Mark point through stack

[kekie]

I'm counting foci which appear distinctly on only a few Z layers. I need some
way to mark foci so I don't end up counting the same focus more than once.
Currently I'm just selecting the foci on one Z (where it is most visible)
with the rectangle select tool and cutting. Unfortunately, this only cuts
one Z, so I have to scrub through the stack before counting any new foci.

Is there any way to create a mark on an image that can be seen on all Z's?
Preferably one that is obvious (like the big black square created by
cutting) and actually modifes the image and so can be saved into the file
(so not multi-point select).

Thanks!



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[Michael Schmid]

Hi Kekie,

you can add the rectangle selections (=ROIs, regions of interest) to the
ROI Manager (press "t"). In the ROI Manager panel, select "Show All".
If you click on the ROI label in the list of ROIs in the ROI Manager
window, the image stack will jump to the slice where you have selected
the rectangle.

You can save the ROI set with the ROI Managers More>>Save.
If you save the image as .tif or .zip, the ROIs are saved a overlays; if
you open the image again they are only visible at the slice where they
are selected.
Use Image>Overlay>To ROI Manager and select "Show All" to make them
visible in all slices.

More about the ROI Manager:
https://imagej.nih.gov/ij/docs/guide/146-30.html#toc-Subsubsection-30.14.5

If you really want to modify your image stack in a destructive manner,
use Edit>Clear, Edit>Fill or Process>Math>Set and select that you want
to modify all slices. You may also use the macro recorder to record that
command and create a macro that you can assign to a shortcut. See, e.g.
   https://imagej.net/Introduction_into_Macro_Programming


Michael
________________________________________________________________
On 08/10/2018 11:02, kekie wrote:

> I'm counting foci which appear distinctly on only a few Z layers. I need some
> way to mark foci so I don't end up counting the same focus more than once.
> Currently I'm just selecting the foci on one Z (where it is most visible)
> with the rectangle select tool and cutting. Unfortunately, this only cuts
> one Z, so I have to scrub through the stack before counting any new foci.
>
> Is there any way to create a mark on an image that can be seen on all Z's?
> Preferably one that is obvious (like the big black square created by
> cutting) and actually modifes the image and so can be saved into the file
> (so not multi-point select).
>
> Thanks!

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[Kenneth Sloan-2]

My approach to this may be overkill for your application - but here's what I have done:

a) I write custom data-collection plugins in Java
b) My code uses Java Classes that extend things like "StackWindow" to provide
   extra functionality.
c) My code keeps it's own "database" of marked points, keeping track of x,y,z
d) For display purposes, the code is notified whenever the stack slice is changed.
   When that happens, it re-displays all the relevant markers.  Sometimes, that's
   the markers for that particular slice - but more often I provide a user-defined
   "slab" and display all markers "close to" the current z value.  This is particularly
   useful when the same physical object can appear in multiple adjacent slices.

Now...as I said above, this is a fair amount of work.  I don't know of any easy way
to do this using the standard ImageJ interface.  But, I recognize that I resort to
custom Java code very quickly - because its the most natural way for me to define such things.
Sometimes too quickly - which means I may be overlooking a standard way to do this.


--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.

> On 8 Oct 2018, at 11:02 , kekie <[hidden email]> wrote:
>
> I'm counting foci which appear distinctly on only a few Z layers. I need some
> way to mark foci so I don't end up counting the same focus more than once.
> Currently I'm just selecting the foci on one Z (where it is most visible)
> with the rectangle select tool and cutting. Unfortunately, this only cuts
> one Z, so I have to scrub through the stack before counting any new foci.
>
> Is there any way to create a mark on an image that can be seen on all Z's?
> Preferably one that is obvious (like the big black square created by
> cutting) and actually modifes the image and so can be saved into the file
> (so not multi-point select).
>
> Thanks!
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Krs5]

Hi Kekie,

Michael is correct but easier is to add the marks to the ROI Manager and select from the ROI menu More > Options... and deselect "Associate "Show All" ROIs with slices. Only problem I notice is that this works for most ROI types but not for points/multi-points, so use one of the other selection options. Now your selections are visible on all slices.

My guess is that this is a bug?

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
www.le.ac.uk/advanced-imaging-facility


Postal address:

-----Original Message-----
From: Michael Schmid <[hidden email]>
Sent: 08 October 2018 11:25
To: [hidden email]
Subject: Re: Mark point through stack

Hi Kekie,

you can add the rectangle selections (=ROIs, regions of interest) to the ROI Manager (press "t"). In the ROI Manager panel, select "Show All".
If you click on the ROI label in the list of ROIs in the ROI Manager window, the image stack will jump to the slice where you have selected the rectangle.

