Mailman 3 April 2017 - scikit-image

Re: [scikit-image] Segmentation
by Cedric Espenel May 2, 2017

May 2, 2017

Hi, Sorry, I guess I can just mask the result with the watershed segmentation. I guess I wonder if it is the proper way to do it? And also, from your point of view, if it's the way to go to segment these cells or if you think of a better way? Cedric

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Using EllipseModel
by Surya Kasturi April 28, 2017

April 28, 2017

Hi, I’m trying to use skimage.measure.EllipseModel to estimate an ellipse around a contour. The results seems to be not so satisfying. I am wondering if I am using “orientation” parameter correctly. Could anyone please let me know whether “theta” is in radians or degrees? / I am doing anything wrong? from skimage.measure import EllipseModel # create ellipse model ellipse = EllipseModel() ellipse.estimate(cnt) xc, yc, a, b, theta = np.array(ellipse.params, dtype=int) # find perimeter rr, cc = draw.ellipse_perimeter(xc, yc, a, b, orientation=theta) # plot ax.scatter(cc, rr, s=5, label="EllipseModel”) Thank you, Surya

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Re: [scikit-image] GLCM with scikit-image
by Kosovan,Sofiia April 28, 2017

April 28, 2017

Dear Neil, I have found your post from 2013 about the graycomatrix implementation differences in Matlab and Python. I would ask you few questions. Please reply. Best regards, Sofiia Kosovan Reifenh?user Reicofil GmbH & Co. KG Spicher Stra?e 46, 53844 Troisdorf, Germany Registergericht Siegburg, Reg.Nr. HR A 4534 USt-IdNr. DE 814359351, Steuer-Nr. 5220/5760/0426 Reifenh?user Reicofil Verwaltungs-GmbH Registergericht Siegburg, Reg.Nr. HR B 788 Gesch?ftsf?hrer: Dr.-Ing. Bernd Kunze Please note: This message may contain information which is privileged, confidential and proprietary.

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Convert data to image and then image to numpy.ndarray
by Carlton Banks April 27, 2017

April 27, 2017

Is it possible to convert a data set stored as a numpy.ndarray -> plot the data with a colormap , possibly cm.jet. -> and then store the image pixels to a numpy.ndarray. The data array of the image should have the same shape of the data array used to make the array. The image conversion is only used for getting a visual representation of the data, and normalise it using the cm.jet. So I actually just interested in the RGB values of the colormap normalised input data. IS this possible?

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Re: [scikit-image] Segmentation
by Brian Perea April 25, 2017

April 25, 2017

Hey Cedric, Have you thought of applying the background mask from the simple watershed to the final split mask? It seems that you should expect your foreground and background areas to be constant, so you should be able to create a boolean background mask (in code: > boolean_mask = watershed_mask == bg_label) from the first segmentation step and multiply the boolean mask by your split mask (> final_mask = boolean_mask * split_mask). This should preserve the foreground labels and set the background to zero uniformly. Best wishes, Brian On Tue, Apr 25, 2017 at 12:37 PM Cedric Espenel <cedric.espenel(a)gmail.com> wrote: > Hi everyone, > > I work on a project where I try to track cell and cell division over-time. > If cells are well separated, a simple watershed is fine, however, if cells > start to overlap it doesn't work anymore. > > If I had another step using random walker followed by a > "join_segmentations" I can split touching cells as in follow: > > > > > > > So my foreground (the cells) were split in 3 which is what I want, but my > background is also split. I might be missing something, but is there an > easy way to "unify" my background, while keeping the foreground > segmentation? > > Best, > > Cedric > > > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image >

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Segmentation
by Cedric Espenel April 25, 2017

April 25, 2017

Hi everyone, I work on a project where I try to track cell and cell division over-time. If cells are well separated, a simple watershed is fine, however, if cells start to overlap it doesn't work anymore. If I had another step using random walker followed by a "join_segmentations" I can split touching cells as in follow: So my foreground (the cells) were split in 3 which is what I want, but my background is also split. I might be missing something, but is there an easy way to "unify" my background, while keeping the foreground segmentation? Best, Cedric

