scikit-image paper

[Juan Nunez-Iglesias]

Hi All,

I'm moving the discussion of the paper to the mailing list, as requested by Stefan. Here's a summary of the points so far:

* Josh brought up a Computational Science and Discovery special issue as not only a possible venue for the paper but a general renewed call to action about this paper.

* I vetoed the CSD special issue, despite having no formal power of veto =P, and suggested we opt instead for a fully open access journal, such as F1000Research.

* This and Johannes's email sparked a discussion about possible homes for it. Current suggestions:

   - F1000 Research

   - JMLR MLOSS [sklearn published here]

   - Journal of Open Research Software [mahotas published here]

   - Image Processing On Line (ipol.im)

   - Journal on Image and Video Processing (jivp.eurasipjournals.com)

* Stefan suggested as the author list, "currently active core contributors", but would certainly add more authors that have "made a substantial contribution to the package." I feel the same way and I imagine other current core devs would not object to this either. (?)

* There is a markdown template PR here:

https://github.com/scikit-image/scikit-image-paper/pull/2

Johannes gave a +1 to merging that, and I give another, so that makes +2, I'll merge following this email. =)

(I have a question about this point: for managing LaTeX papers on git, I have usually stuck to the convention of "1 sentence: 1 line". Do we want this for this paper, or wrap at 72 characters, or something else?)

I think that's everything, though I'm sure the discussion will continue!

Stefan asked me to elaborate on my suggestion of F1000. I must admit I don't know much about the other journals on the list, and would need to look into them. Things that I expect from our eventual home are:

 - open access.

 - CC or similar licensing that allows text mining applications.

Further niceties offered by F1000Res:

 - papers published immediately as preprint.

 - open peer review

 - once two reviewers have signed off on the paper, it is considered "peer reviewed". Reviewers can request modifications, and full paper and revision history is maintained.

 - peer reviewed articles are indexed by PubMed.

Essentially, the review model is quite similar to the GitHub PR process, which sounds great to me. PeerJ offers a similar (identical?) model, but is currently not LaTeX friendly, which pretty much rules it out for this.

Juan.

[Stéfan van der Walt]

On Mon, Nov 18, 2013 at 3:23 AM, Juan Nunez-Iglesias <jni....@gmail.com> wrote:
> * This and Johannes's email sparked a discussion about possible homes for
> it. Current suggestions:
> - F1000 Research

I'm a bit concerned by what I read here:

http://scholarlykitchen.sspnet.org/2013/01/15/pubmed-and-f1000-research-unclear-standards-applied-unevenly/

> - JMLR MLOSS [sklearn published here]

Impact factor is about 3.4, which at least gives some indication that
its content is valued.

> - Journal on Image and Video Processing (jivp.eurasipjournals.com)

And about 0.5 for this one.

Let's stick to using wrapped lines, otherwise editing using our normal
configurations becomes painful.

Stéfan

[Juan Nunez-Iglesias]

Hey Stéfan,

On Mon, Nov 18, 2013 at 6:13 PM, Stéfan van der Walt <ste...@sun.ac.za> wrote:

>    - F1000 Research

I'm a bit concerned by what I read here:
http://scholarlykitchen.sspnet.org/2013/01/15/pubmed-and-f1000-research-unclear-standards-applied-unevenly/

Scholarly Kitchen have it in for open access in general and seem to think there is nothing wrong with the business-as-usual model of scientific publishing. I imagine that this is not true of the present list of authors, but am happy to be corrected. Just have a quick browse of their past posts and try to find something positive about OA.

You can just read a few of Fernando Perez's blog posts, particularly the recent one about the Sloan/Moore data science initiative, to find out what I think of business-as-usual science and publishing.

Quick rebuttals of the post's two main points:

"unclear standards applied unevenly" "cynical and confusing mélange of incomplete editorial practices"

Yeah, welcome to peer review. This is true of all journals — the fact that it's not open doesn't mean it's not there.

"Yet, these rejected articles continue to be published on the F1000 Research site."

It's called a preprint. arXiv papers don't get taken down when they don't pass peer review (ditto for closed github PRs). Why should these? They are clearly marked as Rejected. F1000 Research is an experiment in openness in publishing and I think it's a worthwhile one.

