Mailman 3 March 2014 - scikit-image

Feature freeze for 0.10
by Johannes Schönberger March 16, 2014

March 16, 2014

Hi everyone, I suggest to stop merging new features at this moment until we release 0.10. There are lot’s of new features on the PR wait list, but merging them just before releasing 0.10 is imo not wise; we want a stable release. Let’s defer them for 0.11 and work hard to fix the remaining issues for 0.10. We already managed to make this list shorter: https://github.com/scikit-image/scikit-image/issues?milestone=3&state=open Johannes

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Re: Code Coverage?
by Stéfan van der Walt March 14, 2014

March 14, 2014

On 14 Mar 2014 06:08, "Ronnie Ghose" <ronnie.ghose(a)gmail.com> wrote: > > so why don't we use Code Climate / CircleCI / similar? We do: have a look at any PR, and you'll see a comment by Coveralls. You can also visit the project directly at coveralls.io. Stéfan

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Code Coverage?
by Ronnie Ghose March 14, 2014

March 14, 2014

so why don't we use Code Climate / CircleCI / similar?

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Re: ANN: SciPy 2014 Conference, July 6th - 12th, Austin, TX!
by Tony Yu March 14, 2014

March 14, 2014

On Mar 13, 2014 3:47 AM, "Juan Nunez-Iglesias" <jni.soma(a)gmail.com> wrote: > > Tony, just to be clear, can I put you down as additional speaker? Yes, count me in! Johannes, how's it looking for you coming? Do you want to be listed too? =) > > > > On Mon, Mar 10, 2014 at 8:26 AM, Tony Yu <tsyu80(a)gmail.com> wrote: >> >> I started sketching out an IPython notebook for a talk, but I didn't get too far (see attached). I also have a tutorial proposal from last year that I've attached. There might be some useful bits in some of it. >> >> Best, >> -Tony >> >> >> On Sun, Mar 9, 2014 at 3:47 AM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: >>> >>> I am submitting a science talk proposal *and* writing up grant apps, *but* I was really looking forward to this so I'll try to get something in. If someone (Emmanuelle?) has some pre-existing materials, that would be helpful! =) >>> >>> Juan. >>> >>> >>> On Sun, Mar 9, 2014 at 1:39 AM, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: >>>> >>>> On 8 Mar 2014 21:44, "Tony Yu" <tsyu80(a)gmail.com> wrote: >>>> > >>>> > I didn't realize the tutorial deadline was coming up in a week. Unfortunately, my next week will be busy, so I won't have much time to put together a tutorial proposal. Anyone else interested writing something up? >>>> >>>> It's looking less likely that I'll be able to attend, so unfortunately I won't be able to do it this time around. >>>> >>>> Regards >>>> Stéfan >>>> >>>> -- >>>> 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+unsubscribe(a)googlegroups.com. >>>> 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+unsubscribe(a)googlegroups.com. >>> 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+unsubscribe(a)googlegroups.com. >> 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+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/d/optout.

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robust ring (and circle) detection algorithm
by Eldad Afik March 13, 2014

March 13, 2014

Dear Devs, In the process of tracking objects under the microscope I was confronted with an image analysis problem, for which I could not find a satisfactory solution in איק standard scientific packages (nor in the literature survey I made). At the time I started this, scikit-image did not include a circle Hough transform and OpenCV's was not good enough. I ended up developing an algorithm myself, which can be regarded as an off-spring of the circle Hough transform. I summarised the work in a manuscript titled: "*Robust and highly performant ring detection algorithm for 3d particle tracking using 2d microscope imaging*" (a pre-print is available at arXiv:1310.1371 <http://arxiv.org/abs/1310.1371>). NB, it was written minded at potential users and applications rather than computer scientists, which I am not. I would like to make the code publicly available. I believe it may be beneficial to the scikit-image community and users as a practical alternative to the current Standard Circle Hough transform. I contacted Stéfan van der Walt, who expressed interest in the algorithm. I would be grateful to have your feedback, any input would be helpful! With kind thanks to all contributors, Eldad -- Eldad Afik Physics of Complex Systems Weizmann Institute of Science *Some technical notes:* A* typical example *of the images I need to analyse can be found in the manuscript arXiv:1310.1371 <http://arxiv.org/abs/1310.1371> (Fig. 1a as well as S2a). The *results* of the software I wrote exhibit a detection rate which exceeds 94% and have only 1% false-detection, providing sub-pixel accuracy. The conceptual steps in making the algorithm* robust* are sketched in Fig. 2. The main steps to make it* efficient*, both in execution-time as well as memory consumption, are outlines on page 8; more technical details in this respect can be found in the "Supporting Information" Text section. The "methods" section of the manuscript provides some details regarding the *benchmarking*.

