LUT applied to a 3d stack

classic Classic list List threaded Threaded
5 messages Options
Reply | Threaded
Open this post in threaded view
|

LUT applied to a 3d stack

aget
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
Reply | Threaded
Open this post in threaded view
|

Re: LUT applied to a 3d stack

lechristophe
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
Reply | Threaded
Open this post in threaded view
|

Re: LUT applied to a 3d stack

lechristophe
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
Reply | Threaded
Open this post in threaded view
|

Re: LUT applied to a 3d stack

Wayne Rasband-2
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
Reply | Threaded
Open this post in threaded view
|

Re: LUT applied to a 3d stack

aget
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