Having said these things, it's definitely a risk publishing there. (My impression though is that scikit-image as a library speaks for itself and the choice of journal is a choice of what model we want to support, rather than which journal will be more prestigious.) But, more importantly, it seems that F1000 Research is indeed slanted towards the biological sciences; I was under the impression that it was a catchall journal. So, it might not be the best fit.

[rant over] =)

>    - JMLR MLOSS [sklearn published here]

Impact factor is about 3.4, which at least gives some indication that
its content is valued.

If we are going to worry about JIF, PLOS ONE has 3.7, and does accept papers from all disciplines. (You will also find a Scholarly Kitchen post about how a JIF of 3.7 is a sign that PLOS and open access are doomed.)

Currently my two top candidates then are JMLR MLOSS and PLOS ONE. (The latter does charge $1300 US per article.)

Let's stick to using wrapped lines, otherwise editing using our normal
configurations becomes painful.

Agreed.

Juan.

[Stéfan van der Walt]

On Mon, Nov 18, 2013 at 10:47 AM, Juan Nunez-Iglesias
<jni....@gmail.com> wrote:
> If we are going to worry about JIF, PLOS ONE has 3.7, and does accept papers
> from all disciplines. (You will also find a Scholarly Kitchen post about how
> a JIF of 3.7 is a sign that PLOS and open access are doomed.)

Thanks, I won't take Scholarly Kitchen too seriously then. I know
that impact factors are a lousy way (by itself) to determine where to
publish, but that's a whole other kettle of fish.

> Currently my two top candidates then are JMLR MLOSS and PLOS ONE. (The
> latter does charge $1300 US per article.)

Open access fees should not pose too much of a problem:

http://library.sun.ac.za/English/services/oa/Pages/su-oafund.aspx

Let's get started on some content!

I think we would do well to emphasize the following in the paper:

- Pythonic API
- Building block for reproducible research, use in academic world (we
need a list of publications of work that used skimage)
- Educational aspects (skimage.novice)
- Google Summer of Code contributions
- Use in industry (do we have examples here?)
- ... other ideas?

Stéfan

[Johannes Schönberger]

> Currently my two top candidates then are JMLR MLOSS and PLOS ONE.

+1

> Let's get started on some content!

+1, but I must mention that I might be short of time over the coming weeks as I am about to move to another continent, so unfortunately I have a ton of other things to do :-)

> I think we would do well to emphasize the following in the paper:
>
> - Pythonic API
> - Building block for reproducible research, use in academic world (we
> need a list of publications of work that used skimage)
> - Educational aspects (skimage.novice)
> - Google Summer of Code contributions
> - Use in industry (do we have examples here?)
> - ... other ideas?

- Extensive documentation (although the docs need some more „love“ for 0.10)
- Easy to use API for prototyping and testing algorithms (probably covered by "Pythonic API“)

I have mainly used skimage for prototyping, but did not directly mention it in a publication.

Johannes

[Adam Hughes]

It may be non-disclosable, but I know that Enthought may have some industrial examples.

[Marianne Corvellec]

Hello all,

What an exciting project!

On Monday, November 18, 2013 3:59:22 AM UTC-5, Stefan van der Walt wrote:

Let's get started on some content!

I think we would do well to emphasize the following in the paper:

- Pythonic API
- Building block for reproducible research, use in academic world (we
need a list of publications of work that used skimage)
- Educational aspects (skimage.novice)
- Google Summer of Code contributions
- Use in industry (do we have examples here?)
- ... other ideas?

I believe it would be fitting to cite Dharhas Pothina's recent work.

Stéfan (and possibly others) know more about it than I do, but it could be considered both academic and industrial.

I believe Tony S Yu would have lots to share as well. :)

Marianne

[Tony Yu]

Thanks for pinging me.

Unfortunately, the current project I'm working on isn't public (at least when I last checked). There's another enthought project that is public: I'll ask around to see if it's OK to make a direct reference to the project.

-T

[Johannes Schönberger]

So, how should we get started with this? Any roadmap / plan?