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Re: ANN: SciPy 2014 Conference, July 6th - 12th, Austin, TX!
by Juan Nunez-Iglesias March 13, 2014

March 13, 2014

Tony, just to be clear, can I put you down as additional speaker? Johannes, how's it looking for you coming? Do you want to be listed too? =) On Mon, Mar 10, 2014 at 8:26 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > I started sketching out an IPython notebook for a talk, but I didn't get > too far (see attached). I also have a tutorial proposal from last year that > I've attached. There might be some useful bits in some of it. > > Best, > -Tony > > > On Sun, Mar 9, 2014 at 3:47 AM, Juan Nunez-Iglesias <jni.soma(a)gmail.com>wrote: > >> I am submitting a science talk proposal *and* writing up grant apps, >> *but* I was really looking forward to this so I'll try to get something in. >> If someone (Emmanuelle?) has some pre-existing materials, that would be >> helpful! =) >> >> Juan. >> >> >> On Sun, Mar 9, 2014 at 1:39 AM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: >> >>> On 8 Mar 2014 21:44, "Tony Yu" <tsyu80(a)gmail.com> wrote: >>> > >>> > I didn't realize the tutorial deadline was coming up in a week. >>> Unfortunately, my next week will be busy, so I won't have much time to put >>> together a tutorial proposal. Anyone else interested writing something up? >>> >>> It's looking less likely that I'll be able to attend, so unfortunately I >>> won't be able to do it this time around. >>> >>> Regards >>> Stéfan >>> >>> -- >>> 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+unsubscribe(a)googlegroups.com. >>> 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+unsubscribe(a)googlegroups.com. >> 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+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/d/optout. >

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Re: A problem scikit-image could solve?
by Stéfan van der Walt March 13, 2014

March 13, 2014

On 13 Mar 2014 02:24, "Stuart Mumford" <stuart(a)mumford.me.uk> wrote: > > I agree, I think it could be a combined scipy effort. Going to need some Astropy magic for the data io (probably) and the Ra/Dec coordinate handling. Then we can use sklearn and potentially astroml once we have a detection routine? That sounds about right. Do you have ties to the AstroPy community? Perhaps someone there would be willing to lead the charge. Regards Stéfan

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Re: A problem scikit-image could solve?
by Deepak Pandian March 13, 2014

March 13, 2014

On Thu, Mar 13, 2014 at 6:02 AM, Ronnie Ghose <ronnie.ghose(a)gmail.com>wrote: > nope sounds accurate :) . we need to recruit more people then haha If you need people, I am in. I have no previous experience in ML, but I do foresee a lot of future experience:) and some free time this summer. -- With Regards, Deepak Pandian "Deconstructing world one piece at a time"

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Re: A problem scikit-image could solve?
by Josh Warner March 13, 2014

March 13, 2014

I don't have the time to coordinate a multi-Python project effort, but would gladly contribute. Agreed that ML will probably be required. On Wednesday, March 12, 2014 7:32:01 PM UTC-5, Ronnie Ghose wrote: > > nope sounds accurate :) . we need to recruit more people then haha > > > On Wed, Mar 12, 2014 at 8:23 PM, Stuart Mumford <stu...(a)mumford.me.uk<javascript:> > > wrote: > >> I agree, I think it could be a combined scipy effort. Going to need some >> Astropy magic for the data io (probably) and the Ra/Dec coordinate >> handling. Then we can use sklearn and potentially astroml once we have a >> detection routine? >> >> Stop me if this sounds crazy. >> >> Stuart >> On 13 Mar 2014 00:21, "Michael Aye" <kmicha...(a)gmail.com <javascript:>> >> wrote: >> >>> I would be joining. But I believe this is not winnable without ML, i.e. >>> only image processing won't do the job. >>> Michael >>> >>> >>> On Wednesday, March 12, 2014 4:53:26 PM UTC-7, Ronnie Ghose wrote: >>>> >>>> i'll go get my sword @stefan :) >>>> >>>> but great application of ML :3, NASA gets a lot of those false positive >>>> things >>>> >>>> >>>> On Wed, Mar 12, 2014 at 7:42 PM, Stéfan van der Walt <ste...(a)sun.ac.za>wrote: >>>> >>>>> On Thu, Mar 13, 2014 at 1:36 AM, Stuart Mumford <stu...(a)mumford.me.uk>wrote: >>>>> >>>>>> I would be willing to contribute but I am already run off my feet, so >>>>>> I really can't offer much. >>>>>> >>>>> >>>>> Josh? >>>>> >>>>> Stéfan >>>>> >>>>> -- >>>>> 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. >>>>> 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. >>> >> -- >> 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. >> > >

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Re: A problem scikit-image could solve?
by Ronnie Ghose March 13, 2014

March 13, 2014

nope sounds accurate :) . we need to recruit more people then haha On Wed, Mar 12, 2014 at 8:23 PM, Stuart Mumford <stuart(a)mumford.me.uk>wrote: > I agree, I think it could be a combined scipy effort. Going to need some > Astropy magic for the data io (probably) and the Ra/Dec coordinate > handling. Then we can use sklearn and potentially astroml once we have a > detection routine? > > Stop me if this sounds crazy. > > Stuart > On 13 Mar 2014 00:21, "Michael Aye" <kmichael.aye(a)gmail.com> wrote: > >> I would be joining. But I believe this is not winnable without ML, i.e. >> only image processing won't do the job. >> Michael >> >> >> On Wednesday, March 12, 2014 4:53:26 PM UTC-7, Ronnie Ghose wrote: >>> >>> i'll go get my sword @stefan :) >>> >>> but great application of ML :3, NASA gets a lot of those false positive >>> things >>> >>> >>> On Wed, Mar 12, 2014 at 7:42 PM, Stéfan van der Walt <ste...(a)sun.ac.za>wrote: >>> >>>> On Thu, Mar 13, 2014 at 1:36 AM, Stuart Mumford <stu...(a)mumford.me.uk>wrote: >>>> >>>>> I would be willing to contribute but I am already run off my feet, so >>>>> I really can't offer much. >>>>> >>>> >>>> Josh? >>>> >>>> Stéfan >>>> >>>> -- >>>> 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. >>>> 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+unsubscribe(a)googlegroups.com. >> 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+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/d/optout. >

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