Ok, I can give it a try... Some questions then: - skivi is pure Qt, so must I keep it that way (no matplotlib dependency)? - skivi is good for RGB images, but not so much for greyscale... Also data conversion from uint16 to uint8 turns everything black (it set anything > 256 to 0), shall this be corrected? -Christoph Gohlke tifffile.imshow() is somehow closer to what us microscopy guys are expecting (more suitable for those greyscale multipage tiffs), though some features of the fancy viewer such as the contrast settings, are great. Also it is a pure matplotlib implementation and the intensity value reading is already there. So my question is: Are those tools needed by the general image analysis skimage community are more by scientific tiff users? If the latest, my guess is that building on top of matplotlib and Christoph's implementation of imshow is a better tactic (plus it would be more cross platform, as this can be a widget irrespective of the backend). Cheers, Guillaume Le 20/02/2012 08:04, Stéfan van der Walt a écrit :
On Fri, Feb 17, 2012 at 6:53 AM, Guillaume Gay <guillaume@mitotic-machine.org> wrote:
I just happen to code a simple linescan function, if that helps... Thanks, Guillaume! If you could integrate this with the fancy Qt imshow to display the line, that would be wonderful, but otherwise I'm sure we'll still be able to use this code.
Stéfan
I agree that there are some benefits of both viewers. However, I work a lot with 16-bit greyscale, and I like the pan & zoom of the matplotlib-based viewer. Therefore, I've found myself using the TIFFFile one more lately. Adding the line profile & some contrast adjustment to this viewer would be great. Neil On Feb 20, 11:11 am, Guillaume Gay <guilla...@mitotic-machine.org> wrote:
Ok, I can give it a try...
Some questions then:
- skivi is pure Qt, so must I keep it that way (no matplotlib dependency)? - skivi is good for RGB images, but not so much for greyscale... Also data conversion from uint16 to uint8 turns everything black (it set anything > 256 to 0), shall this be corrected? -Christoph Gohlke tifffile.imshow() is somehow closer to what us microscopy guys are expecting (more suitable for those greyscale multipage tiffs), though some features of the fancy viewer such as the contrast settings, are great. Also it is a pure matplotlib implementation and the intensity value reading is already there. So my question is: Are those tools needed by the general image analysis skimage community are more by scientific tiff users? If the latest, my guess is that building on top of matplotlib and Christoph's implementation of imshow is a better tactic (plus it would be more cross platform, as this can be a widget irrespective of the backend).
Cheers,
Guillaume
Le 20/02/2012 08:04, Stéfan van der Walt a écrit :
On Fri, Feb 17, 2012 at 6:53 AM, Guillaume Gay <guilla...@mitotic-machine.org> wrote:
I just happen to code a simple linescan function, if that helps... Thanks, Guillaume! If you could integrate this with the fancy Qt imshow to display the line, that would be wonderful, but otherwise I'm sure we'll still be able to use this code.
Stéfan
guillaume.vcf < 1KViewDownload
Ok, sounds good to me too, if nobody objects... Guillaume Le 21/02/2012 08:04, Neil Yager a écrit :
I agree that there are some benefits of both viewers. However, I work a lot with 16-bit greyscale, and I like the pan& zoom of the matplotlib-based viewer. Therefore, I've found myself using the TIFFFile one more lately. Adding the line profile& some contrast adjustment to this viewer would be great.
Neil
On Feb 20, 11:11 am, Guillaume Gay<guilla...@mitotic-machine.org> wrote:
Ok, I can give it a try...
Some questions then:
- skivi is pure Qt, so must I keep it that way (no matplotlib dependency)? - skivi is good for RGB images, but not so much for greyscale... Also data conversion from uint16 to uint8 turns everything black (it set anything> 256 to 0), shall this be corrected? -Christoph Gohlke tifffile.imshow() is somehow closer to what us microscopy guys are expecting (more suitable for those greyscale multipage tiffs), though some features of the fancy viewer such as the contrast settings, are great. Also it is a pure matplotlib implementation and the intensity value reading is already there. So my question is: Are those tools needed by the general image analysis skimage community are more by scientific tiff users? If the latest, my guess is that building on top of matplotlib and Christoph's implementation of imshow is a better tactic (plus it would be more cross platform, as this can be a widget irrespective of the backend).
Cheers,
Guillaume
Le 20/02/2012 08:04, Stéfan van der Walt a écrit :
On Fri, Feb 17, 2012 at 6:53 AM, Guillaume Gay <guilla...@mitotic-machine.org> wrote:
I just happen to code a simple linescan function, if that helps... Thanks, Guillaume! If you could integrate this with the fancy Qt imshow to display the line, that would be wonderful, but otherwise I'm sure we'll still be able to use this code. Stéfan
guillaume.vcf < 1KViewDownload
On Mon, Feb 20, 2012 at 11:04 PM, Neil Yager <yager.neil@gmail.com> wrote:
I agree that there are some benefits of both viewers. However, I work a lot with 16-bit greyscale, and I like the pan & zoom of the matplotlib-based viewer. Therefore, I've found myself using the TIFFFile one more lately. Adding the line profile & some contrast adjustment to this viewer would be great.
