Mailman 3 March 2015 - scikit-image

Re: skimage and opencv
by Emmanuelle Gouillart 22 Sep '16

22 Sep '16

Hi FranÃ¯Â¿Â½ois, that's an excellent question, and not a troll :-). Opencv is a very powerful library, but it focuses primarily on computer vision (feature detection and extraction, classification, ...), as opposed to image processing in general (with other tasks such as denoising, segmentation, ...). The other big difference is that skimage builds on numpy ndarrays, and uses the full power of the numpy API (including of course the basic facilities for processing arrays as images that come with numpy), as well as some of scipy functions (you could have added scipy.ndimage to your list -- a few functions in skimage are wrappers around scipy.ndimage, that exist for the sake of completeneness). One important consequence is that algorithms working for 3-d or even n-d images can be easily implemented in 3-d/n-d in skimage, whereas opencv is restricted to 2-D images (as far as I know). Thanks to the use of numpy arrays, the API of skimage is also quite pleasant for a numpy user, more than the API of opencv. A related difference is that skimage is written in python and cython, whereas opencv is a C++ library. The two libraries attract a different crowd of developers, and a Python/Cython toolkit based on numpy arrays is easier to develop and maintain inside the Scientific Python ecosystem. I'm sure that other devs/users will have things to add to this discussion! Cheers, Emmanuelle On Thu, Dec 27, 2012 at 02:06:08PM -0800, FranÃ¯Â¿Â½ois wrote: > Hi users and devs, > It came to my knowledge that another python library (based on C++ and C > codes) for image processing exists too : opencv > I understand that numpy intregrates some basic features and we need some > advanced features but I have the feeling that skimages is redoundant with > opencv in some ways. > What's the position of skimage about that? (Don't read this question as a > troll but like a real question). > I mean that similar features exist in both. Would not be possible to > reuse/integrate opencv or merge? what's the reason for keeping them apart? > My observation is there is 4 libraries to manipulate images: > * PIL > * numpy > * skimages > * opencv > That's a lot. > Cheers,

3 2

Improving HoG
by Martin Savc 17 Nov '15

17 Nov '15

I've been implementing my own HoG transform looking at different sources. While the implementation in scikit-image seems to lack certain features (multiple normalization schemes, general block overlap, Gaussian block window, trillinear interpolation/weighting of bin assignments,...) these don't seem to be that important, at least when applied to my current problem (eye blink analysis). Most of these would increase complexity, giving the implementation a complicated look, with little gain. I've also been looking into some practical improvements - integral histogram, separating the cell-block histogram feature to use it with other dense feature transforms such as LBP, a HoG visualization function that would render the visualization at higher resolutions that the original image. Would any of these be welcomed additions to scikit-image? Regards, Martin Savc PuppySaturation

3 3

Problems with coordinate ranges when doing conversion from LCH to LAB to RGB
by Matteo 16 Nov '15

16 Nov '15

A while ago I wrote a post on my blog with code on how to import in Python a colour palette in an ASCII file and convert it to a Matplotlib colormap: mycarta.wordpress.com/2014/04/25/convert-color-palettes-to-python-matplotli… Following that post I wrote a tutorial on a geoscience magazine on how to evaluate and compare colormaps using Python: wiki.seg.org/wiki/How_to_evaluate_and_compare_color_maps In the accompanying notebook I show how to convert a 256x3 RGB colormap to a 256x256x3 RGB image, then convert it to CIELAB using scikit-image's rgb2lab, then plot the 256x1 lightness (L) array to evaluate the colormaps perceptually. You can read the relevant extract of the notebook using this nbviewer link: http://nbviewer.ipython.org/urls/dl.dropbox.com/s/54zoax2qesb71wn/evaluate_… In that case scikit-image worked really well for me. Now I am trying to follow up with a new tutorial and I run into problems with the color space conversions. You can follow what I am trying to do in this other notebook extract: http://nbviewer.ipython.org/urls/dl.dropbox.com/s/noli66nzrlk0676/make_colo… The goal of this new tutorial is to show how to build colormaps from scratch using perceptual principles. I design a color palette in LCH (polar version of CIELAB) by keeping Chroma and Lightness fixed and interpolating Hue around the circle, then convert to LAB, then to RGB. As far as I know the code I wrote should work, but the result is a black colormap. I am thinking I got wrong one or more of the ranges for the LCH coordinates. I assumed L between (0,1), Ch between (0,1), and H between (0, 2*pi). Is that wrong, and if that's the case, what are the ranges? Many of them are not stated clearly in the documentation in here: http://scikit-image.org/docs/dev/api/skimage.color.html Is it possible to update the documentation to clearly state all ranges for all colour spaces. Thanks for your help. Matteo

