Mailman 3 - scikit-image

Installation question about skimage developer version
by Hung, C. (Chien-Cheng) 12 Dec '20

12 Dec '20

Dear scikit team, My name is Chien-Cheng and I am trying to use scikit-image to do some image segmentation. The method I choose is called "Training segmentation" (https://scikit-image.org/docs/dev/auto_examples/segmentation/plot_trainable…). Currently, I am trying to run the example of the training method and I got a few questions. The latest skimage version I have in the Anaconda is 0.17.2. But I found the training method seems only applicable for the developer version 0.19.0.dev0 since some of the attribute in the script is missing in the version of 0.17.2 (for example, there is an error called AttributeError: module 'skimage.feature' has no attribute 'multiscale_basic_features' after running the example script with 0.17.2). Also, I cannot find the example of the training method in the version of 0.17.2 so I figure the training methods require the developer version. I have tried installing the contributor/developer version in the conda environment by following the instruction (https://scikit-image.org/docs/dev/install.html#id6) but when I was running the third comment "conda install `for i in requirements/{default,build,test}.txt; do echo -n " --file $i "; done`. The console shows me the error below: [cid:image002.jpg@01D6CFE7.99D9EF80] I really don't know what the problem might be so I would like to turn to your help. There are two questions I have so far: 1. Do I need to install the developer version to use the training methods? 2. If so, did I install the developer version with the correct procedure? If yes, how to solve the issue I have above? Looking forward to your reply, thanks! Best regards, Chien-Cheng

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Smil release 0.10.0
by Jose-Marcio Martins da Cruz 10 Dec '20

10 Dec '20

Hello, Although Smil is not part os Scikit-image, it may be of interest to some of you. I'm glad to announce the release 0.11.0 of Smil, our Mathematical Morphology library. Smil is a library completely written in C++ with a Python interface (thanks to Swig). This is maintenance release with some few changes. Smil is the successor of other Mathematical Morphology software we created since the 70s : Xlim, Xlim3D, Micromorph, Morph-M and now Smil. Mathematical Morphology is a discipline created at our research department in the 60s by Georges Matheron and Jean Serra. The web site of the library is : http://smil.cmm.mines-paristech.fr You can have have a quick global view of what functions are available inside Smil here : http://smil.cmm.mines-paristech.fr/publis/SmilQuickReference.pdf Release notes here : http://smil.cmm.mines-paristech.fr/doc/_release_notes.html Feel free to make comments or give some feedback. Best regards -- --------------------------------------------------------------- Jose Marcio MARTINS DA CRUZ, Ph.D. Ecole des Mines de Paris Centre de Morphologie Mathématique --------------------------------------------------------------- Spam : http://amzn.to/LEscRu ou http://bit.ly/SpamJM ---------------------------------------------------------------

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Smil release 0.10.0
by Jose Marcio Martins da Cruz 10 Dec '20

10 Dec '20

Hello, Although Smil is not part os Scikit-image, it may be of interest to some of you. I'm glad to announce the release 0.11.0 of Smil, our Mathematical Morphology library. Smil is a library completely written in C++ with a Python interface (thanks to Swig). This is maintenance release with some few changes. Smil is the successor of other Mathematical Morphology software we created since the 70s : Xlim, Xlim3D, Micromorph, Morph-M and now Smil. Mathematical Morphology is a discipline created at our research department in the 60s by Georges Matheron and Jean Serra. The web site of the library is : http://smil.cmm.mines-paristech.fr You can have have a quick global view of what functions are available inside Smil here : http://smil.cmm.mines-paristech.fr/publis/SmilQuickReference.pdf Release notes here : http://smil.cmm.mines-paristech.fr/doc/_release_notes.html Feel free to make comments or give some feedback. Best regards -- --------------------------------------------------------------- Jose Marcio MARTINS DA CRUZ, Ph.D. Ecole des Mines de Paris Centre de Morphologie Mathématique --------------------------------------------------------------- Spam : http://amzn.to/LEscRu ou http://bit.ly/SpamJM ---------------------------------------------------------------

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Release 0.18
by Juan Nunez-Iglesias 02 Nov '20

02 Nov '20

Hi everyone, I intend to branch v0.18.x and release version 0.18.0 tomorrow or Wednesday. If you have any pull requests that you think are *critical* to get into 0.18, or that would be nice and you think are super close, please tag the appropriate PR with the 0.18 milestone. Juan.