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[Stéfan van der Walt]

On Wed, Nov 20, 2013 at 11:06 AM, Johannes Schönberger <js...@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

[Johannes Schönberger]

Maybe a feature / speed comparison with other libs (primarily Matlab, maybe Mahotas,...)?

> Am 20.11.2013 um 10:50 schrieb "Stéfan van der Walt" <ste...@sun.ac.za>:
>
>> On Wed, Nov 20, 2013 at 11:06 AM, Johannes Schönberger <js...@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
>

[Stéfan van der Walt]

On Wed, Nov 20, 2013 at 11:55 AM, Johannes Schönberger <js...@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

[Johannes Schönberger]

> 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

[Stéfan van der Walt]

On Wed, Nov 20, 2013 at 12:41 PM, Johannes Schönberger <js...@demuc.de> wrote:
> 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.

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

Stéfan

[Johannes Schönberger]

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

+1

[Johannes Schönberger]

Any plans on how long each of those sections and the whole article should be?

[Stéfan van der Walt]

On Wed, Nov 20, 2013 at 12:46 PM, Johannes Schönberger <js...@demuc.de> wrote:
> Any plans on how long each of those sections and the whole article should be?

I was thinking around 4 to 5 pages or so?

Volunteering for sections: I will do the big picture overview
(introduction + motivation) for now.

Stéfan

[Johannes Schönberger]

> 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?

[Juan Nunez-Iglesias]

@stefanv, I've found a flaw in your structure:

=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.

[Stéfan van der Walt]

Hi Juan

On Wed, Nov 20, 2013 at 3:19 PM, Juan Nunez-Iglesias <jni....@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

[Johannes Schönberger]

> 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?

The functional style is imo the preferred style, especially for raw image processing functionality, which only takes some image and produces some output.

But there are parts where object-oriented style makes a lot of sense. I only know of the following excessive cases:

- skimage.transform.GeometricTransforms
- skimage.measure.fit.*Models
- skimage.viewer

And in some places internally, mostly where actually appropriate. But only the interface is relevant in my opinion.

I can only speak for the estimation functionality in skimage, where objects help a lot to make a sane implementation - a purely functional interface would be horribly complicated.

Maybe it’s easier to keep track of the status of the discussion for everyone with a new PR: https://github.com/scikit-image/scikit-image-paper/pull/3

Please, raise your voice for more ideas and if you are volunteering for a section :-)

[Adam Hughes]

Is there currently a preferred way to cite scikit image while this paper is in the works?

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[Stéfan van der Walt]

On Wed, Nov 20, 2013 at 7:52 PM, Adam Hughes <hughes...@gmail.com> wrote:
> Is there currently a preferred way to cite scikit image while this paper is
> in the works?

I think unfortunately not until we at least upload the pre-print on arxiv.

Stéfan

[Stuart Mumford]

The paper I have contributed to that uses skimage references the website.

Stuart

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[Tony Yu]

On Mon, Nov 18, 2013 at 10:49 PM, Tony Yu <tsy...@gmail.com> wrote:

On Mon, Nov 18, 2013 at 8:50 PM, Marianne Corvellec <marianne....@ens-lyon.org> wrote:

<snip> 

I believe Tony S Yu would have lots to share as well. :)

 

Thanks for pinging me.

Unfortunately, the current project I'm working on isn't public (at least when I last checked). There's another enthought project that is public: I'll ask around to see if it's OK to make a direct reference to the project.

Unfortunately, it's a no-go on mentioning the specific companies we've worked with, but its OK to say something like "Enthought, Inc uses scikit-image extensively in their consulting projects related to geophysics and microscopy".

-T

[Stéfan van der Walt]

On Thu, Nov 21, 2013 at 6:39 AM, Tony Yu <tsy...@gmail.com> wrote:
> Unfortunately, it's a no-go on mentioning the specific companies we've
> worked with, but its OK to say something like "Enthought, Inc uses
> scikit-image extensively in their consulting projects related to geophysics
> and microscopy".

That's great, thank you! Could I use [1] as a reference?