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Re: [scikit-image] Image Processing short course in IAMG 2017
by Juan Nunez-Iglesias April 24, 2017

April 24, 2017

Cool! Are you stopping in Melbourne? =D On 25 Apr 2017, 3:49 AM +1000, Stefan van der Walt <stefanv(a)berkeley.edu>, wrote: > On Mon, Apr 24, 2017, at 09:58, Alexandre Fioravante de Siqueira wrote: > > I'll present a short course in the International Association for > > Mathematical Geosciences (IAMG) [1] meeting, on Sep 03 [2]. This course > > will be given using scikit-image for processing microscopy images. > > If you're close, please check it out! Also, the materials will be > > available in [3]. > > Great, thanks for doing that! > > We'll be building up material for SciPy2017 at the usual location: > > https://github.com/scikit-image/skimage-tutorials > > Use whatever seems useful. > > Best regards > Stéfan > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image

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Image Processing short course in IAMG 2017
by Alexandre Fioravante de Siqueira April 24, 2017

April 24, 2017

Dear all, I'll present a short course in the International Association for Mathematical Geosciences (IAMG) [1] meeting, on Sep 03 [2]. This course will be given using scikit-image for processing microscopy images. If you're close, please check it out! Also, the materials will be available in [3]. Kind regards and have a nice week, Alex [1] IAMG's website: https://iamg.org/ [2] Short Course 8 in: http://iamg2017.com/courses/. [3] github's dedicated folder: https://github.com/alexandrejaguar/lectu res/tree/master/2017/iamg2017 -- ----------------------------------------------------------------------- Dr. Alexandre 'Jaguar' Fioravante de Siqueira Grupo de Cronologia - Sala 12 Departamento de Raios Cósmicos e Cronologia - DRCC Instituto de Física "Gleb Wataghin" - IFGW Unicamp - Universidade Estadual de Campinas Rua Sérgio Buarque de Holanda, 777 Cidade Universitária Zeferino Vaz - CEP 13083-859 Campinas - SP - Brazil Phone: +55(19)3521-5362 Lattes curriculum: http://lattes.cnpq.br/3936721630855880/ Personal site: http://www.programmingscience.org/ Github: http://www.github.com/alexandrejaguar/ Skype: alexandrejaguar Twitter: http://www.twitter.com/alexdesiqueira/ -----------------------------------------------------------------------

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Re: [scikit-image] New core team member
by Alexandre Fioravante de Siqueira April 24, 2017

April 24, 2017

Hi all, welcome Greg! It's nice to have the opportunity to work with you. I'm very fond of your work in PyWavelets and wavelets in general. Thanks for that! Kind regards, Alex On Sat, 2017-04-22 at 10:28 -0700, Stefan van der Walt wrote: > Hi everyone, > > I'd like to welcome Greg Lee to the scikit-image core team. > > Greg has been a contributor to scikit-image since September 2014, and > has been doing some great work on improving N-dimensional support. > > Greg, we're glad to have you on board, and look forward to our future > collaboration! > > Best regards > Stéfan > -- ----------------------------------------------------------------------- Dr. Alexandre 'Jaguar' Fioravante de Siqueira Grupo de Cronologia - Sala 12 Departamento de Raios Cósmicos e Cronologia - DRCC Instituto de Física "Gleb Wataghin" - IFGW Unicamp - Universidade Estadual de Campinas Rua Sérgio Buarque de Holanda, 777 Cidade Universitária Zeferino Vaz - CEP 13083-859 Campinas - SP - Brazil Phone: +55(19)3521-5362 Lattes curriculum: http://lattes.cnpq.br/3936721630855880/ Personal site: http://www.programmingscience.org/ Github: http://www.github.com/alexandrejaguar/ Skype: alexandrejaguar Twitter: http://www.twitter.com/alexdesiqueira/ -----------------------------------------------------------------------

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Re: [scikit-image] New core team member
by François Boulogne April 23, 2017

April 23, 2017

Welcome on board Greg! :) I'm looking forward working with you in the future. -- François Boulogne. http://www.sciunto.org GPG: 32D5F22F

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