev/api/skimage.feature.html#skimage.feature.p… says "Minimum intensity of peaks", but I am not sure how this applies to a binary image where intensity of a pixel is either 1 or zero. When set the parameter equal to an integer, say 12, it removes the smaller particles from the image, which is nice because that is something I need to do, but I am just not sure why it does this. Below is a comparison of the results with and with out the parameter. Could someone please explain what is happening? Images are attached for: With threshold_abs = 12 Without threshold_abs (I assume default is threshold_abs = zero?)

3 3

Re: hough ellipse fit inaccurate?
by Arno Dietz 12 Mar '15

12 Mar '15

Hi Stéfan, I don't know if I did something wrong. But I think there are not that much possibilities to do something wrong with canny. I also just realised.. when I use cv2.fitEllipse() with the same canny input, the ellipses are detected very accurate with no outliers. So maybe canny is not the problem? Regards, Arno

1 0

Re: SciPy 2015 Conference: Call for proposals
by Josh Warner 12 Mar '15

12 Mar '15

I'm definitely in this year! Blocked off the entire week for SciPy. Josh On Wednesday, March 11, 2015 at 2:24:02 PM UTC-5, stefanv wrote: > > On Mon, Mar 9, 2015 at 5:19 PM, Tony Yu wrote: > > SciPy 2015 is requesting proposals for tutorials, talks, and posters for > > this year's conference. Note that there's a mini-symposium on > > "Visualization, Vision and Imaging", so this year will be particularly > > relevant for people here. > > I am interested in presenting a tutorial this year, but will be gone > most of June, so I need a partner in crime to share in the fun. Any > volunteers? > > Stéfan >

2 1