If you can improve the matplotlib version of imshow, that would be much appreciated. Let me know if you need a hand with anything. The source is in: skimage/io/_plugins/matplotlib_plugin.py Currently it just sets interpolation to 'nearest' and 'cmap' to gray by default (behaviour that is important to keep). Stéfan
Hi all, Here is a first version of the linescan implementation. It sort of works, but I have some issues: -the major one is that when I instantiate the LineScanInteractor within the imshow() function definition, I don't catch the events any more. So this is not usable in an interactive session. -I can't get the ticks on the linescan plot to update properly... -also there should be some kind of a reset mechanism, because if the image is zoomed in, you can lost the handles of the line So if any one have a hint on how to do this... Meanwhile I can try to have this work in conjunction tifffile's imshow (which should not be so complicated). With all that maybe it would be better to implement a subclass of FigureCanvas, so that linescan appears only when a button (at the bottom of the window) is pressed, and it is easy to add e.g. a histogram plot or a contrast setter... what do you think? Bye Guillaume Le 20/02/2012 12:11, Guillaume Gay a écrit :
Ok, I can give it a try...
Some questions then:
- skivi is pure Qt, so must I keep it that way (no matplotlib dependency)? - skivi is good for RGB images, but not so much for greyscale... Also data conversion from uint16 to uint8 turns everything black (it set anything > 256 to 0), shall this be corrected? -Christoph Gohlke tifffile.imshow() is somehow closer to what us microscopy guys are expecting (more suitable for those greyscale multipage tiffs), though some features of the fancy viewer such as the contrast settings, are great. Also it is a pure matplotlib implementation and the intensity value reading is already there. So my question is: Are those tools needed by the general image analysis skimage community are more by scientific tiff users? If the latest, my guess is that building on top of matplotlib and Christoph's implementation of imshow is a better tactic (plus it would be more cross platform, as this can be a widget irrespective of the backend).
Cheers,
Guillaume
Le 20/02/2012 08:04, Stéfan van der Walt a écrit :
On Fri, Feb 17, 2012 at 6:53 AM, Guillaume Gay <guillaume@mitotic-machine.org> wrote:
I just happen to code a simple linescan function, if that helps... Thanks, Guillaume! If you could integrate this with the fancy Qt imshow to display the line, that would be wonderful, but otherwise I'm sure we'll still be able to use this code.
Stéfan
On Thu, Feb 23, 2012 at 6:22 AM, Guillaume Gay < guillaume@mitotic-machine.org> wrote:
Hi all,
Here is a first version of the linescan implementation. It sort of works, but I have some issues:
-the major one is that when I instantiate the LineScanInteractor within the imshow() function definition, I don't catch the events any more. So this is not usable in an interactive session.
-I can't get the ticks on the linescan plot to update properly...
-also there should be some kind of a reset mechanism, because if the image is zoomed in, you can lost the handles of the line
So if any one have a hint on how to do this...
Meanwhile I can try to have this work in conjunction tifffile's imshow (which should not be so complicated).
With all that maybe it would be better to implement a subclass of FigureCanvas, so that linescan appears only when a button (at the bottom of the window) is pressed, and it is easy to add e.g. a histogram plot or a contrast setter... what do you think?
Bye
Guillaume
HI Guillaume, I don't actually see a link or attachment in this email. Could you point me to the code you mention above? Thanks, -Tony
Le 20/02/2012 12:11, Guillaume Gay a écrit :
Ok, I can give it a try...
Some questions then:
- skivi is pure Qt, so must I keep it that way (no matplotlib dependency)? - skivi is good for RGB images, but not so much for greyscale... Also data conversion from uint16 to uint8 turns everything black (it set anything > 256 to 0), shall this be corrected? -Christoph Gohlke tifffile.imshow() is somehow closer to what us microscopy guys are expecting (more suitable for those greyscale multipage tiffs), though some features of the fancy viewer such as the contrast settings, are great. Also it is a pure matplotlib implementation and the intensity value reading is already there. So my question is: Are those tools needed by the general image analysis skimage community are more by scientific tiff users? If the latest, my guess is that building on top of matplotlib and Christoph's implementation of imshow is a better tactic (plus it would be more cross platform, as this can be a widget irrespective of the backend).
Cheers,
Guillaume
Le 20/02/2012 08:04, Stéfan van der Walt a écrit :
On Fri, Feb 17, 2012 at 6:53 AM, Guillaume Gay <guillaume@mitotic-machine.org**> wrote:
I just happen to code a simple linescan function, if that helps...
Thanks, Guillaume! If you could integrate this with the fancy Qt imshow to display the line, that would be wonderful, but otherwise I'm sure we'll still be able to use this code.
Stéfan
participants (4)
-
Guillaume Gay -
Neil Yager -
Stéfan van der Walt -
Tony Yu