howdyjessie
commented
8 years ago @carlkesselman Does 'combo' count as a channel?
Open carlkesselman opened 9 years ago
howdyjessie
commented
8 years ago @carlkesselman Does 'combo' count as a channel?
carlkesselman
commented
8 years ago Yes. So we may have RGB (combo channel) which already has color assigned, so no color selector is needed, or the other channels, which are grayscale and can have color assigned to them. Actually, I wonder if there is a good way to determine what we have, other then looking at the channel name….
Carl
Dr. Carl Kesselman Dean’s Professor, Epstein Department of Industrial and Systems Engineering Fellow, Information Sciences Institute Viterbi School of Engineering
Professor, Preventive Medicine Keck School of Medicine
University of Southern California 4676 Admiralty Way, Suite 1001, Marina del Rey, CA 90292-6695 Phone: +1 (310) 448-9338 Email: carl@isi.edumailto:carl@isi.edu Web: http://www.isi.edu/~carl
On Nov 23, 2015, at 3:12 PM, Jessie Wong notifications@github.com<mailto:notifications@github.com> wrote:
@carlkesselmanhttps://github.com/carlkesselman Does 'combo' count as a channel?
— Reply to this email directly or view it on GitHubhttps://github.com/informatics-isi-edu/microscopy/issues/18#issuecomment-159097402.
meihuisu
commented
8 years ago Both 'combo'(we can change it to RGBcombo, it is named by us anyway) and 'TL Brightfield' assume color is assigned and the hue slider is not visible nor selectable.
mei
----- Original Message ----- From: "Carl Kesselman" notifications@github.com To: "informatics-isi-edu/microscopy" microscopy@noreply.github.com Sent: Monday, November 23, 2015 3:17:00 PM Subject: Re: [microscopy] Modify UI so channel selector is not avialable if only one channel. (#18)
Yes. So we may have RGB (combo channel) which already has color assigned, so no color selector is needed, or the other channels, which are grayscale and can have color assigned to them. Actually, I wonder if there is a good way to determine what we have, other then looking at the channel name….
Carl
Dr. Carl Kesselman Dean’s Professor, Epstein Department of Industrial and Systems Engineering Fellow, Information Sciences Institute Viterbi School of Engineering
Professor, Preventive Medicine Keck School of Medicine
University of Southern California 4676 Admiralty Way, Suite 1001, Marina del Rey, CA 90292-6695 Phone: +1 (310) 448-9338 Email: carl@isi.edumailto:carl@isi.edu Web: http://www.isi.edu/~carl
On Nov 23, 2015, at 3:12 PM, Jessie Wong notifications@github.com<mailto:notifications@github.com> wrote:
@carlkesselmanhttps://github.com/carlkesselman Does 'combo' count as a channel?
— Reply to this email directly or view it on GitHubhttps://github.com/informatics-isi-edu/microscopy/issues/18#issuecomment-159097402.
Reply to this email directly or view it on GitHub: https://github.com/informatics-isi-edu/microscopy/issues/18#issuecomment-159098365
carlkesselman
commented
8 years ago Is there a more robust way of indicating this? In particular, I’m concerned that we will be getting pyramids generated from other microscopes, and it would be good to have our expectations well defined, and even documented so we can tell the people generating the images exactly what we expect.
Carl
Dr. Carl Kesselman Dean’s Professor, Epstein Department of Industrial and Systems Engineering Fellow, Information Sciences Institute Viterbi School of Engineering
Professor, Preventive Medicine Keck School of Medicine
University of Southern California 4676 Admiralty Way, Suite 1001, Marina del Rey, CA 90292-6695 Phone: +1 (310) 448-9338 Email: carl@isi.edumailto:carl@isi.edu Web: http://www.isi.edu/~carl
On Nov 23, 2015, at 4:36 PM, meihuisu notifications@github.com<mailto:notifications@github.com> wrote:
Both 'combo'(we can change it to RGBcombo, it is named by us anyway) and 'TL Brightfield' assume color is assigned and the hue slider is not visible nor selectable.
mei
----- Original Message ----- From: "Carl Kesselman" notifications@github.com<mailto:notifications@github.com> To: "informatics-isi-edu/microscopy" microscopy@noreply.github.com<mailto:microscopy@noreply.github.com> Sent: Monday, November 23, 2015 3:17:00 PM Subject: Re: [microscopy] Modify UI so channel selector is not avialable if only one channel. (#18)
Yes. So we may have RGB (combo channel) which already has color assigned, so no color selector is needed, or the other channels, which are grayscale and can have color assigned to them. Actually, I wonder if there is a good way to determine what we have, other then looking at the channel name….
Carl
Dr. Carl Kesselman Dean’s Professor, Epstein Department of Industrial and Systems Engineering Fellow, Information Sciences Institute Viterbi School of Engineering
Professor, Preventive Medicine Keck School of Medicine
University of Southern California 4676 Admiralty Way, Suite 1001, Marina del Rey, CA 90292-6695 Phone: +1 (310) 448-9338 Email: carl@isi.edumailto:carl@isi.edumailto:carl@isi.edu Web: http://www.isi.edu/~carl
On Nov 23, 2015, at 3:12 PM, Jessie Wong notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:
@carlkesselmanhttps://github.com/carlkesselman Does 'combo' count as a channel?
— Reply to this email directly or view it on GitHubhttps://github.com/informatics-isi-edu/microscopy/issues/18#issuecomment-159097402.