3 5

Issue with morphological filters
by Matteo 16 Nov '15

16 Nov '15

*Issues with morphological filters when trying to remove white holes in black objects in a binary images. Using opening or filling holes on inverted (or complement) of the original binary.* Hi there I have a series of derivatives calculated on geophysical data. Many of these derivatives have nice continuous maxima, so I treat them as images on which I do some cleanup with morphological filter. Here's one example of operations that I do routinely, and successfully: # threshold theta map using Otsu method thresh_th = threshold_otsu(theta) binary_th = theta > thresh_th # clean up small objects label_objects_th, nb_labels_th = sp.ndimage.label(binary_th) sizes_th = np.bincount(label_objects_th.ravel()) mask_sizes_th = sizes_th > 175 mask_sizes_th[0] = 0 binary_cleaned_th = mask_sizes_th[label_objects_th] # further enhance with morphological closing (dilation followed by an erosion) to remove small dark spots and connect small bright cracks # followed by an extra erosion selem = disk(1) closed_th = closing(binary_cleaned_th, selem)/255 eroded_th = erosion(closed_th, selem)/255 # Finally, extract lienaments using skeletonization skeleton_th=skeletonize(binary_th) skeleton_cleaned_th=skeletonize(binary_cleaned_th) # plot to compare fig = plt.figure(figsize=(20, 7)) ax = fig.add_subplot(1, 2, 1) imshow(skeleton_th, cmap='bone_r', interpolation='none') ax2 = fig.add_subplot(1, 3, 2) imshow(skeleton_cleaned_th, cmap='bone_r', interpolation='none') ax.set_xticks([]) ax.set_yticks([]) ax2.set_xticks([]) ax2.set_yticks([]) Unfortunately I cannot share the data as it is proprietary, but I will for the next example, which is the one that does not work. There's one derivative that shows lots of detail but not continuous maxima. As a workaround I created filled contours in Matplotlib exported as an image. The image is attached. Now I want to import back the image and plot it to test: # import back image cfthdr=io.imread('filled_contour.png') # threshold using using Otsu method thresh_thdr = threshold_otsu(cfthdr) binary_thdr = cfthdr > thresh_thdr # plot it fig = plt.figure(figsize=(5, 5)) ax = fig.add_subplot(1, 1, 1) ax.set_xticks([]) ax.set_yticks([]) plt.imshow(binary_thdr, cmap='bone') plt.show() The above works without issues. Next I want to fill the white holes inside the black blobs. I thought of 2 strategies. The first would be to use opening; the second to invert the image, and then fill the holes as in here: http://scikit-image.org/docs/dev/auto_examples/plot_holes_and_peaks.html By the way, I found a similar example for opencv here http://stackoverflow.com/questions/10316057/filling-holes-inside-a-binary-o… Let's start with opening. When I try: selem = disk(1) opened_thdr = opening(binary_thdr, selem) or: selem = disk(1) opened_thdr = opening(cfthdr, selem) I get an error message like this: --------------------------------------------------------------------------- ValueError Traceback (most recent call last) <ipython-input-49-edc0d01ba327> in <module>() 1 #binary_thdr=img_as_float(binary_thdr,force_copy=False) ----> 2 opened_thdr = opening(binary_thdr, selem)/255 3 4 # plot it 5 fig = plt.figure(figsize=(5, 5)) C:\...\skimage\morphology\grey.pyc in opening(image, selem, out) 160 shift_y = True if (h % 2) == 0 else False 161 --> 162 eroded = erosion(image, selem) 163 out = dilation(eroded, selem, out=out, shift_x=shift_x, shift_y=shift_y) 164 return out C:\...\skimage\morphology\grey.pyc in erosion(image, selem, out, shift_x, shift_y) 58 selem = img_as_ubyte(selem) 59 return cmorph._erode(image, selem, out=out, ---> 60 shift_x=shift_x, shift_y=shift_y) 61 62 C:\...\skimage\morphology\cmorph.pyd in skimage.morphology.cmorph._erode (skimage\morphology\cmorph.c:2658)() ValueError: Buffer has wrong number of dimensions (expected 2, got 3) --------------------------------------------------------------------------- Any idea of what is going on and how I can fix it? As for inverting (or finding the complement) and then hole filling, that would be my preferred option. However, I have not been able to invert the image. I tried numpy.invert, adapting the last example from here: http://docs.scipy.org/doc/numpy/reference/generated/numpy.invert.html I tried something like this: http://stackoverflow.com/a/16724700 and this: http://stackoverflow.com/a/2498909 But none of these methods worked. Is there a way in scikit.image to do that, and if not, do you have any suggestions? Thank you, Matteo

2 7

Finding pairs of images (homologous chromosomes)
by Jean-Patrick Pommier 15 Nov '15

15 Nov '15

Dear All, I am trying to make pairs of images from the following set of images (chromosomes sorted by size after rotation). The idea is to make a feature vector for unsupervised classification (kmeans with 19 clusters) >From each chromosome an integral image was calculated: plt.figure(figsize = (15,15)) gs1 = gridspec.GridSpec(6,8) gs1.update(wspace=0.0, hspace=0.0) # set the spacing between axes. for i in range(38): # i = i + 1 # grid spec indexes from 0 ax1 = plt.subplot(gs1[i]) plt.axis('off') ax1.set_xticklabels([]) ax1.set_yticklabels([]) ax1.set_aspect('equal') image = sk.transform.integral_image(reallysorted[i][:,:,2]) imshow(image , interpolation='nearest') Then each integral image was flatten and combined with the others: Features =[] for i in range(38): Feat = np.ndarray.flatten(sk.transform.integral_image(reallysorted[i][:,:,2])) Features.append(Feat) X = np.asarray(Features) print X.shape The X array contains *38* lines and 9718 features, which is not good. However, I trried to submit these raw features to kmeans classification with sklearn using a direct example <http://scikit-learn.org/stable/modules/neighbors.html> : from sklearn.neighbors import NearestNeighbors nbrs = NearestNeighbors(n_neighbors=*19*, algorithm='ball_tree').fit(X) distances, indices = nbrs.kneighbors(X) connection = nbrs.kneighbors_graph(X).toarray() Ploting the connection graph shows that a chromosomes is similar to more than one ... - Do you think that integral images can be used to discriminate the chromosomes pairs? - If so, how to reduce the number of features to 10~20? (to get a better discrimination) Thanks for your advices. Jean-Patrick

