Z-Axis Plot: Multi-Channel?

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Z-Axis Plot: Multi-Channel?

Jacob Keller-2
Dear Imagers,

I am very fond of the "plot z-axis" feature in imageJ (especially the
"live" part), but would love a version which could plot multiple color
channels together, hopefully each scaled separately to the plot window and
overlayed and in a representative color. I guess it would be good to be
able to select which channels to plot somewhere before or during plotting.
Is something like this out there? If not, I think this feature gets a good
amount of use, it would benefit many people to have a slightly suped-up
version.

Also, I would note that sometimes the plots in live mode get snaggled with
longer stacks and fast movements of the ROI--the plots look disjointed and
resolve with a slight jiggle of the ROI. Perhaps a bug?

All the best,

Jacob Keller

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Re: Z-Axis Plot: Multi-Channel?

Tiago Ferreira-2
Jacob,

The BAR update site (https://imagej.net/BAR) provides that functionality.
(Some screencasts here: https://git.io/vy2SN)


> sometimes the plots in live mode get snaggled with longer stacks and
> fast movements of the ROI. Perhaps a bug?

Ultimately it will be a performance issue, specially if you resize or
redraw the ROI. I never experienced lagging or jitter from just moving
the ROI around the image canvas.

HTH,
T.

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Re: Z-Axis Plot: Multi-Channel?

Jacob Keller-2
I am excited to get this working--I've downloaded it, but see something
strange happening. The temporal signal is supposed to be an oscillation in
intensity over time, which I see in the normal plotter, but in the
multi-channel, it looks like perhaps it's doing a running average, or when
I play with other things, even a running sum. I have attached an image with
the old plotter on the left, and the new one on the right. It may be
something I am doing wrong, or perhaps a bug in the program. Is there a
required input format, perhaps, or something that must be true about the
arrangement of the channels?

All the best,

Jacob

On Thu, Mar 9, 2017 at 9:56 AM, Tiago Ferreira <
[hidden email]> wrote:

> Jacob,
>
> The BAR update site (https://imagej.net/BAR) provides that functionality.
> (Some screencasts here: https://git.io/vy2SN)
>
>
> > sometimes the plots in live mode get snaggled with longer stacks and
> > fast movements of the ROI. Perhaps a bug?
>
> Ultimately it will be a performance issue, specially if you resize or
> redraw the ROI. I never experienced lagging or jitter from just moving
> the ROI around the image canvas.
>
> HTH,
> T.
>
>
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plot_malfunction.png (25K) Download Attachment
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Re: Z-Axis Plot: Multi-Channel?

Tiago Ferreira-2
On Thu, Mar 9, 2017 at 10:38 AM, Jacob Keller <[hidden email]> wrote:
> something strange happening. The temporal signal is supposed to be an oscillation in intensity over time, which I see in the normal plotter, but in the multi-channel, it looks like perhaps it's doing a running average, or when I play with other things, even a running sum.

Just fixed it (https://git.io/vya4H).
It was an overlook when implementing the StdDev error bars while ago.
It will be available through the updater later in the week once I arrive to the lab (I am traveling right now)

HTH,
-tiago

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Re: Z-Axis Plot: Multi-Channel?

Glyn Nelson
In reply to this post by Jacob Keller-2
Hi Jacob,

I think the multi colour plot written by Kees Straatman in Leicester might do z stacks as well:

http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/AIF/software-1/imagej-macros#Multi%20colour%20profile

Glyn


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Re: Z-Axis Plot: Multi-Channel?

Tiago Ferreira-2
In reply to this post by Tiago Ferreira-2
Dear Jacob,

Just pushed a new release (BAR 1.1.13) to the updater [1].

You can access 'BAR>Analysis>Multichannel ZT-axis Profile' after running
'Help>Update Fiji..' and subscribing to the BAR update site[2]
If you need to edit the script, you can do so using the 'Shift-trick'[3]

This release has also a 'Multi_ROI_Profiler' script that plots ROI intensities over
time that you may find useful. (I wrote it to monitor iGluSnFR/jRGECO fluorescence)

[1] https://github.com/tferr/Scripts/releases
[2] http://imagej.net/BAR#Installation
[3] http://imagej.net/BAR#OpeningBAR


On Mar 9, 2017, at 12:31, Keller, Jacob <[hidden email]> wrote:
> How can I get this into the code?

Sorry, I do not understand that question.
If you bump into any issues, it is better to use http://forum.imagej.net

HTH,
-tiago

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Re: Z-Axis Plot: Multi-Channel?

Jacob Keller-2
Yes! It works, and I'll give the multiplot a shot as well--you are right,
it should be useful. I noticed that the y-axis of the plot always has zero
at the bottom, whereas the native plotter scales to fit, apparently, the
min/max of the trace. Unless you know off-hand, I will try to figure out
where to toggle this, since sometimes it's helpful to have the
min/max-scaled y-axis.

Thanks very much--I've been looking for something like this for a long time!

Jacob

On Fri, Mar 10, 2017 at 10:12 AM, Tiago Ferreira <
[hidden email]> wrote:

> Dear Jacob,
>
> Just pushed a new release (BAR 1.1.13) to the updater [1].
>
> You can access 'BAR>Analysis>Multichannel ZT-axis Profile' after running
> 'Help>Update Fiji..' and subscribing to the BAR update site[2]
> If you need to edit the script, you can do so using the 'Shift-trick'[3]
>
> This release has also a 'Multi_ROI_Profiler' script that plots ROI
> intensities over
> time that you may find useful. (I wrote it to monitor iGluSnFR/jRGECO
> fluorescence)
>
> [1] https://github.com/tferr/Scripts/releases
> [2] http://imagej.net/BAR#Installation
> [3] http://imagej.net/BAR#OpeningBAR
>
>
> On Mar 9, 2017, at 12:31, Keller, Jacob <[hidden email]> wrote:
> > How can I get this into the code?
>
> Sorry, I do not understand that question.
> If you bump into any issues, it is better to use http://forum.imagej.net
>
> HTH,
> -tiago
>
>
>

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