Reply to this email directly or view it on GitHub: https://github.com/informatics-isi-edu/microscopy/issues/18#issuecomment-159098365
— Reply to this email directly or view it on GitHubhttps://github.com/informatics-isi-edu/microscopy/issues/18#issuecomment-159114297.
karlcz
commented
8 years ago I'm not sure what you can base it on other than one of these:
Basically, we've only seen single-sample (grayscale) channels in fluorescence images and 3-sample (RGB) channels in brightfield imagery. I don't know if/when we'll encounter anything more unusual...
karl
meihuisu
commented
8 years ago I think next thing is to rework it so it is easier to extend the option without any need to edit the source. A 2dViewer config setup or something. This is going to be true for all those greayscale/color/channelname table or relation.
mei
----- Original Message ----- From: "karlcz" notifications@github.com To: "informatics-isi-edu/microscopy" microscopy@noreply.github.com Cc: "meihuisu" mei@isi.edu Sent: Tuesday, November 24, 2015 8:21:29 AM Subject: Re: [microscopy] Modify UI so channel selector is not avialable if only one channel. (#18)
I'm not sure what you can base it on other than one of these:
Basically, we've only seen single-sample (grayscale) channels in fluorescence images and 3-sample (RGB) channels in brightfield imagery. I don't know if/when we'll encounter anything more unusual...
karl
Reply to this email directly or view it on GitHub: https://github.com/informatics-isi-edu/microscopy/issues/18#issuecomment-159320337
howdyjessie
commented
8 years ago Well anyway, here's what I've got so far: http://vm-dev-030.misd.isi.edu/~jessie/openseadragon-viewer/mview.html?url=http://vm-dev-030.misd.isi.edu/~mei/data/real3/DZC/Alexa%20Fluor%20488/ImageProperties.xml&x=0.5000000000000001&y=0.6452489905787349&z=0.6100553130613549
For now, when there's only one channel, I display the channel name in lieu of the channel selector dropdown.
carlkesselman
commented
8 years ago I think that is good.
There was one other issue related to contrast setting. For the time being, we don’t want it displayed, and we need to make sure that internally the setting is at 1. Not sure if this is the UI or app where this needs to happen.
Carl
Dr. Carl Kesselman Dean’s Professor, Epstein Department of Industrial and Systems Engineering Fellow, Information Sciences Institute Viterbi School of Engineering
Professor, Preventive Medicine Keck School of Medicine
University of Southern California 4676 Admiralty Way, Suite 1001, Marina del Rey, CA 90292-6695 Phone: +1 (310) 448-9338 Email: carl@isi.edumailto:carl@isi.edu Web: http://www.isi.edu/~carl
On Nov 24, 2015, at 3:55 PM, Jessie Wong notifications@github.com<mailto:notifications@github.com> wrote:
For now, when there's only one channel, I display the channel name in lieu of the channel selector dropdown.
— Reply to this email directly or view it on GitHubhttps://github.com/informatics-isi-edu/microscopy/issues/18#issuecomment-159442630.
carlkesselman
commented
8 years ago Actually, I see Mei has committed a new contrast function…so perhaps what I’m suggesting should’d be done, although defaulting to a contrast setting of 1 should still happen,
Carl
Dr. Carl Kesselman Dean’s Professor, Epstein Department of Industrial and Systems Engineering Fellow, Information Sciences Institute Viterbi School of Engineering
Professor, Preventive Medicine Keck School of Medicine
University of Southern California 4676 Admiralty Way, Suite 1001, Marina del Rey, CA 90292-6695 Phone: +1 (310) 448-9338 Email: carl@isi.edumailto:carl@isi.edu Web: http://www.isi.edu/~carl
On Nov 25, 2015, at 7:50 AM, Carl Kesselman carl@exchange.isi.edu<mailto:carl@exchange.isi.edu> wrote:
I think that is good.
There was one other issue related to contrast setting. For the time being, we don’t want it displayed, and we need to make sure that internally the setting is at 1. Not sure if this is the UI or app where this needs to happen.
Carl
Dr. Carl Kesselman Dean’s Professor, Epstein Department of Industrial and Systems Engineering Fellow, Information Sciences Institute Viterbi School of Engineering
Professor, Preventive Medicine Keck School of Medicine
University of Southern California 4676 Admiralty Way, Suite 1001, Marina del Rey, CA 90292-6695 Phone: +1 (310) 448-9338 Email: carl@isi.edumailto:carl@isi.edu Web: http://www.isi.edu/~carl
On Nov 24, 2015, at 3:55 PM, Jessie Wong notifications@github.com<mailto:notifications@github.com> wrote:
For now, when there's only one channel, I display the channel name in lieu of the channel selector dropdown.
— Reply to this email directly or view it on GitHubhttps://github.com/informatics-isi-edu/microscopy/issues/18#issuecomment-159442630.
howdyjessie
commented
8 years ago Should the contrast setting be hidden only when there's 1 channel or even when there's multiple channels?
carlkesselman
commented
8 years ago Assuming the contrast filter is working now, it makes sense to have this for any number of channels.
Carl
Dr. Carl Kesselman Dean’s Professor, Epstein Department of Industrial and Systems Engineering Fellow, Information Sciences Institute Viterbi School of Engineering
Professor, Preventive Medicine Keck School of Medicine
University of Southern California 4676 Admiralty Way, Suite 1001, Marina del Rey, CA 90292-6695 Phone: +1 (310) 448-9338 Email: carl@isi.edumailto:carl@isi.edu Web: http://www.isi.edu/~carl
On Nov 25, 2015, at 3:47 PM, Jessie Wong notifications@github.com<mailto:notifications@github.com> wrote:
Should the contrast setting be hidden only when there's 1 channel or even when there's multiple channels?
— Reply to this email directly or view it on GitHubhttps://github.com/informatics-isi-edu/microscopy/issues/18#issuecomment-159757703.
Right now if there is only one image channel the channel selector still shows, even thought it does nothing. This thould be changed so it doesn't show up unless there is more then one channel.