Stéfan

[1] Personal communications with Tony S Yu, <insert title> [or insert
other name here]

[Tony Yu]

On Thu, Nov 21, 2013 at 12:30 AM, Stéfan van der Walt <ste...@sun.ac.za> wrote:

On Thu, Nov 21, 2013 at 6:39 AM, Tony Yu <tsy...@gmail.com> wrote:
> Unfortunately, it's a no-go on mentioning the specific companies we've
> worked with, but its OK to say something like "Enthought, Inc uses
> scikit-image extensively in their consulting projects related to geophysics
> and microscopy".

That's great, thank you!  Could I use [1] as a reference?

Oops, I forgot to reply to this. Yes, definitely.

-Tony

 

Stéfan

[1] Personal communications with Tony S Yu, <insert title> [or insert
other name here]

[Johannes Schönberger]

Ping to all involved people. what's the status in this project?

[Stéfan van der Walt]

Johannes, sorry for the delay on this; the paper is a top priority for me, and I should have quite a bit of time to work on this starting Sunday evening.

[Johannes Schönberger]

Good to hear.

Let me know how to improve the Development section and I could certainly contribute another example - not sure how many examples we want to include?

On Jan 18, 2014, at 4:30, Stéfan van der Walt <ste...@sun.ac.za> wrote:

> Johannes, sorry for the delay on this; the paper is a top priority for me, and I should have quite a bit of time to work on this starting Sunday evening.
>
>

[Juan Nunez-Iglesias]

Thanks for the ping, Johannes! I myself dropped the ball on this but ready to pick it up again! 

[Johannes Schönberger]

@Juan That'd be great :-)

[François Boulogne]

Hi,

I think we should decide where and how we write codes, in the text with
a snippet style and/or at the end with a full code.
I don't know how it depends on the journal where you want to submit the
paper. Have you reached a consensus about that?

Thank you.
Best.

--
François Boulogne.
http://www.sciunto.org
GPG fingerprint: 25F6 C971 4875 A6C1 EDD1 75C8 1AA7 216E 32D5 F22F

[Stéfan van der Walt]

On Fri, 24 Jan 2014 17:57:17 -0500, François Boulogne wrote:
> I think we should decide where and how we write codes, in the text with
> a snippet style and/or at the end with a full code.
> I don't know how it depends on the journal where you want to submit the
> paper. Have you reached a consensus about that?

If you want to show something specific, e.g. the simplicity of building a
pipeline, for which you need just 3-5 lines of code, then it should probably
go inline. If it is a longer snippet, attach it at the end or perhaps think
whether it should be included at all.

We can very easily write an IPython notebook and simply reference that from
the paper for examples.

Stéfan

[Adam Hughes]

Hi guys,

Just a curiosity following up on the notebook question:  Is there a standard practice to submitting journal articles with iPython notebooks?  We were looking to do the same with a few papers in our lab and wondered if this was common yet, if there were guidelines set forth by the journals to this regard, and if only certain journals accepted notebook as accompanying materials.

[Stéfan van der Walt]

Hi Adam

On Mon, 27 Jan 2014 12:53:49 -0800, Adam Hughes wrote:
> Just a curiosity following up on the notebook question: Is there a
> standard practice to submitting journal articles with iPython notebooks?
> We were looking to do the same with a few papers in our lab and wondered
> if this was common yet, if there were guidelines set forth by the journals
> to this regard, and if only certain journals accepted notebook as
> accompanying materials.

Perhaps have a chat to Konrad Hinsen about his ActivePapers project:

http://python.6.x6.nabble.com/Interfacing-ActivePapers-with-IPython-notebooks-td5044882.html

Regards
Stéfan

[Juan Nunez-Iglesias]

Hi all,

Although we need a paper before we need to find a home for it, I came across this blog post from PeerJ, which appears to be moving up in the world! Also, they apparently accept latex submissions, even if they don't provide a template.

http://blog.peerj.com/post/74392709695/two-reviews-of-peerj

Just thought I'd add the journal to the pile.

Juan.

Stéfan

[Juan Nunez-Iglesias]

On Tue, Jan 28, 2014 at 11:48 PM, Juan Nunez-Iglesias <jni....@gmail.com> wrote:

Also, they apparently accept latex submissions, even if they don't provide a template.