3 5

Pattern and object recognition with COSFIRE
by Almar Klein 06 Jul '15

06 Jul '15

Hi all, Just wanted to mention an algorithm which I was very impressed by and which might be an awesome addition to scikit-image. The algorithm is called COSFIRE (Combination of Shifted Filter Responses). I saw a talk by Geore Azzopardi, who presented the use of the algorithm for object and patter recognition. I was very impressed with the quality of segmentation of the shown examples, but also with the wide variety of image data (e.g. retina images, traffic signs, hand-written characters, and more). The filter is inspired by how the brain processes visual information, and according to the author the algorithm is actually quite simple. The algorithm was the topic of his PhD and he's going to continue working on it in his new job. The code (in Matlab) is available, so it might be worth a shot to try and port it to Python. Some links: - PhD thesis: http://www.cs.rug.nl/~george/phd-thesis/ - Matlab code: nl.mathworks.com/matlabcentral/fileexchange/37395 - Paper in MIA: http://www.medicalimageanalysisjournal.com/article/S1361-8415%2814%2900136-… - Almar

5 4

ANN: imageio v1.0
by Almar Klein 03 Jul '15

03 Jul '15

Hi all, I'm pleased to announce version 1.0 of imageio - a library for reading and writing images. This library started as a spin-off of the freeimage plugin in skimage, and is now a fully-fledged library with unit tests and all. Imageio provides an easy interface to read and write a wide range of image data, including animated images, volumetric data, and scientific formats. It is cross-platform, runs on Python 2.x and 3.x, and is easy to install. Imageio is plugin-based, making it easy to extend. It could probably use more scientific formats. I welcome anyone who's interested to contribute! install: pip install imageio website: http://imageio.github.io release notes: http://imageio.readthedocs.org/en/latest/releasenotes.html Regards, Almar

4 12

Re: Pattern and object recognition with COSFIRE
by George Azzopardi 26 Jun '15

26 Jun '15

Dear all, I am pleased to see interest in the COSFIRE approach that I started during my PhD studies. The COSFIRE approach is a trainable pattern recognition approach which can be applied to several applications, including feature detection, object recognition and localization, image classification, contour detection and vessel segmentation. The selectively for a pattern of interest is automatically configured in a training process. The method involves several computations that are independent of each other, and thus it can be easily implemented using parallel programming (e.g. on a GPU). The original paper (http://www.cs.rug.nl/~george/articles/PAMI2013.pdf) combines information about the contours of the concerned pattern. We now have another paper which is currently being reviewed for CVPR2015 where we show that by adding colour information COSFIRE filters become even more robust. Please feel free to send me other ideas on how this work can be developed further. I would be very happy and available to work with an undergraduate or a postgraduate student (or any other person) to have this parallel implementation in Python. I see that you already added it to the Requested-features page. You can also add my contact details (geazzo@gmail) there for the interested readers. All my papers can be freely downloaded from my website: http://www.cs.rug.nl/~george/research-activities/ regards, George On Tuesday, 16 December 2014 15:22:45 UTC+1, Stefan van der Walt wrote: > > On Tue, Dec 16, 2014 at 1:57 PM, Pratap Vardhan <prat...(a)gmail.com > <javascript:>> wrote: > > I found few copies of the paper hosted by universities. I haven't > checked if > > these are the actual pre-prints - However, by the citation it looks like > it. > > Thanks! I've added it to the list: > > https://github.com/scikit-image/scikit-image/wiki/Requested-features > > Stéfan >

2 2

Re: hough ellipse fit inaccurate?
by Arno Dietz 05 May '15

05 May '15

Ok sorry, maybe I need to explain my project better. I have a Autodesk Maya Model of a simplified eyeball with the pupil (see image). I render the images of the eyeball from different angles and try to detect the pupil center as accurate as possible. Since I know the geometry <http://www.dict.cc/englisch-deutsch/geometry.html> and rotation of the eyeball, I can calculate the mapping of the real center of the pupil on my virtual maya camera sensor. I proved the validity <http://www.dict.cc/englisch-deutsch/validity.html> of my calculation with several other methods of ellipse center detection (center of mass, distance transform, opencv ellipse fit, starbust) where I get errors between my calculation and measurement with sometimes less than 0.02 pixels. But nevertheless <http://www.dict.cc/englisch-deutsch/nevertheless.html> I want to try the hough ellipse approach, because it may be more robust against noise or other errors I want to simulate later. And it seems so far only the hough ellipse approach is quite inaccurate so I was wondering why. I think the reason could be the ellipse center detection has only a half pixel accuracy while my other approaches have sub-pixel accuracy. I think posting the calculation code would be too much, but I am quite sure the calculation is right. Kind regards Arno

3 2

regionprops - displaying region properties
by ciaran.robb＠googlemail.com 07 Apr '15

07 Apr '15

Hello everyone, I have recently been attempting to modify some existing skimage code to display regionprops for a labeled image (e.g. area or eccentricity) I initially tried to translate a vectorized bit of old matlab code I had, but gave up on that and decided to alter the existing label2rgb skimage function I am attempting to change each label value to it's area property value similar to the label2rgb "avg" function. so I have: labels = a labeled image out = np.zeros_like(labels) #a blank array labels2 = np.unique(labels) #a vector of label vals out = np.zeros_like(labels) Props = regionprops(labels, ['Area']) bg_label=0 bg = (labels2 == bg_label) if bg.any(): labels2 = labels2[labels2 != bg_label] out[bg] = 0 for label in labels2: mask = (labels == label).nonzero() color = Props[label].area out[mask] = color but the "out" props image does not correspond to the correct area values? Can anyone help me with this? It also throws the following error: "list index out of range" It would certainly be useful to have a way to view the spatial distribution of label properties in this way - perhaps in a future skimage version?

