Hi,
Could anyone advise on how to apply LUT along the z-axis of an image stack? Googled a while, but no results, maybe i did not get the right keyword? Thanks! Kevin -- Truth Shall Make You Free -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Hi,
The plugin for that is "Temporal Color-Code", available by default in Fiji (Image > Hyperstacks > Temporal-Color Code) Christophe On Sun, 5 Apr 2020 at 18:25, aget liang <[hidden email]> wrote: > Hi, > Could anyone advise on how to apply LUT along the z-axis of an image stack? > Googled a while, but no results, maybe i did not get the right keyword? > Thanks! > Kevin > -- > Truth Shall Make You Free > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Hi ,
Sorry for the misunderstanding - if you need something that will apply a LUT but nor project afterwards, I added a "No projection" option to Kiota Miura "Temporal Color Code" macro (it's actually not a plugin). I actually started from the version modified by Eugene Katrukha that includes another projection method (weighted sum). The modified macro i here: http://www.neurocytolab.org/up/Temporal-Color_Code.ijm By selecting "None" in the projection methods, you'll get the RGB colored stack using the selected LUT. Best regards, Christophe On Sun, 5 Apr 2020 at 20:52, aget liang <[hidden email]> wrote: >> >>> Thanks Christophe, that one will generate a projection. How to prevent >>> the projecting function but keep the LUT application? I found similar >>> questions online, but no solutions there. >>> https://forum.image.sc/t/time-lapse-color-code-without-projection/24037 >>> Z_code_stack seems to be the way to go, but i did not get it working yet >>> (got error messages, no experiences with java plugins). >>> https://github.com/fiji/cookbook/blob/master/src/main/java/sc/fiji/cookbook/Z_Code_Stack.java >>> Any idea? Thanks! >>> >>> >>> On Sun, Apr 5, 2020 at 12:51 PM Christophe Leterrier < >>> [hidden email]> wrote: >>> >>>> Hi, >>>> >>>> The plugin for that is "Temporal Color-Code", available by default in >>>> Fiji (Image > Hyperstacks > Temporal-Color Code) >>>> >>>> Christophe >>>> >>>> On Sun, 5 Apr 2020 at 18:25, aget liang <[hidden email]> wrote: >>>> >>>>> Hi, >>>>> Could anyone advise on how to apply LUT along the z-axis of an image >>>>> stack? >>>>> Googled a while, but no results, maybe i did not get the right keyword? >>>>> Thanks! >>>>> Kevin >>>>> -- >>>>> Truth Shall Make You Free >>>>> >>>>> -- >>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >>>>> >>>> >>> >>> -- >>> Truth Shall Make You Free >>> >> >> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
In reply to this post by aget
> On Apr 5, 2020, at 12:24 PM, aget liang <[hidden email]> wrote:
> > Hi, > Could anyone advise on how to apply LUT along the z-axis of an image stack? > Googled a while, but no results, maybe i did not get the right keyword? There is an updated version of the macro by Kota Miura that implements the commands Plugins > Stacks> Time-Lapse Color Coder (ImageJ) Image > Hyperstacks > Temporal-Color Code (Fiji) available at http://wsr.imagej.net/macros/Time-Lapse_Color_Coder.ijm that displays a colorized version of the stack, not just the maximum projection of the colorized stack. -wayne -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Thank you Wayne and Christophe! This updated code from Kota Miura is
perfect. Wonder if it could be put into one of the update sites from imageJ/Fiji, so it will be available to broader users. Kevin On Sun, Apr 5, 2020 at 3:51 PM Wayne Rasband <[hidden email]> wrote: > > On Apr 5, 2020, at 12:24 PM, aget liang <[hidden email]> wrote: > > > > Hi, > > Could anyone advise on how to apply LUT along the z-axis of an image > stack? > > Googled a while, but no results, maybe i did not get the right keyword? > > There is an updated version of the macro by Kota Miura that implements the > commands > > Plugins > Stacks> Time-Lapse Color Coder (ImageJ) > Image > Hyperstacks > Temporal-Color Code (Fiji) > > available at > > http://wsr.imagej.net/macros/Time-Lapse_Color_Coder.ijm > > that displays a colorized version of the stack, not just the maximum > projection of the colorized stack. > > -wayne > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- Truth Shall Make You Free -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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