scikit-image November 2013

scikit-image@python.org

24 participants
88 discussions

Re: Advice on improving a analysis on images of nanoparticles
by Brickle Macho 20 Nov '13

20 Nov '13

I can always adapt this example (http://pythonvision.org/basic-tutorial) which uses pymorph and mahotaos to counting nuceli and segments the image as a gallery example for skimage (obviously acknowledging the original tutorial). Or is it bad form to copy/use another example. Michael. -- On 20/11/2013 2:13 pm, StÃ¯Â¿Â½fan van der Walt wrote: > > On 20 Nov 2013 07:33, "Juan Nunez-Iglesias" <jni.soma(a)gmail.com > <mailto:jni.soma@gmail.com>> wrote: > > > > I'm guessing you are applying label() directly to your image, which > is not the right way to use it. > > Looks like isolating objects is a common problem. Time for another > gallery example? We already have the coins, but perhaps something more > realistic with some biological data. > > StÃ¯Â¿Â½fan > > -- > 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/groups/opt_out.

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Re: scikit-image paper
by Stéfan van der Walt 20 Nov '13

20 Nov '13

Hi Juan On Wed, Nov 20, 2013 at 3:19 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > > @stefanv, I've found a flaw in your structure: > I don't quite get the joke (doh). > I think it's worth spending a bit of time on the actual outline (e.g. bullet points on each section), before launching into writing, to avoid redundancy. We can do this directly on the github template. For example, I would add my chromosome finding example (with code) to the gallery/science applications. Sure, make a few suggestions here then we can pen down the outline. > Speaking of development practices, I've recently noticed that there's a bit of heterogeneity in the API, with some parts being object-oriented in style and others (most) being functional, which is my preference. Do we want to emphasise that this is the preferred style? I think the majority of the library consists of functions, unless there is a big benefit to doing it differently. Can you elaborate? Stéfan

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Re: scikit-image paper
by Juan Nunez-Iglesias 20 Nov '13

20 Nov '13

@stefanv, I've found a flaw in your structure: [image: Inline image 1] =P Section 2 sounds to me like it would be made of examples, maybe merged with 3? I think it's worth spending a bit of time on the actual outline (e.g. bullet points on each section), before launching into writing, to avoid redundancy. We can do this directly on the github template. For example, I would add my chromosome finding example (with code) to the gallery/science applications. Speaking of development practices, I've recently noticed that there's a bit of heterogeneity in the API, with some parts being object-oriented in style and others (most) being functional, which is my preference. Do we want to emphasise that this is the preferred style? +1 for a roadmap section. Juan. On Wed, Nov 20, 2013 at 9:57 PM, Johannes Schönberger <jsch(a)demuc.de> wrote: > > I was thinking around 4 to 5 pages or so? > > Probably also a question of funding and if the journal charges for > excessive page lengths...? > > > Volunteering for sections: I will do the big picture overview > > (introduction + motivation) for now. > > > > I could do the Development practice and parts of the gallery? > > -- > 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/groups/opt_out. >

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Re: Fun with skimage
by Juan Nunez-Iglesias 20 Nov '13

20 Nov '13

Haha it took me a while to realise that it was within a notebook!!! I was like, looks pretty much identical to the viewer to me... =P That's bloody awesome, can't wait to use it! Juan. PS: Brian, please look at my recent PR<https://github.com/scikit-image/scikit-image/pull/810>for the viewer to get output from overlays. Would be excellent to get the same capability from this! On Wed, Nov 20, 2013 at 9:16 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > How cool is this? > > ---------- Forwarded message ---------- > From: Brian Granger > Date: Fri, Nov 1, 2013 at 11:43 PM > Subject: Fun with skimage > > I am working on some demos of the new IPython widget stuff and wrote a > simple skimage one. Thought you might find this interesting. Should be > pretty trivial to re-write the skimage viewer/plugin stuff using > this... > > Cheers, > > Brian > > -- > Brian E. Granger > Cal Poly State University, San Luis Obispo > bgranger(a)calpoly.edu and ellisonbg(a)gmail.com > > -- > 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/groups/opt_out. >

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Re: scikit-image paper
by Johannes Schönberger 20 Nov '13

20 Nov '13

> I was thinking around 4 to 5 pages or so? Probably also a question of funding and if the journal charges for excessive page lengths...? > Volunteering for sections: I will do the big picture overview > (introduction + motivation) for now. > I could do the Development practice and parts of the gallery?

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Re: scikit-image paper
by Johannes Schönberger 20 Nov '13

20 Nov '13

> Let's do first drafts, and then review and rework one another's sections? +1

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Re: scikit-image paper
by Johannes Schönberger 20 Nov '13

20 Nov '13

> I am hesitant to do that, because we expressly decided not have > feature-hunting as a goal. Speed comparisons are fine: it will > probably show that we are comparable, but not the fastest (not > currently one of our primary aims--but that could change in the > future). Just an idea… I’m also hesitant as it is always very difficult to compare functions, which itself have different parameters and options. > 1. Introduction and motivation > 2. Purpose > a) Research > b) Education > c) Industry > 3. Gallery of examples > 4. Development practices > 5. Conclusion Looks like a sane choice. Another idea: „Outlook & Future roadmap“? Splitting up the sections is a good idea, I think, although the text may sound a bit conglomerate as everyone has a different style and level of writing. So, I absolutely encourage you to correct me. Johannes

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Fwd: Fun with skimage
by Stéfan van der Walt 20 Nov '13

20 Nov '13

How cool is this? ---------- Forwarded message ---------- From: Brian Granger Date: Fri, Nov 1, 2013 at 11:43 PM Subject: Fun with skimage I am working on some demos of the new IPython widget stuff and wrote a simple skimage one. Thought you might find this interesting. Should be pretty trivial to re-write the skimage viewer/plugin stuff using this... Cheers, Brian -- Brian E. Granger Cal Poly State University, San Luis Obispo bgranger(a)calpoly.edu and ellisonbg(a)gmail.com

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Re: scikit-image paper
by Stéfan van der Walt 20 Nov '13

20 Nov '13

On Wed, Nov 20, 2013 at 11:55 AM, Johannes Schönberger <jsch(a)demuc.de> wrote: > Maybe a feature / speed comparison with other libs (primarily Matlab, maybe Mahotas,...)? I am hesitant to do that, because we expressly decided not have feature-hunting as a goal. Speed comparisons are fine: it will probably show that we are comparable, but not the fastest (not currently one of our primary aims--but that could change in the future). Stéfan

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Re: scikit-image paper
by Johannes Schönberger 20 Nov '13

20 Nov '13

Maybe a feature / speed comparison with other libs (primarily Matlab, maybe Mahotas,...)? > Am 20.11.2013 um 10:50 schrieb "Stéfan van der Walt" <stefan(a)sun.ac.za>: > >> On Wed, Nov 20, 2013 at 11:06 AM, Johannes Schönberger <jsch(a)demuc.de> wrote: >> So, how should we get started with this? Any roadmap / plan? > > Shall we split the paper into sections, and each take responsiblity > for part of it? > > Something like: > > 1. Introduction and motivation > 2. Purpose > a) Research > b) Education > c) Industry > 3. Gallery of examples > 4. Development practices > 5. Conclusion > > Ideas welcome. A slightly more exciting structure could be more fun > to write, but this will get the job done. > > 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/groups/opt_out. >

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scikit-image November 2013