Aaaaand, on cue:

http://blog.peerj.com/post/74820148558/peerj-partners-with-writelatex

[Stéfan van der Walt]

Hi all,

Working on the scikit-image paper, I've had some further thoughts
about authorship (yes, this is much harder than writing the paper :).

I suggest the following (what I consider to be) fair guideline:

1) Anyone who contributes significantly to the writing of the paper
gets their name in the authors list
2) All other contributors are included in the "scikit-image contributors" author

To me, this feels like the fairest way to reward those who time into
writing the paper, while also giving credit to all of those whose work
is described therein. I felt uncomfortable adding all "core
contributors" to the authors list, since that concept is becoming more
and more nebulous with GitHub PRs.

I'd like to hear your thoughts.

Stéfan

[Johannes Schönberger]

Fully agree on all your thoughts!

[Johannes Schönberger]

I also thought about contributing one example covering feature detection, extraction, matching and some simple image stitching using projective transformations... your thoughts? Is this too long?

[Stéfan van der Walt]

On Wed, Feb 5, 2014 at 4:01 PM, Johannes Schönberger <js...@demuc.de> wrote:
> I also thought about contributing one example covering feature detection, extraction, matching and some simple image stitching using projective transformations... your thoughts? Is this too long?

I think that is a powerful usage example, and doesn't need to take up
too much space--let's do it.

[Stéfan van der Walt]

On Wed, Feb 5, 2014 at 4:25 PM, Stéfan van der Walt <ste...@sun.ac.za> wrote:
> On Wed, Feb 5, 2014 at 4:01 PM, Johannes Schönberger <js...@demuc.de> wrote:
>> I also thought about contributing one example covering feature detection, extraction, matching and some simple image stitching using projective transformations... your thoughts? Is this too long?

By the way, you can make really nice panoramas if you export the
transformed images to TIFF and stitch them together using "enblend".
Since blending is not really in our scope, it's probably fine to use
that as the final component, if you want a particularly shiny result.

Stéfan

[Juan Nunez-Iglesias]

I'm not positive about this new criterion. My gut feeling is that it should be a bit nuanced on either side. For example, even if Tony doesn't write a single line for the paper, I still think he should be an author. Conversely, I don't think someone who has not thus far contributed a single line of code, issue, or tutorial should be able to jump in, write a few paragraphs, and be an author on the paper.

Having said that, I do agree that "core contributors" is too nebulous, so, for example, I'd be perfectly comfortable having François on the author list.

Juan.

[Tony Yu]

On Wed, Feb 5, 2014 at 10:49 PM, Juan Nunez-Iglesias <jni....@gmail.com> wrote:

I'm not positive about this new criterion. My gut feeling is that it should be a bit nuanced on either side. For example, even if Tony doesn't write a single line for the paper, I still think he should be an author. Conversely, I don't think someone who has not thus far contributed a single line of code, issue, or tutorial should be able to jump in, write a few paragraphs, and be an author on the paper.

 As much as I love scikit-image, I hate writing academic papers (there's a reason I left academia!). I would feel a bit guilty having my name on the paper without contributing any text to it; I'm not sure yet if that guilt is strong enough to make me contribute to the writing (again, because I hate writing papers---I still love scikit-image).

In short, I would be fine if I were left off the authors list (assuming I haven't guilted myself into writing a section of the paper)---it would great to be listed, but I also think an author on a paper should contribute to the writing (... which, sadly, isn't always the case in academia... actually you don't even have to contribute that much to the research either... sorry I may still have some post-academia hang ups:P).

Best,

-Tony

P.S. Sorry I haven't contributed much to the paper discussion.

[Juan Nunez-Iglesias]

On Thu, Feb 6, 2014 at 4:05 PM, Tony Yu <tsy...@gmail.com> wrote:

(there's a reason I left academia!)

And here I thought it was greed! =P

I also think an author on a paper should contribute to the writing

The criterion for inclusion that is usually brandished about, and that I tend to agree with, is "significant intellectual contribution", where "significant" allows for some wiggle room. Even though that wiggle room is sometimes abused in academia, as you bitterly recall, I don't think there is any question about whether your contribution was significant.