3 7

Re: Apply segmentation to a large binary image
by Juan Nunez-Iglesias 03 Apr '15

03 Apr '15

Hey Yuta, You'll need to do some stitching out-of-core. That's a really tricky problem and I don't have any ready-made solutions for you. The solution will depend on the nature of your segments. The only thing I would recommend is that you use a format such as HDF5 (you can use the excellent h5py library) that allows random access into the underlying disk data. Other than that, as I said, to my knowledge you'll have to develop your own stitching: segment *overlapping* tiles independently in memory, and when it comes time to write to disk, load the tile and overlapping tiles that have already been segmented, and resolve label mapping then... Generally, think of it this way: tile i has already been segmented and written out. We now want to write out tile j, which overlaps tile i. Labels from tile i that intersect labels from tile j in the overlap region should be matched. labels in tile j that *don't* intersect tile i should be relabelled to ensure they are unique with respect to tile i. Of course this gets a bit more complicated in 2D or 3D... Juan. On Fri, Mar 13, 2015 at 7:20 PM, Yuta Sato <yutaxsato(a)gmail.com> wrote: > 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. > -- > 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.

3 3

Steerable pyramid
by Dzung Nguyen 31 Mar '15

31 Mar '15

Hi all, I implemented Steerable pyramid (similar to Gabor transform). Would skimage community be interested in this? I am thinking of adding API for image transforms, and have all popular transform out there? (orthogonal, Gabor, steerable etc) https://github.com/andreydung/Steerable-filter

3 4

Re: GSoC: Rewriting scipy.ndimage in Cython
by Jérôme Kieffer 30 Mar '15

30 Mar '15

On Fri, 27 Mar 2015 07:04:10 -0700 Jaime Fernández del Río <jaime.frio(a)gmail.com> wrote: > Similarly, you suggest using Cython's prange to parallelize computations. I > haven't seen OpenMP used anywhere in NumPy or SciPy, and have the feeling > that parallel implementations are left out on purpose. Am I right, or would > parallelizing were possible be OK? OpenMP is tricky under MacOSX: 10.7-10.9 had no support at all (they use clang <3.6). Since 10.10, the support is incomplete, well at least many code I tested fail with OpenMP (they run under linux and windows), I noticed wrong results, not only failure to compile ! Of course on can install gcc or icc, but this is not in Python's philosophy -- Jérôme Kieffer <google(a)terre-adelie.org>

1 0

Lab Color space vs RGB
by Dzung Nguyen 29 Mar '15

29 Mar '15

Is it true that Lab color space is larger than RGB color space? For example, there exists a color in Lab that can't be reproduced in RGB space ( outside of monitor's gamut)? How does the function rgb2lab deal with this case? From the code, I saw that there's always a corresponding mapping one to one between Lab and RGB.

1 1

Re: Water-shedding non-circular particles
by Claiborne Morton 28 Mar '15

28 Mar '15

Hey thanks for all the help, here is the original image. Also I am removing the smallest particles later on in the process using a function that does the removal based on the average size of healthy (highly circular) cells, which is why I had not removed them in the images I have already posted. On Thursday, March 19, 2015 at 6:07:58 PM UTC-4, Claiborne Morton wrote: > > 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] > > >

2 1

Re: Website designer volunteer
by Tony Yu 28 Mar '15

28 Mar '15

Hey Stéfan, Do you have some ideas for what improvements you're looking for? -Tony On Wed, Mar 25, 2015 at 9:09 PM, Stéfan van der Walt <stefanv(a)berkeley.edu> wrote: > Hi folks, > > I know it's a bit of a long shot, but I'd like to find a volunteer to > work on the layout and readability of our website. > > If you know of anyone interested in doing design work the same way we > do software development, please let me know. They will have to be > able to work with our current workflow, so good technical chops are a > must. > > Thanks, > 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. >

1 0

Re: GSoC: Rewriting scipy.ndimage in Cython
by Jaime Fernández del Río 27 Mar '15

27 Mar '15

On Fri, Mar 27, 2015 at 2:27 AM, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: > > > On Thu, Mar 26, 2015 at 8:40 PM, AMAN singh <ug201310004(a)iitj.ac.in> > wrote: > >> Thank you everyone for your insightful comments. >> I have tried to incorporate your suggestion in the proposal. Kindly have >> a look at the new proposal here >> <https://docs.google.com/document/d/11RTVaDQDu38mrEv3WPdguxprJ-ha5kGnx2LhpEU…> >> and suggest the improvements. >> > > Hi Aman, this looks quite good to me. For the timeline I think it will > take longer to get the iterators right and shorter to port the last > functions at the end - once you get the hang of it you'll be able to do the > last ones quickly I expect. > That sounds about right. I think that breaking down the schedule to what function will be ported what week is little more than wishful thinking, and that keeping things at the file level would make more sense. But I think you are getting your proposal there. One idea that just crossed my mind: checking your implementation of the iterators and other stuff in support.c for correctness and performance is going to be an important part of the project. Perhaps it is a good idea to identify, either now or very early on the project, a few current ndimage top level functions that use each of those objects, if possible without interaction with the others, and build a sequence that could look something like (I am making this up in a hurry, so don't take the actual function names proposed too seriously, although they may actually make sense): Port NI_PointIterator -> Port NI_CenterOfMass, benchmark and test Port NI_LineBuffer -> Port NI_UniformFilter1D, benchmark and test ... This would very likely extend the time you will need to implement all the items in support.c. But by the time you were finished with that we would both have high confidence that things were going well, plus a "Rosetta Stone" that should make it a breeze to finish the job, both for you and anyone else. We would also have an intermediate milestone (everything in support ported plus a working example of each being used, with correctness and performance verified), that would be a worthy deliverable on its own: if we are terribly miscalculating task duration, and everything slips and is delayed, getting there could still be considered a success, since it would make finishing the job for others much, much simpler. One little concern of mine, and the questions don't really go to Aman, but to the scipy devs: the Cython docs on fused types have a big fat warning at the top on support still being experimental. Also, this is going to bump the version requirements for Cython to a very recent one. Are we OK with this? Similarly, you suggest using Cython's prange to parallelize computations. I haven't seen OpenMP used anywhere in NumPy or SciPy, and have the feeling that parallel implementations are left out on purpose. Am I right, or would parallelizing were possible be OK? Jaime -- (\__/) ( O.o) ( > <) Este es Conejo. Copia a Conejo en tu firma y ayúdale en sus planes de dominación mundial.

