Mailman 3 February 2012 - scikit-image

Re: Object detection
by Zachary Pincus 25 Feb '12

25 Feb '12

> I'd love to be able to solve Siggi's problem--this is exactly the > kinds of things our toolbox should be able to address. Is there a template matching module? That'd be a good wish-list item for a simple cython implementation. (Convolution is easy, but sum-of-[absolute|squared]-differences can't be done through convolution alone, right? Or am I being daft?) Zach

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0.5 Release
by Stéfan van der Walt 25 Feb '12

25 Feb '12

Hi all, I'm slightly behind on the release, but I have to cut it before PyData this upcoming week, so if there's anything urgent that you'd like to go in still, please let me know by tomorrow. I'll try to push out the release Sunday evening, Pacific time. Thanks! Stéfan

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Re: Imshow and Linescan - first version
by Christoph Gohlke 25 Feb '12

25 Feb '12

On 2/25/2012 11:10 AM, Tony Yu wrote: > > 2012/2/24 StÃ¯Â¿Â½fan van der Walt <stefan(a)sun.ac.za <mailto:stefan@sun.ac.za>> > > On Fri, Feb 24, 2012 at 12:02 AM, Guillaume Gay > <guillaume(a)mitotic-machine.org > <mailto:guillaume@mitotic-machine.org>> wrote: > > I forked sckimage on github and pushed the plugin there: > > > > https://github.com/glyg/scikits-image/blob/master/skimage/io/_plugins/matpl… > > Cute! I like it. > > StÃ¯Â¿Â½fan > > > Hi Guillaume, > > Hmm, this is much more interesting than what I expected when you > mentioned a line scan tool. :) > > I made a PR to your repo, which I guess you already noticed (and > merged) and I have some more specific comments I want to add to your > PR, but I had some more general thoughts (i.e. probably not stuff that > should be implemented in this PR) that I want to post here: > > Plugin system > ------ > It might be nice to have some sort of plugin system for the image > viewer. That way, tools like this could be implemented a bit more > easily and, also, easily added to the viewer or ignored by the user. I > think someone mentioned on the list that scikits-image should be > careful not to stray too far into GUI tools (I could be completely > mis-representing the idea here), and I agree to an extent. > Nevertheless, I think providing a viewer that supplies *an > infrastructure* for creating GUI tools might be really valuable. I > haven't really thought through what this plugin system would look > like, so it may just be a pipe dream. > > TIFFFile Viewer > ------ > There was talk of integrating the viewer from TIFFFile---was the idea > to write a wrapper around the viewer (like Zach did for > `imread`/`imsave`) or to copy it into skimage and modify it. If it's > the latter, we should make sure that Christophe Gohlke is OK with that > (Christophe mentioned that it wouldn't make sense to fork TIFFFile > into skimage, but presumably, this would be different for > `tifffile.imshow` since we would likely want to modify it). > > Best, > -Tony Hi Tony, sure it's OK to take imview or parts of it out of tifffile.py. I'm not sure how much of its functionality applies to skimage, which seems to limit itself to well defined image formats. Tifffile has to deal with n-dimensional, planar, any bit depth per channel, two channel "RGB", and 16 bit paletted images. The tifffile.imshow function is a hack to provide a preview of such (often ambiguous) data. Christoph

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Re: downscaling float32 image to uint12 via scikits.img_as_uint()
by Sigmund 25 Feb '12

25 Feb '12

Am Samstag, 25. Februar 2012 17:46:33 UTC+1 schrieb Tony S Yu: > > Hi Siggi, > > It sounds like you may have a float32 image with values outside of the > assumed range of 0--1 (see user guide<http://scikits-image.org/docs/dev/user_guide/data_types.html>). > > correct! > A couple of solutions; unfortunately, both require you to run skimage from > github (there's been a lot of activity since the last release): > no issues with the 0.5dev installation and use so fare on Mac OSX 10.6.8 > * Assuming you have float values outside the range, use > `rescale_intensity`<http://scikits-image.org/docs/dev/api/skimage.exposure.html#rescale-intensi…> to > rescale your image to the correct range. (You can also do this manually > too, of course). > kept the float values since conversion is not needed anymore > * Use `threshold_otsu`<http://scikits-image.org/docs/dev/api/skimage.filter.html#threshold-otsu> from > skimage instead of mahotas. > works great! > Also, all conversion functions should now (i.e. github master) raise an > error when given a float image outside of the 0--1 range, so this shouldn't > happen in the future. > in my case they raise the error > Best, > -Tony > > Thanks! Great job! Siggi