You can save the ROI set with the ROI Managers More>>Save.
If you save the image as .tif or .zip, the ROIs are saved a overlays; if you open the image again they are only visible at the slice where they are selected.
Use Image>Overlay>To ROI Manager and select "Show All" to make them visible in all slices.

More about the ROI Manager:
https://imagej.nih.gov/ij/docs/guide/146-30.html#toc-Subsubsection-30.14.5

If you really want to modify your image stack in a destructive manner, use Edit>Clear, Edit>Fill or Process>Math>Set and select that you want to modify all slices. You may also use the macro recorder to record that command and create a macro that you can assign to a shortcut. See, e.g.
   https://imagej.net/Introduction_into_Macro_Programming


Michael
________________________________________________________________
On 08/10/2018 11:02, kekie wrote:

> I'm counting foci which appear distinctly on only a few Z layers. I
> need some way to mark foci so I don't end up counting the same focus more than once.
> Currently I'm just selecting the foci on one Z (where it is most
> visible) with the rectangle select tool and cutting. Unfortunately,
> this only cuts one Z, so I have to scrub through the stack before counting any new foci.
>
> Is there any way to create a mark on an image that can be seen on all Z's?
> Preferably one that is obvious (like the big black square created by
> cutting) and actually modifes the image and so can be saved into the
> file (so not multi-point select).
>
> Thanks!

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[jmutterer]

Dear all,
Here's a macro set with
- a tool that places dots with colors reflecting their z position
- slice navigation with 'q' and 'w' that adjusts dot size to according to
distance to the current slice.
It sometimes allows to better perceive dots already marked in neighbouring
slices.

https://gist.github.com/mutterer/29660e44fb273627cf9508d1d4e3e2f8

Jerome

Le lun. 8 oct. 2018 à 13:20, Straatman, Kees (Dr.) <[hidden email]> a
écrit :

> Hi Kekie,
>
> Michael is correct but easier is to add the marks to the ROI Manager and
> select from the ROI menu More > Options... and deselect "Associate "Show
> All" ROIs with slices. Only problem I notice is that this works for most
> ROI types but not for points/multi-points, so use one of the other
> selection options. Now your selections are visible on all slices.
>
> My guess is that this is a bug?
>
> Best wishes
>
> Kees
>
>
> Dr Ir K.R. Straatman
> Senior Experimental Officer
> Advanced Imaging Facility
> Centre for Core Biotechnology Services
> University of Leicester
> www.le.ac.uk/advanced-imaging-facility
>
>
> Postal address:
>
> -----Original Message-----
> From: Michael Schmid <[hidden email]>
> Sent: 08 October 2018 11:25
> To: [hidden email]
> Subject: Re: Mark point through stack
>
> Hi Kekie,
>
> you can add the rectangle selections (=ROIs, regions of interest) to the
> ROI Manager (press "t"). In the ROI Manager panel, select "Show All".
> If you click on the ROI label in the list of ROIs in the ROI Manager
> window, the image stack will jump to the slice where you have selected the
> rectangle.
>
> You can save the ROI set with the ROI Managers More>>Save.
> If you save the image as .tif or .zip, the ROIs are saved a overlays; if
> you open the image again they are only visible at the slice where they are
> selected.
> Use Image>Overlay>To ROI Manager and select "Show All" to make them
> visible in all slices.
>
> More about the ROI Manager:
> https://imagej.nih.gov/ij/docs/guide/146-30.html#toc-Subsubsection-30.14.5
>
> If you really want to modify your image stack in a destructive manner, use
> Edit>Clear, Edit>Fill or Process>Math>Set and select that you want to
> modify all slices. You may also use the macro recorder to record that
> command and create a macro that you can assign to a shortcut. See, e.g.
>    https://imagej.net/Introduction_into_Macro_Programming
>
>
> Michael
> ________________________________________________________________
> On 08/10/2018 11:02, kekie wrote:
> > I'm counting foci which appear distinctly on only a few Z layers. I
> > need some way to mark foci so I don't end up counting the same focus
> more than once.
> > Currently I'm just selecting the foci on one Z (where it is most
> > visible) with the rectangle select tool and cutting. Unfortunately,
> > this only cuts one Z, so I have to scrub through the stack before
> counting any new foci.
> >
> > Is there any way to create a mark on an image that can be seen on all
> Z's?
> > Preferably one that is obvious (like the big black square created by
> > cutting) and actually modifes the image and so can be saved into the
> > file (so not multi-point select).
> >
> > Thanks!
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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