Dear,
I am struggling with making a plugging in ImageJ / FiJi. What I want to do, is from a TIFF file from a 13 stacks in Z, several point in time, and 4 channels, to create a new file (extraction) from the slice where there is more intensity. Indeed, during my acquisition, I made a Z stack, I am only interested on having one slice, which is the more intense in the fluorescent channel. Up-to-there, I am able to measure intensity in all the channel, all the time, and all the slice, but unable to from that to extract data in a way that I can ask the following: "for each slice, which slice present the highest value in intensity" Indeed, from that, I would be able to extract the given slice (for the 4 channels) and make a new file containing only the brightest slice for each time, based only on the value of the fluorescent channel (here channel 4 on the figure below). Would it be possible to help me on this macro or maybe some have idea about an easiest way? Many thanks by advance! :) |
Hi cbenji59,
the following ImageJ forum post might help you in achieving your goal. The macro, presented there basically measures the intensity and extracts the respective brightest slice from a xyzt-stack. You can accordingly adjust this to make it work for your type of stacks. kind regards, Jan 2016-08-01 9:38 GMT+02:00 cbenji59 <[hidden email]>: > Dear, > > I am struggling with making a plugging in ImageJ / FiJi. > What I want to do, is from a TIFF file from a 13 stacks in Z, several point > in time, and 4 channels, to create a new file (extraction) from the slice > where there is more intensity. > Indeed, during my acquisition, I made a Z stack, I am only interested on > having one slice, which is the more intense in the fluorescent channel. > > Up-to-there, I am able to measure intensity in all the channel, all the > time, and all the slice, but unable to from that to extract data in a way > that I can ask the following: > > "for each slice, which slice present the highest value in intensity" > > Indeed, from that, I would be able to extract the given slice (for the 4 > channels) and make a new file containing only the brightest slice for each > time, based only on the value of the fluorescent channel (here channel 4 on > the figure below). > > Would it be possible to help me on this macro or maybe some have idea about > an easiest way? > Many thanks by advance! :) > > > > <http://imagej.1557.x6.nabble.com/file/n5016959/results.png> > > > > -- > View this message in context: > http://imagej.1557.x6.nabble.com/Extraction-of-slice-having-the-maximum-intensity-in-a-specific-channel-tp5016959.html > Sent from the ImageJ mailing list archive at Nabble.com. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- CEO: Dr. rer. nat. Jan Brocher phone: +49 (0)6234 917 03 39 mobile: +49 (0)176 705 746 81 e-mail: [hidden email] info: [hidden email] inquiries: [hidden email] web: www.biovoxxel.de -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Sorry, link missing. So, here we go:
http://forum.imagej.net/t/maximum-intensity-z-project-alters-values-randomly/2193/2 Am 01.08.2016 13:09 schrieb "BioVoxxel" <[hidden email]>: > Sorry, link missing. So, here we go: > > http://forum.imagej.net/t/maximum-intensity-z-project-alters-values-randomly/2193/2 > > Am 01.08.2016 12:12 schrieb "BioVoxxel" <[hidden email]>: > >> Hi cbenji59, >> >> the following ImageJ forum post might help you in achieving your goal. >> The macro, presented there basically measures the intensity and extracts >> the respective brightest slice from a xyzt-stack. >> You can accordingly adjust this to make it work for your type of stacks. >> >> kind regards, >> Jan >> >> 2016-08-01 9:38 GMT+02:00 cbenji59 <[hidden email]>: >> >>> Dear, >>> >>> I am struggling with making a plugging in ImageJ / FiJi. >>> What I want to do, is from a TIFF file from a 13 stacks in Z, several >>> point >>> in time, and 4 channels, to create a new file (extraction) from the slice >>> where there is more intensity. >>> Indeed, during my acquisition, I made a Z stack, I am only interested on >>> having one slice, which is the more intense in the fluorescent channel. >>> >>> Up-to-there, I am able to measure intensity in all the channel, all the >>> time, and all the slice, but unable to from that to extract data in a way >>> that I can ask the following: >>> >>> "for each slice, which slice present the highest value in intensity" >>> >>> Indeed, from that, I would be able to extract the given slice (for the 4 >>> channels) and make a new file containing only the brightest slice for >>> each >>> time, based only on the value of the fluorescent channel (here channel 4 >>> on >>> the figure below). >>> >>> Would it be possible to help me on this macro or maybe some have idea >>> about >>> an easiest way? >>> Many thanks by advance! :) >>> >>> >>> >>> <http://imagej.1557.x6.nabble.com/file/n5016959/results.png> >>> >>> >>> >>> -- >>> View this message in context: >>> http://imagej.1557.x6.nabble.com/Extraction-of-slice-having-the-maximum-intensity-in-a-specific-channel-tp5016959.html >>> Sent from the ImageJ mailing list archive at Nabble.com. >>> >>> -- >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >>> >> >> >> >> -- >> >> CEO: Dr. rer. nat. Jan Brocher >> phone: +49 (0)6234 917 03 39 >> mobile: +49 (0)176 705 746 81 >> e-mail: [hidden email] >> info: [hidden email] >> inquiries: [hidden email] >> web: www.biovoxxel.de >> > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Great! Many thanks for this link, I didn't find it out.
I made few modification for extracting the channels referring to the same slice, and it works perfectly! Many thanks for your help! :) |
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