Mailman 3 June 2017 - scikit-image

Re: [scikit-image] Techniques for Aligning images to GIS data
by K.-Michael Aye 01 Jul '17

01 Jul '17

I don’t know your status of knowledge, so I apologize if I state the obvious. Your issue is that of the co-registration of images. You have to always decide what your “prime” or “truth” is. How was your “GIS” data precisely located? How do you know it’s not that which is off? (Even so, if you have “ground truth” measurements, they are usually more precisely located than remote sensing data. Are the satellite images “map-projected” ? If so, against what ground truth was that projection performed? What geographical coordinate system of Earth was used for the map projection? This stackexchange might help. There are a bazillion books out there for that, don’t really have a recommendation, mostly learned my stuff by internet searches. ;) HTH, Michael > On Jun 30, 2017, at 09:49, Vighnesh Birodkar <vighneshbirodkar(a)gmail.com> wrote: > > Hello > > Has anyone here worked with satellite images before ? I am dealing with the problem of aligning satellite images to GIS data which can be off by upto 15pixels. Could someone point me to good literature to read on the topic ? > > Thanks > Vighnesh > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image

3 3

Re: [scikit-image] building scikit-image plugin and tool set.
by Dongyao Li 30 Jun '17

30 Jun '17

Hi YXDragon and Stefan: I am a process engineer in semiconductor industry. I wrote a SEM/STEM/TEM analysis software with UI based on scikit-image, pyqt, and others, using the concept of plugins. I agree with Stefan's point that there is a market for this. However my experience is that the images from scientific instruments like SEM/STEM/TEM/MRI are quite different with images from cameras. And people in semiconductor industry and people working on biology have very different needs. I feel like the focus right now is mostly on the biology community. I am very happy to hear that we can possibly build a web-based UI for image analysis now. It will integrate the image analysis and further data analysis greatly, which is the our future direction. It would be great if scikit-image could include some demo of it in the future, just like the "viewer" package skimage has right now. Best, Dongyao On Fri, Jun 30, 2017 at 10:48 AM, Stefan van der Walt <stefanv(a)berkeley.edu> wrote: > Hi, YXDragon > > On Fri, Jun 30, 2017, at 01:46, imagepy(a)sina.com wrote: > > Now I think It is time to build a project named skimg-plgs > <https://github.com/Image-Py/skimg-plgs>. And I had wrote some > presentative demo <https://github.com/Image-Py/skimg-plgs> with friendly > interact. these demo are all from the gallery, (interactive snake contours, > interactive watershed...) I want to build a full plugin system and tool set > covering scikit-image's every module. Then we can build a large user > community like ImageJ, not only programers but also the doctors and > biologists. > > > Given the immense success of projects such as ImageJ, and based on > feedback I've received from practitioners in microscopy, there is certainly > a market for a GUI built on top of scikit-image. > > I don't personally have the time to contribute to such an effort at the > moment (my focus is probably best spent keeping skimage on track!), but I > am appreciative of the work you are doing, and encourage you to continue. > > I may have mentioned this to you before, but I am not sure about the > long-term viability of WXPython. I heard that they have a Phoenix rewrite > underway, but looking at the latest PyPI release ( > https://pypi.python.org/pypi/wxPython/4.0.0a1) they also only support > Windows and MacOS. > > With a Jupyter Lab release imminent, I would strongly consider using the > web as UI, and building components that integrate with that project. I can > put you in contact with their developers, if you like. > > Best regards > Stéfan > > > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image > >

1 0

building scikit-image plugin and tool set.
by imagepy＠sina.com 30 Jun '17

30 Jun '17

Hi everyone: In the past half year, I am working on a project ImagePy. I had communicated with several expert here privately, and got many advice. It is a plugin Frame work just like ImageJ, which can wrap any numpy based library. I had reconstructed it many a time, Up to now, It still has many bug, But it is right in general orientation. Now I think It is time to build a project named skimg-plgs. And I had wrote some presentative demo with friendly interact. these demo are all from the gallery, (interactive snake contours, interactive watershed...) I want to build a full plugin system and tool set covering scikit-image's every module. Then we can build a large user community like ImageJ, not only programers but also the doctors and biologists. I wrote this email to ask some advice, and If anyone agree with this opinion, If it's OK, Let's start! Best regardsYXDragon

2 1

Re: [scikit-image] Techniques for Aligning images to GIS data
by Ömer Özak 30 Jun '17

30 Jun '17

Hi Vigresh, Not sure what you're proven is exactly but you can try Geoandas and Georasters which are socialized packages for GIS. Best, Ömer Sent from my mobile Please excuse any typos > On Jun 30, 2017, at 10:49 AM, Vighnesh Birodkar <vighneshbirodkar(a)gmail.com> wrote: > > Hello > > Has anyone here worked with satellite images before ? I am dealing with the problem of aligning satellite images to GIS data which can be off by upto 15pixels. Could someone point me to good literature to read on the topic ? > > Thanks > Vighnesh > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image

1 0

Techniques for Aligning images to GIS data
by Vighnesh Birodkar 30 Jun '17

30 Jun '17

Hello Has anyone here worked with satellite images before ? I am dealing with the problem of aligning satellite images to GIS data which can be off by upto 15pixels. Could someone point me to good literature to read on the topic ? Thanks Vighnesh

1 0

Re: [scikit-image] Parallel processing segmentation while keeping labels
by Juan Nunez-Iglesias 28 Jun '17