[Stéfan van der Walt]

On Wed, Jan 29, 2014 at 12:43 AM, Juan Nunez-Iglesias
<jni....@gmail.com> wrote:
> Aaaaand, on cue:
> http://blog.peerj.com/post/74820148558/peerj-partners-with-writelatex

PeerJ is currently offering free publication (if you submit a
pre-print first) until March 31st:

http://blog.peerj.com/post/67476390580/free-publications-in-peerj

This does look very appealing. I am sure we can hit that deadline
(Johannes is done with his section, mine is nearing completion and we
have two examples in the works).

Stéfan

[Johannes Schönberger]

> This does look very appealing. I am sure we can hit that deadline
> (Johannes is done with his section, mine is nearing completion and we
> have two examples in the works).

What other sections do we need?

Introduction: Stefan

Usage examples: Francois 1, Stefan 2 (?)

Development practices: Johannes

Roadmap: ??? (me?)

Conclusion: (Stefan?)

[Stéfan van der Walt]

On Sat, 08 Feb 2014 10:00:59 -0500, Johannes Schönberger wrote:
> Usage examples: Francois 1, Stefan 2 (?)

Should you and I add the panorama example as #2?

> Roadmap: ??? (me?)

The roadmap is pretty much non-existent at the moment, I'm afraid.

> Conclusion: (Stefan?)

Sure, I'll write that.

We still need someone to do the sections on Education and Industry
Application.

Stéfan

[Johannes Schönberger]

> Should you and I add the panorama example as #2?

Yes, I'd be happy to work with you on that. One major first contribution to that example would be some suitable set of images for stitching :-) Do you have some in your collection, I couldn't find anything useful in my collection?

> The roadmap is pretty much non-existent at the moment, I'm afraid.

Remove the section entirely or can we come up with a roadmap?

>> Conclusion: (Stefan?)
> Sure, I'll write that.

Perfect. The same person should imo write the introduction and conclusion.

> We still need someone to do the sections on Education and Industry
> Application.

Yes, maybe Juan and Josh can collaborate on one example?

What was the status about the industry example from Tony?

[Stéfan van der Walt]

On Sat, 08 Feb 2014 18:21:55 -0500, Johannes Schönberger wrote:
> > Should you and I add the panorama example as #2?
>
> Yes, I'd be happy to work with you on that. One major first contribution to
> that example would be some suitable set of images for stitching :-) Do you
> have some in your collection, I couldn't find anything useful in my
> collection?

I've had a look at the ones in my collection, and I'm not too excited about
them. Let me mail a photographer friend and see.

> > The roadmap is pretty much non-existent at the moment, I'm afraid.
>
> Remove the section entirely or can we come up with a roadmap?

I don't have any immediate suggestions, other than the fact that I want to
make the gallery interactive soon.

> > We still need someone to do the sections on Education and Industry
> > Application.
>
> Yes, maybe Juan and Josh can collaborate on one example?

+1

> What was the status about the industry example from Tony?

He said we may mention that they use it, but that we cannot give screenshots.
I will also tweet and fish for some more.

Cheers
Stéfan

[Neil]

He said we may mention that they use it, but that we cannot give screenshots.
I will also tweet and fish for some more.

I saw your tweet, and I may be able to help with an industry application. At BT Imaging (http://www.btimaging.com/) we do photoluminescent imaging of silicon wafers. We use skimage for image processing (along with the other usual suspects, such as OpenCV, scipy.ndimage, cython, etc). What sort of information would you need? I wouldn't be able to give any low-level details of our algorithms, but perhaps some screenshots of the input & output. Let me know, and I'll run it past the CEO.

[Stéfan van der Walt]

Hi Neil

On Sat, 08 Feb 2014 22:15:24 -0800, Neil wrote:
> I saw your tweet, and I may be able to help with an industry application.
> At BT Imaging (http://www.btimaging.com/) we do photoluminescent imaging of
> silicon wafers. We use skimage for image processing (along with the other
> usual suspects, such as OpenCV, scipy.ndimage, cython, etc). What sort of
> information would you need? I wouldn't be able to give any low-level
> details of our algorithms, but perhaps some screenshots of the input &
> output. Let me know, and I'll run it past the CEO.