1 0

GSoC: Rewriting scipy.ndimage in Cython
by AMAN singh 27 Mar '15

27 Mar '15

Hi developers My name is Aman Singh and I am currently a second year undergraduate student of Computer Science department at Indian Institute of Technology, Jodhpur. I want to participate in GSoC'15 and the project I am aiming for is *porting scipy.ndimage to cython*. I have been following scipy for the last few months and have also made some contributions. I came across this project on their GSoC'15 ideas' page and found it interesting. I have done some research in the last week on my part. I am going through Cython documentation, scipy lecture on github and Richard's work of GSoC' 14 in which he ported cluster package to cython. While going through the module scipy.ndimage I also found that Thouis Jones had already ported a function ndimage.label() to cython. I can use that as a reference for the rest of the project. 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. Regards, Aman Singh

4 6

Re: Water-shedding non-circular particles
by Claiborne Morton 27 Mar '15

27 Mar '15

Also Juan, When you say, "There have been some recent developments on that function," are you referring to the peak_local_max() function? On Thursday, March 19, 2015 at 6:07:58 PM UTC-4, Claiborne Morton wrote: > > 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] > > >

2 1

Re: The right way to access red channel in Lena
by Adam Hughes 27 Mar '15

27 Mar '15

Thanks! On Thu, Mar 26, 2015 at 8:38 PM, Stéfan van der Walt <stefanv(a)berkeley.edu> wrote: > Hi Adam > > On Thu, Mar 26, 2015 at 4:31 PM, Adam Hughes <hughesadam87(a)gmail.com> > wrote: > >> ax1.imshow(lena*(1,0,0)) >> ax2.imshow(lena*(255,0,0)) >> > > The multiplication turns your image's dtype into uint64, which causes the > scaling problems. > > I prefer with float images, always ensuring that they are in [0, 1] and > then specifying vmin=0 and vmax=1 to matplotlib. > > Regards > Stéfan > > -- > 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/JzmfEbBJKYU/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > scikit-image+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/d/optout. >

1 0

The right way to access red channel in Lena
by Adam Hughes 27 Mar '15

27 Mar '15

I'm trying to build a filter to show only the red channel in the lena image. I defined two masks: (1,0,0) (255,0,0) Oddly, the (255,0,0) gives me the correct plot when doing imshow(), but (1,0,0) doesn't. Why does the (1,0,0) mask lead to light regions being dark and dark regions being light? Here's a working example: %pylab inline from skimage.data import lena lena = lena() f, (ax1, ax2) = plt.subplots(1,2, figsize=(8,6)) ax1.imshow(lena*(1,0,0)) ax2.imshow(lena*(255,0,0))

3 4

Re: Face detection
by Daniil Pakhomov 26 Mar '15

26 Mar '15

Here it is https://docs.google.com/document/d/19omiz31ewE-oWcveSCq7hSFWRsnRPjF39np6yL_… четверг, 28 марта 2013 г., 10:35:31 UTC+1 пользователь Stefan van der Walt написал: > > Hi everyone > > I've been interested in getting face detection into skimage for a > while. This morning, Nathan Faggian reminded me that the highly > popular Viola-Jones detector is patent encumbered (yes, if you're not > careful you can use patented code in packages like OpenCV). However, > the following link seems to suggest that we can work around that by > training our own classifier with different features: > > > http://rafaelmizrahi.blogspot.com/2007/02/intel-opencv-face-detection-licen… > > If there's any interest in working on this, or if you already have an > algorithm available, please get in touch. > > Stéfan >

1 0

Re: Face detection
by Daniil Pakhomov 26 Mar '15

26 Mar '15

Hello, Stefan. Could I ask you to review my proposal, please? Because I have a little confusion on how we can avoid the patent. Thank you. четверг, 28 марта 2013 г., 10:35:31 UTC+1 пользователь Stefan van der Walt написал: > > Hi everyone > > I've been interested in getting face detection into skimage for a > while. This morning, Nathan Faggian reminded me that the highly > popular Viola-Jones detector is patent encumbered (yes, if you're not > careful you can use patented code in packages like OpenCV). However, > the following link seems to suggest that we can work around that by > training our own classifier with different features: > > > http://rafaelmizrahi.blogspot.com/2007/02/intel-opencv-face-detection-licen… > > If there's any interest in working on this, or if you already have an > algorithm available, please get in touch. > > Stéfan >

1 0

Re: Digest for scikit-image@googlegroups.com - 2 updates in 2 topics
by Jérôme Kieffer 26 Mar '15

26 Mar '15

On Wed, 25 Mar 2015 22:40:13 +0900 Raphael Okoye <raphael(a)aims.ac.za> wrote: > hi guys, > > Can one implement SIFT and SURF functionalities available in openCV > in Sckit-image?Thanks Hi I worked a bit on it ... Here are Python wrapper to C++ libraries (included) https://github.com/kif/imageAlignment This is the Sift version on GPU (OpenCL, so it also runs multithreaded on CPU): https://github.com/kif/sift_pyocl The patent issue mentioned by Stefan applies even if the code is GPL or MIT... HTH -- Jérôme Kieffer <google(a)terre-adelie.org>