28 Jun '17

Hi Cedric, Stitching of separate regions is not a trivial problem… You’ll basically have to: a) overlap the blocks by a certain amount. You might be able to use skimage.util.apply_parallel more easily here than joblib. b) compute which labels overlap the most between each neighbouring pair of images c) relabel as necessary to make those labels match It’s not super-hard, just a lot of annoying bookkeeping. If you come up with a reasonably robust method to do this, I for one would very much welcome such a contribution into the library! Here’s a paper from an old colleague of mine who had to deal this on a large-scale problem, and they created a robust method to do the matching: https://arxiv.org/pdf/1604.00385.pdf (page 6) Juan. On 27 Jun 2017, 9:20 AM +1000, Cedric Espenel <cedric.espenel(a)gmail.com>, wrote: > Hi, > > I'm working on a project where I have to segment out nucleus of cells in a volume. I use random_walker with define markers for every nuclei. If I try to run it on the all volume the segmentation works well but it's very slow. So I used util.view_as_blocks function from scikit to split my image and markers and I loop over the different block using joblib: > > > rw_dapi_chunks = Parallel(n_jobs = 4)(delayed(segmentation.random_walker)(chunks[i,j], > > chunks_markers[i,j], beta = 3000, mode='cg_mg') for > > i in range(2) for j in range(2)) > > So I end up with a list of 4 images and if I combine these images (btw I'm not sure what is the best way for doing that? I just add them up in an empty array) everything work well, except that I end-up with nuclei with 2 different labels: > > > Am I doing something wrong? Is there a way to split your images in block for parallel computing but being able to get the labeling right at the end? > > Best, > > Cedric > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image

2 1

Re: [scikit-image] Refactoring ndimage
by K.-Michael Aye 27 Jun '17

27 Jun '17

Awesome effort! ;) Is it maybe worth, during the refactor, to evaluate how NDimage could be supportive for auto-parallelization? I’m thinking that it somehow would be able to split off into embarrassingly parallel n tasks, if thrown to a n-core machine? I’m sorry if I talk non-sense, I’m just fighting to get GLCM faster, when running it via “generic_filter” over large-ish images, so far not successful, even trying to use numba, but as many things are already running in Cython, so I guess I can’t expect much auto-improvements. ;) So, I’m anticipating to have to go to a cluster for my hundreds of images I want to run multiple/many GLCM analyses on. Thanks again for the developer docs, they are great! Regards, Michael > On Jun 27, 2017, at 09:06, Stefan van der Walt <stefanv(a)berkeley.edu> wrote: > > On Tue, Jun 27, 2017, at 07:49, Egor Panfilov wrote: >> - Not sure that I'll find enough time to contribute to the code by myself, but it won't harm if you could provide to the public some directions on where to start with `scipy.ndimage` C-code. > > Making ndimage developer notes along the way would be extremely helpful! > > Stéfan > > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image

2 1

Re: [scikit-image] Refactoring ndimage
by Ralf Gommers 27 Jun '17

27 Jun '17

On Wed, Jun 28, 2017 at 3:20 AM, Jaime Fernández del Río < jaime.frio(a)gmail.com> wrote: > On Tue, Jun 27, 2017 at 5:06 PM, Stefan van der Walt <stefanv(a)berkeley.edu > > wrote: > >> On Tue, Jun 27, 2017, at 07:49, Egor Panfilov wrote: >> >> - Not sure that I'll find enough time to contribute to the code by >> myself, but it won't harm if you could provide to the public some >> directions on where to start with `scipy.ndimage` C-code. >> >> >> Making ndimage developer notes along the way would be extremely helpful! >> > > I started trying to document how ndimage internals work here: > > https://docs.google.com/document/d/1IJagsIVK9UAR0CU4kriipb0z3uxJD > OdK1eTjBTlC5KU/edit?usp=sharing > > I was mostly trying to document my own understanding of ndimage, but at > some point I needed to start writing code, not literature! But I guess it > could be repurposed to become those developer notes. > That's an awesome start for dev notes, much better than anything we have in the scipy docs now! Ralf

1 0

Re: [scikit-image] Refactoring ndimage
by Jaime Fernández del Río 27 Jun '17

27 Jun '17

On Tue, Jun 27, 2017 at 5:06 PM, Stefan van der Walt <stefanv(a)berkeley.edu> wrote: > On Tue, Jun 27, 2017, at 07:49, Egor Panfilov wrote: > > - Not sure that I'll find enough time to contribute to the code by myself, > but it won't harm if you could provide to the public some directions on > where to start with `scipy.ndimage` C-code. > > > Making ndimage developer notes along the way would be extremely helpful! > I started trying to document how ndimage internals work here: https://docs.google.com/document/d/1IJagsIVK9UAR0CU4kriipb0z3uxJDOdK1eTjBTl… I was mostly trying to document my own understanding of ndimage, but at some point I needed to start writing code, not literature! But I guess it could be repurposed to become those developer notes. Jaime

1 0

Re: [scikit-image] Refactoring ndimage
by Stefan van der Walt 27 Jun '17

27 Jun '17

On Tue, Jun 27, 2017, at 07:49, Egor Panfilov wrote: > - Not sure that I'll find enough time to contribute to the code by > myself, but it won't harm if you could provide to the public some > directions on where to start with `scipy.ndimage` C-code. Making ndimage developer notes along the way would be extremely helpful! Stéfan

1 0