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Re: Object detection
by Stéfan van der Walt 25 Feb '12

25 Feb '12

Hi Tony On Thu, Feb 23, 2012 at 7:57 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > I have a hough-circles implementation (which I've been meaning to > contribute). Unfortunately, my implementation does a pretty poor job when > there's a large range of circle size and when the circles are > close/overlapping. I'm not sure this is your implementation's fault--aren't the parameters just overly sensitive in general? I searched for a different parametrization, and found this paper on the arxiv: http://arxiv.org/abs/cs/0301001v1 Have you ever seen the Hough transform implemented using this formulation? (A(x^2 + y^2) + B(x) + C(y) + D). Maybe we're on to something :) I'd love to be able to solve Siggi's problem--this is exactly the kinds of things our toolbox should be able to address. Stéfan

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Re: Imshow and Linescan - first version
by Tony Yu 25 Feb '12

25 Feb '12

2012/2/24 Stéfan van der Walt <stefan(a)sun.ac.za> > On Fri, Feb 24, 2012 at 12:02 AM, Guillaume Gay > <guillaume(a)mitotic-machine.org> wrote: > > I forked sckimage on github and pushed the plugin there: > > > > > https://github.com/glyg/scikits-image/blob/master/skimage/io/_plugins/matpl… > > Cute! I like it. > > Stéfan > Hi Guillaume, Hmm, this is much more interesting than what I expected when you mentioned a line scan tool. :) I made a PR to your repo, which I guess you already noticed (and merged) and I have some more specific comments I want to add to your PR, but I had some more general thoughts (i.e. probably not stuff that should be implemented in this PR) that I want to post here: Plugin system ------ It might be nice to have some sort of plugin system for the image viewer. That way, tools like this could be implemented a bit more easily and, also, easily added to the viewer or ignored by the user. I think someone mentioned on the list that scikits-image should be careful not to stray too far into GUI tools (I could be completely mis-representing the idea here), and I agree to an extent. Nevertheless, I think providing a viewer that supplies *an infrastructure* for creating GUI tools might be really valuable. I haven't really thought through what this plugin system would look like, so it may just be a pipe dream. TIFFFile Viewer ------ There was talk of integrating the viewer from TIFFFile---was the idea to write a wrapper around the viewer (like Zach did for `imread`/`imsave`) or to copy it into skimage and modify it. If it's the latter, we should make sure that Christophe Gohlke is OK with that (Christophe mentioned that it wouldn't make sense to fork TIFFFile into skimage, but presumably, this would be different for `tifffile.imshow` since we would likely want to modify it). Best, -Tony

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Object detection
by Sigmund 25 Feb '12

25 Feb '12

Dear Group, I'm trying to do object detecting on images as shown on the end of the post. I tried to adapt the coin example in the gallery but the results are not good. My problem is that both the background (bg) and the objects have large variations in there gray value. By the way, these are tiny little ice spheres (30-100 microns) A second approach was to do a laplace filter and threshold the result but even there, the variability is to big (see below). Well, before I change the measurement technique (change bg) or start working on sorting out which group of segments form a sphere, I thought, I better ask some adepts in image processing if there is an easier way. Thanks in advance! Siggi <https://lh3.googleusercontent.com/-PeS-7pVfM6Y/T0T09jyQD5I/AAAAAAAAADs/s3N1…> <https://lh4.googleusercontent.com/-xhi_BdlNmS0/T0T5Mc56y8I/AAAAAAAAAD4/XRAL…>

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downscaling float32 image to uint12 via scikits.img_as_uint()
by Sigmund 25 Feb '12

25 Feb '12

Hi! its me again... I'm using the scikits.img_as_uint() function for downscaling a float32 gray scale image. The downscaling is needed to use the mahotas.thresholding.otsu() function. I noticed that the img_as_uint() function is not scaling the intensity. It looks like that in areas where the intensity is exceeding the uint16 space, it shows wrong values. Does it show 0+the exceeding part? Is the behavior volitional ? Siggi

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Re: Imshow and Linescan - first version
by Guillaume Gay 24 Feb '12