If you have a result that made significant use of skimage, then a picture of
that result with a description of what it depicts, as well as the role skimage
played, would be perfect. We do not need to know the exact details of the
algorithm.

Thanks very much for offering to help!

Stéfan

[Stéfan van der Walt]

On Sat, 08 Feb 2014 18:21:55 -0500, Johannes Schönberger wrote:

> Yes, I'd be happy to work with you on that. One major first contribution to
> that example would be some suitable set of images for stitching :-) Do you
> have some in your collection, I couldn't find anything useful in my
> collection?

I asked a friend and he has some photos for us--it may take a day or two to
get hold of them.

Stéfan

[Johannes Schönberger]

> I saw your tweet, and I may be able to help with an industry application. At BT Imaging (http://www.btimaging.com/) we do photoluminescent imaging of silicon wafers. We use skimage for image processing (along with the other usual suspects, such as OpenCV, scipy.ndimage, cython, etc). What sort of information would you need? I wouldn't be able to give any low-level details of our algorithms, but perhaps some screenshots of the input & output. Let me know, and I'll run it past the CEO.

Hi Neil, thanks for sharing this and this sounds great!

[Jérôme Kieffer]

On Sun, 9 Feb 2014 01:53:21 +0200

Stéfan van der Walt <ste...@sun.ac.za> wrote:

> > Yes, I'd be happy to work with you on that. One major first contribution to
> > that example would be some suitable set of images for stitching :-) Do you
> > have some in your collection, I couldn't find anything useful in my
> > collection?

I have plenty of panorama (already stitched) ... but raw images are
available if you need for the publication.

http://photo.terre-adelie.org/Panoramiques/html/dirindex.html

Cheers,
--
Jérôme Kieffer <goo...@terre-adelie.org>

[Stéfan van der Walt]

On Sun, Feb 9, 2014 at 7:41 PM, Jérôme Kieffer <goo...@terre-adelie.org> wrote:
> I have plenty of panorama (already stitched) ... but raw images are
> available if you need for the publication.
>
> http://photo.terre-adelie.org/Panoramiques/html/dirindex.html

That's awesome, thanks! We'll have a look through those and get in touch.

Would it be acceptable to distribute the images freely with attribution?

Stéfan

[Jérôme Kieffer]

On Sun, 9 Feb 2014 19:47:06 +0200

Stéfan van der Walt <ste...@sun.ac.za> wrote:

All those panorama (maybe there are 1 or 2 exceptions) have been
assembled from images I took myself. I can specify a licence, probably
CC-By it it fits you. Please take one without anybody on the image to
avoid issues with what we call "droit à l'image" in French... (and
doesn't exist in many counties: People appearing in content may have a
right to control use of their image and to maintain their privacy.)
http://fr.wikipedia.org/wiki/Droit_%C3%A0_l%27image

Those panorama were assembled using gimp (before 2004) then with the help of
Hugin. More recently I tested AutoPanoPro which is great while
proprietary...

Cheers,
--
Jérôme Kieffer <goo...@terre-adelie.org>

PS: I miss-used the word raw as they were all shout in JPEG mode.

[Juan Nunez-Iglesias]

Hi all,

1. I'm unsure about writing the education or industry sections of the paper, as I have little experience in either. I'm currently working on another research example. I think we can have two, since it's scikit-image! Who worked on the Novice module? They might be a good candidate for the Education section. And Neil might be your man for industry... =)

2. For stitching, some electron microscopy tiled images are another alternative, see e.g.: http://www.ini.uzh.ch/~acardona/trakem2_manual.html

3. Big fan of PeerJ so let's get this show started! =) 

Juan.

[Adam Hughes]

Hey guys,

I'm curious on your approach for introducing scikit image in the context of other available image processing libraries, without really stepping on anyone's toes so to speak.  I'm referring to several image processing tools in a paper we're working on, and certainly would be interested in hearing your take on this issue.

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