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Big image sprint at SciPy Japan
by Genevieve Buckley 31 Oct '20

31 Oct '20

Juan and I are going to run a "big image" sprint at SciPy Japan next week (Nov 1-2, 9am-5pm Tokyo time). Anyone who wants to join the sprint (even asynchronously) is welcome to join! There's a hackmd here with some more details about topics people might like to sprint on: https://hackmd.io/qpiRFdIsTdCAfdr_C2mMUA - Genevieve

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Developers' meeting on Thursday October 29th at 11am CEST
by Marianne Corvellec 27 Oct '20

27 Oct '20

Dear all, The next developers' meeting for scikit-image will take place next Thursday (October 29th) at 11am CEST (Paris time). All developers are welcome to attend the meeting. This meeting will focus again on the preparation of the 0.18 release. Other agenda items can be found at: https://hackmd.io/r5oMbIyvQH2K0mhgntAW2g We will use Zoom (https://monash.zoom.us/j/284282585). Best, Marianne

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multidimensional (4D) color conversion
by Matteo Niccoli 17 Oct '20

17 Oct '20

I have 3 3D numpy arrays of shape 600 x 600 x 200 representing the X, Y, Z directions. The arrays contain dip azimuth, dip magnitude, and edge magnitude calculated from a geophysical dataset. I would like to stack them into a 4D array of shape 600x600x600x3 where azimuth is Hue, dip is Saturation, and edge is Value. *Question*: Would color skimage.color.hsv2rg take this 4D array as input and convert it to RGB? My goal is to then split the 3 R,G,B arrays and load them into a commercial software where I can visualize them using RGB blending? Thanks, Matteo Matteo Niccoli P. Geo., M.sc. Geophysics and data science [image: WordPress] <http://mycarta.wordpress.com/>[image: LinkedIn] <http://www.linkedin.com/in/matteo-niccoli-031aa426>[image: Twitter] <http://twitter.com/@my_carta>[image: Custom link] <https://github.com/mycarta>[image: Custom link] <https://www.researchgate.net/profile/Matteo_Niccoli2>

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how to properly save what I see (on my monitor)
by Scott Bryant 11 Oct '20

11 Oct '20

Hi. I am pretty much a beginner in Python and scikit-image. Thank you for all the great resources! I am using sci-kit image for a hobby project involving images of medieval illuminated manuscripts. Here is my question: How do I save images like I see -- in many of your examples, in matplotlib? For example: 1. The last image of colored, segmented coins in https://scikit-image.org/docs/stable/auto_examples/applications/plot_coins_… 2. Or the three results in https://scikit-image.org/docs/dev/auto_examples/segmentation/plot_marked_wa… 3. Or even the three results in https://scikit-image.org/docs/stable/auto_examples/filters/plot_hysteresis.… . I have some test scripts that successfully save using skimage.io.imsave. But the results like in the examples above don't save the color; and/or the results are very dark (like mostly or all black-looking). I also get a lot of warnings about lossy-ness. I've tried a number of things, including matplot's saving methods. But the results are still what I've described. Any help on this would be super-appreciated! Sincerely, Scott PS I can also save what I see pop up when running a script, hitting the disk symbol and saving. But as you probably know, the results not only have the axes and words and such, but they also are very small and poor resolution (though I'm not confident "resolution" is the right term).

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The pinnacle of scikit-image's contributions to the world
by Juan Nunez-Iglesias 22 Sep '20

22 Sep '20

Hello skimagers! I thought you might enjoy reading this blog post as much as I did (a lot): https://www.ethanrosenthal.com/2020/08/25/optimal-peanut-butter-and-banana-… <https://www.ethanrosenthal.com/2020/08/25/optimal-peanut-butter-and-banana-…> Sent to me by dask-image’s (among others) Genevieve Buckley. Juan.

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developers meeting on Monday September 21st, at 2pm CEST
by Emmanuelle Gouillart 14 Sep '20

14 Sep '20

Dear all, the next developers meeting of scikit-image will take place next Monday (September 21st), at 2pm CEST (Paris time). All developers are welcome to attend the meeting. The major subject of the meeting will be the preparation of the 0.18 release. Other agenda items can be found on https://hackmd.io/r5oMbIyvQH2K0mhgntAW2g?view We will use Zoom (https://monash.zoom.us/j/284282585) All the best Emma

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