24 Feb '12

Hi Tony, Mea culpa, I forgot to attach the code: I forked sckimage on github and pushed the plugin there: https://github.com/glyg/scikits-image/blob/master/skimage/io/_plugins/matpl… Guillaume Le 23/02/2012 19:29, Tony Yu a écrit : > > > On Thu, Feb 23, 2012 at 6:22 AM, Guillaume Gay > <guillaume(a)mitotic-machine.org <mailto:guillaume@mitotic-machine.org>> > wrote: > > Hi all, > > Here is a first version of the linescan implementation. It sort of > works, but I have some issues: > > -the major one is that when I instantiate the LineScanInteractor > within the imshow() function definition, I don't catch the events > any more. So this is not usable in an interactive session. > > -I can't get the ticks on the linescan plot to update properly... > > -also there should be some kind of a reset mechanism, because if > the image is zoomed in, you can lost the handles of the line > > So if any one have a hint on how to do this... > > Meanwhile I can try to have this work in conjunction tifffile's > imshow (which should not be so complicated). > > With all that maybe it would be better to implement a subclass of > FigureCanvas, so that linescan appears only when a button (at the > bottom of the window) is pressed, and it is easy to add e.g. a > histogram plot or a contrast setter... what do you think? > > > Bye > > Guillaume > > > HI Guillaume, > > I don't actually see a link or attachment in this email. Could you > point me to the code you mention above? > > Thanks, > -Tony > > > Le 20/02/2012 12:11, Guillaume Gay a écrit : > > Ok, I can give it a try... > > Some questions then: > > - skivi is pure Qt, so must I keep it that way (no matplotlib > dependency)? > - skivi is good for RGB images, but not so much for > greyscale... Also data conversion from uint16 to uint8 turns > everything black (it set anything > 256 to 0), shall this be > corrected? > -Christoph Gohlke tifffile.imshow() is somehow closer to what > us microscopy guys are expecting (more suitable for those > greyscale multipage tiffs), though some features of the fancy > viewer such as the contrast settings, are great. Also it is a > pure matplotlib implementation and the intensity value reading > is already there. So my question is: > Are those tools needed by the general image analysis skimage > community are more by scientific tiff users? If the latest, my > guess is that building on top of matplotlib and Christoph's > implementation of imshow is a better tactic (plus it would be > more cross platform, as this can be a widget irrespective of > the backend). > > Cheers, > > Guillaume > > > > > Le 20/02/2012 08:04, Stéfan van der Walt a écrit : > > On Fri, Feb 17, 2012 at 6:53 AM, Guillaume Gay > <guillaume(a)mitotic-machine.org > <mailto:guillaume@mitotic-machine.org>> wrote: > > I just happen to code a simple linescan function, if > that helps... > > Thanks, Guillaume! If you could integrate this with the > fancy Qt > imshow to display the line, that would be wonderful, but > otherwise I'm > sure we'll still be able to use this code. > > Stéfan > > > >

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Re: GUI tools and upsizing
by Guillaume Gay 23 Feb '12

23 Feb '12

Ok, I can give it a try... Some questions then: - skivi is pure Qt, so must I keep it that way (no matplotlib dependency)? - skivi is good for RGB images, but not so much for greyscale... Also data conversion from uint16 to uint8 turns everything black (it set anything > 256 to 0), shall this be corrected? -Christoph Gohlke tifffile.imshow() is somehow closer to what us microscopy guys are expecting (more suitable for those greyscale multipage tiffs), though some features of the fancy viewer such as the contrast settings, are great. Also it is a pure matplotlib implementation and the intensity value reading is already there. So my question is: Are those tools needed by the general image analysis skimage community are more by scientific tiff users? If the latest, my guess is that building on top of matplotlib and Christoph's implementation of imshow is a better tactic (plus it would be more cross platform, as this can be a widget irrespective of the backend). Cheers, Guillaume Le 20/02/2012 08:04, Stéfan van der Walt a écrit : > On Fri, Feb 17, 2012 at 6:53 AM, Guillaume Gay > <guillaume(a)mitotic-machine.org> wrote: >> I just happen to code a simple linescan function, if that helps... > Thanks, Guillaume! If you could integrate this with the fancy Qt > imshow to display the line, that would be wonderful, but otherwise I'm > sure we'll still be able to use this code. > > Stéfan >

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