1 0

Re: Digest for scikit-image@googlegroups.com - 2 updates in 2 topics
by Stéfan van der Walt 26 Mar '15

26 Mar '15

On Wed, Mar 25, 2015 at 6:40 AM, Raphael Okoye <raphael(a)aims.ac.za> wrote: > Can one implement SIFT and SURF functionalities available in openCV > in Sckit-image?Thanks Unfortunately SIFT and SURF are patent encumbered, so we cannot include them in scikit-image. That said, I have file readers available for the format output by die provided SIFT and SURF binaries. You can also use SIFT and SURF from OpenCV inter-operatively with scikit-image. We also have other kinds of similar feature detectors, such as CenSURE, implemented (see `skimage.feature`). Stéfan

1 0

Website designer volunteer
by Stéfan van der Walt 26 Mar '15

26 Mar '15

Hi folks, I know it's a bit of a long shot, but I'd like to find a volunteer to work on the layout and readability of our website. If you know of anyone interested in doing design work the same way we do software development, please let me know. They will have to be able to work with our current workflow, so good technical chops are a must. Thanks, Stéfan

1 0

Fwd: Opening for Full-Time Postdoctoral Researchers
by Stéfan van der Walt 26 Mar '15

26 Mar '15

Please see below for a postdoc opportunity at my group. ---------- Forwarded message ---------- Full-Time Postdoctoral Researcher Positions Open We are now accepting applications for full-time postdoctoral researchers at BIDS. Successful applicants will join our current cohort of fellows in helping make data analysis easier in the research sciences. We are looking for postdoctoral researchers with excellent credentials in their fields as well as strong interests in advancing data-analysis approaches with a community of like-minded individuals from across campus. Your data does not have to be “big data” for you to be eligible for the program. If you find your data-related problems to be at all unique and challenging, we welcome you to work with us. In particular, we are interested in applications from cross-disciplinary groups and from individuals exploring topics that may broaden the research diversity of our community (e.g., genetics, economics, and the Internet of Things). Each postdoctoral researcher will become part of and contribute to a growing ecosystem that brings together faculty, other postdoctoral scholars, students, staff, and alumni to form a strong network that assists researchers in advancing data-analysis methods and inquiry, expanding and building new software and analytics tools, sharing best practices, and more. To learn more about this position’s requirements and responsibilities, please visit the application page <http://berkeley.us9.list-manage.com/track/click?u=af6553c6218a60168c066d7e2…>. In addition, if you know anyone who would be interested in this program, please feel free to forward this message along. <http://berkeley.us9.list-manage1.com/track/click?u=af6553c6218a60168c066d7e…> Twitter <http://berkeley.us9.list-manage.com/track/click?u=af6553c6218a60168c066d7e2…> <http://berkeley.us9.list-manage.com/track/click?u=af6553c6218a60168c066d7e2…> Website <http://berkeley.us9.list-manage.com/track/click?u=af6553c6218a60168c066d7e2…> Berkeley Institute for Data Science (BIDS) · 190 Doe Library · Berkeley, CA 94720 · USA [image: Email Marketing Powered by MailChimp] <http://www.mailchimp.com/monkey-rewards/?utm_source=freemium_newsletter&utm…>

1 0

Re: Water-shedding non-circular particles
by Kai Wiechen 25 Mar '15

25 Mar '15

I have a problem closely related to this (segmenting touching irregular nuclei in histology images). Is it possible to get the original (RGB ??) image to test something? Best regards, Kai On Thursday, March 19, 2015 at 11:07:58 PM UTC+1, Claiborne Morton wrote: > > 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

Example: Scikit-image and trackpy (bubble tracking in foams)
by François Boulogne 25 Mar '15

25 Mar '15

Hi, Just for your information, I wrote an example based on my research to show the use of scikit-image with trackpy for feature detection and tracking. http://nbviewer.ipython.org/github/soft-matter/trackpy-examples/blob/master… Hopefully, this might be helpful for future workshops or presentations. Best, -- François Boulogne. http://www.sciunto.org GPG: 32D5F22F

8 14

Re: Digest for scikit-image@googlegroups.com - 2 updates in 2 topics
by Raphael Okoye 25 Mar '15

25 Mar '15

hi guys, Can one implement SIFT and SURF functionalities available in openCV in Sckit-image?Thanks Raphael On 24/03/2015, scikit-image(a)googlegroups.com <scikit-image(a)googlegroups.com> wrote: > ============================================================================= > Today's topic summary > ============================================================================= > > Group: scikit-image(a)googlegroups.com > URL: > > https://groups.google.com/forum/?utm_source=digest&utm_medium=email#!forum/… > > > - Dynamic intensity scaling for CollectionViewer [1 Update] > http://groups.google.com/group/scikit-image/t/8aee8a915f035440 > - GSoC: Rewriting scipy.ndimage in Cython [1 Update] > http://groups.google.com/group/scikit-image/t/5c1c936b30cba4d4 > > > ============================================================================= > Topic: Dynamic intensity scaling for CollectionViewer > URL: http://groups.google.com/group/scikit-image/t/8aee8a915f035440 > ============================================================================= > > ---------- 1 of 1 ---------- > From: Ferdinand Greiss <ferdinand.greiss(a)gmail.com> > Date: Mar 23 08:15AM -0700 > URL: http://groups.google.com/group/scikit-image/msg/1d6c8e510adc4334 > > Hallo, > > Thanks for your amazing project on image processing. > > I was wondering whether it would be straight forward to implement automatic > > rescaling of intensity (or y axis on LineProfile widget) in order to > account for bleaching in image sequences. Otherwise the line plot will > vanish below the pre-computed value of the first image and I won't be able > to see much after the first few images. > > Thanks for any help or/and suggestions. > Ferdinand > > > > ============================================================================= > Topic: GSoC: Rewriting scipy.ndimage in Cython > URL: http://groups.google.com/group/scikit-image/t/5c1c936b30cba4d4 > ============================================================================= > > ---------- 1 of 1 ---------- > From: "Stéfan van der Walt" <stefanv(a)berkeley.edu> > Date: Mar 23 01:31AM -0700 > URL: http://groups.google.com/group/scikit-image/msg/cbacf3d255b16d93 > > Hi folks, > >> @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… > > I wasn't aware--thanks for the heads-up! > > Stéfan > > > > > > > -- > You have received this digest because you're subscribed to updates for this > group. You can change your settings on the group membership page: > > https://groups.google.com/forum/?utm_source=digest&utm_medium=email#!forum/… > . > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe(a)googlegroups.com. > >

1 0

Fwd: ANN: SciPy (Scientific Python) 2015 Call for Proposals & Registration Open - tutorial & talk submissions due April 1st
by Nelle Varoquaux 25 Mar '15

25 Mar '15

Hello everyone, (I apologize for the cross posting). This is a quick reminder that the call for submission for Scipy 2015 is open but due April 1st! There is only 7 days left to submit a proposal. Thanks, Nelle ---------- Forwarded message ---------- From: Courtenay Godshall <cgodshall(a)enthought.com> Date: 19 March 2015 at 04:46 Subject: ANN: SciPy (Scientific Python) 2015 Call for Proposals & Registration Open - tutorial & talk submissions due April 1st To: python-list(a)python.org **SciPy 2015 Conference (Scientific Computing with Python) Call for Proposals: Submit Your Tutorial and Talk Ideas by April 1, 2015 at http://scipy2015.scipy.org.** SciPy 2015, the fourteenth annual Scientific Computing with Python conference, will be held July 6-12, 2015 in Austin, Texas. SciPy is a community dedicated to the advancement of scientific computing through open source Python software for mathematics, science, and engineering. The annual SciPy Conference brings together over 500 participants from industry, academia, and government to showcase their latest projects, learn from skilled users and developers, and collaborate on code development. The full program will consist of two days of tutorials by followed by three days of presentations, and concludes with two days of developer sprints. More info available on the conference website at http://scipy2015.scipy.org; you can also sign up on the website for mailing list updates or follow @scipyconf on Twitter. We hope you'll join us - early bird registration is open until May 15, 2015 at http://scipy2015.scipy.org/ehome/115969/259272/?& We encourage you to submit tutorial or talk proposals in the categories below; please also share with others who you'd like to see participate! Submit via the conference website @ http://scipy2015.scipy.org. *SCIPY TUTORIAL SESSION PROPOSALS - DEADLINE EXTENDED TO WED APRIL 1, 2015* The SciPy experience kicks off with two days of tutorials. These sessions provide extremely affordable access to expert training, and consistently receive fantastic feedback from participants. We're looking for submissions on topics from introductory to advanced - we'll have attendees across the gamut looking to learn. Whether you are a major contributor to a scientific Python library or an expert-level user, this is a great opportunity to share your knowledge and stipends are available. Submit Your Tutorial Proposal on the SciPy 2015 website: http://scipy2015.scipy.org *SCIPY TALK AND POSTER SUBMISSIONS - DUE April 1, 2015* SciPy 2015 will include 3 major topic tracks and 7 mini-symposia tracks. Submit Your Talk Proposal on the SciPy 2015 website: http://scipy2015.scipy.org Major topic tracks include: - Scientific Computing in Python (General track) - Python in Data Science - Quantitative and Computational Social Sciences Mini-symposia will include the applications of Python in: - Astronomy and astrophysics - Computational life and medical sciences - Engineering - Geographic information systems (GIS) - Geophysics - Oceanography and meteorology - Visualization, vision and imaging If you have any questions or comments, feel free to contact us at: scipy-organizers(a)scipy.org. -- https://mail.python.org/mailman/listinfo/python-list

1 0

Re: GSoC: Rewriting scipy.ndimage in Cython
by Ralf Gommers 25 Mar '15

25 Mar '15

On Wed, Mar 25, 2015 at 4:26 AM, Jaime Fernández del Río < jaime.frio(a)gmail.com> wrote: > On Tue, Mar 24, 2015 at 5:34 PM, AMAN singh <ug201310004(a)iitj.ac.in> > wrote: > >> Hi Everyone >> >> I have made a basic draft of my proposal here >> <https://docs.google.com/document/d/1-dRqhFzyWnoDJl82KsYECo00B82osR6hujaZ008…> >> . >> Please review it and suggest modifications. >> > > Hi Aman, > > This may not be 100% true for all the functionality, but I believe that > the gist of the ndimage module is in the 4-5 object-like constructs in > ni_support, namely: > > > - NI_Iterator in its three flavors: point, subspace and line iterator, > - NI_LineBuffer and > - NI_FilterIterator. > > Closely linked to this is the choice of a method to deal with multiple > dtypes, a question for which I don't think there is an obvious answer. > Since performance is critical, you may want to take a look at bottleneck's > use of templates that are pre-processed before cythonizing and compiling. > > If you get these right, then rather than the leaves of the tree, you will > have built a solid foundation, more like the the trunk: porting all the > other modules is then going to mostly be little more than an exercise in > translation. So I would suggest that you devote more time to getting these > fundamental questions right, as some trial and error is going to be > inevitable. > This sounds like great advice. Comments on the timeline: - week 1 "reading through the code": I think you should cover, and will have covered this, in the communitiy bonding period. At the start of week 1 you should be at the point where you start tacking the problem. Probably by doing what Jaime says above. - unit tests, docs and benchmarks: these cannot be separated from writing code. Each PR should have decent unit test coverage and a decent docstring. Plus since performance is critical you have to benchmark your code as you go. The only thing you could reserve time for at the end is writing some longer documentation (maybe a tutorial), benchmarks in ASV format (see https://github.com/scipy/scipy/tree/master/benchmarks) and some minor cleanups. Regarding "I will also use better algorithms when possible to improve the time complexity of the functions": it is important to not mix porting code from C to Cython with changing the algorithm, because when output of a function doesn't match the current Scipy output you don't know whether porting or algorithm changes are the cause. Cheers, Ralf

1 0

Fiscal sponsorship
by Stefan van der Walt 25 Mar '15

25 Mar '15

Hi everyone scikit-image is getting enough traction that we can consider finding some development sponsorships (think, e.g., of getting the team together for sprints, etc.). Along that vein, I would like to propose that we sign a fiscal sponsorship agreement with NumFocus to manage the legal aspects of any funds raised. Please let me know if you have any concerns. Regards Stéfan

3 2

Range of a,b in Lab color space
by Dzung Nguyen 25 Mar '15

25 Mar '15

What is the range of a, b coordinate in Lab space?

1 0

Re: Water-shedding non-circular particles
by Emmanuelle Gouillart 25 Mar '15

25 Mar '15

Hi Clay, how do you select the markers and the elevation function used in the watershed algorithm? Could you include the code that results in the segmentation you attached? Cheers, Emmanuelle On Thu, Mar 19, 2015 at 06:07:57PM -0400, Claiborne Morton wrote: > 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 > Inline image 1

3 2

Re: Dynamic intensity scaling for CollectionViewer
by Ferdinand Greiss 24 Mar '15

24 Mar '15

from skimage.viewer import CollectionViewer from skimage.viewer.plugins.lineprofile import LineProfile import numpy as np stack = np.random.randn(100, 50, 50) stack *= np.exp(-0.1*np.arange(stack.shape[0]))[:, np.newaxis, np.newaxis] viewer = CollectionViewer(stack) viewer += LineProfile() viewer.show() I actually did change the source code of tifffile.py written by Christoph Gohlke on line 4660 to include rescaling for min and max of current image in image stack (by pressing r). But it'd be nice to still be able to use your plugins... Thanks for your prompt answer... Ferdinand Am Montag, 23. März 2015 23:57:11 UTC+1 schrieb stefanv: > > Hi Ferdinand > > On Mon, Mar 23, 2015 at 8:15 AM, Ferdinand Greiss > <ferdinan...(a)gmail.com <javascript:>> wrote: > > I was wondering whether it would be straight forward to implement > automatic > > rescaling of intensity (or y axis on LineProfile widget) in order to > account > > for bleaching in image sequences. Otherwise the line plot will vanish > below > > the pre-computed value of the first image and I won't be able to see > much > > after the first few images. > > I think that should be pretty simple. Can you share a code snippet of > how you are using it currently? > > Stéfan >

3 2

Dynamic intensity scaling for CollectionViewer
by Ferdinand Greiss 24 Mar '15

24 Mar '15

Hallo, Thanks for your amazing project on image processing. I was wondering whether it would be straight forward to implement automatic rescaling of intensity (or y axis on LineProfile widget) in order to account for bleaching in image sequences. Otherwise the line plot will vanish below the pre-computed value of the first image and I won't be able to see much after the first few images. Thanks for any help or/and suggestions. Ferdinand

3 2

SpaceX public photo archive
by Stefan van der Walt 23 Mar '15

23 Mar '15

Hi everyone A heads up from Josh Warner on Gitter that SpaceX now has an enormous photo collection in the public domain: https://www.flickr.com/photos/spacexphotos Stéfan

2 1

Light Exhibit
by Stefan van der Walt 23 Mar '15

23 Mar '15

Hi everyone Here's a call for participation in an image exhibition taking place in Paris and San Francisco, among others. """ Light in all of its forms allows us to communicate, entertain, explore, and understand the world we inhabit and the Universe we live in. This exhibit shows you some examples of the myriad of wonderful things that light can do, and how it plays a critical role in our lives every day. WE ARE LOOKING FOR IMAGES THAT: -Illustrate different aspects/phenomena of light in nature, such as lensing, reflection, refraction, atomic collisions, shadows, etc. Examples might include sunsets showing a distorted Sun, auroras, rainbows, sunrises, light rays, lightning, Sun halos, moon dogs, etc. -We are also looking for natural photos of biologic importance tied to light such as sea turtle hatchlings, migrating birds, butterflies, bats at dusk, photosynthesis, sunflowers, etc. -Microscopic images and medically-themed images such as brain scans, images of cells, etc. -Also needed, Earth at Night scences, including our views of the Milky Way at night, "light pollution" themed images, etc. -We have pinned examples to Pinterest: - http://www.pinterest.com/kimberlyarcand/light-beyond-the-bulb-core-30%2B-im… """ http://lightexhibit.org/about.html Stéfan

1 0

Re: GSoC: Rewriting scipy.ndimage in Cython
by Stéfan van der Walt 23 Mar '15

23 Mar '15

Hi folks, On Sun, Mar 15, 2015 at 10:45 AM, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: > @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… I wasn't aware--thanks for the heads-up! Stéfan

1 0

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 14 Mar '15

14 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 13 Mar '15

13 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