Object-Image successor

[H=?ISO-8859-1?Q?=E5kan?= Toresson]

My group does work on dynamic changes within dendritic spines. We thus
analyse at least two channels; one for the spine and one or more for an
organelle or protein of interest.  The analysis is done manually over time
(from three time-points and up) by evaluating, spine by spine, the content
of different markers. Typically a stack will contain a few hundred markers.

For a long time we have been using Object-Image for these analyses. As the
number of MacOS9 computers go down this becomes a less convenient solution
though...

The requirements for the software we need are some key features of Object-Image.
1. That non-destructive labels can be added to time stacks (and sometimes
z-stacks) to mark the position of different classes of spines and,
evidently, that the program records the number and position of the different
labels.
2. That a label set in one of the slices can be seen in all other slices.
This is important because we set one label for a feature observed in one
channel (e.g. stubby spine) and then another feature at a later time-point
(e.g. the presence of GFP-labelled CamKII).

I’m new to ImageJ and would very much appreciate if anyone could let me know
of a suitable plugin for ImageJ to perform such analyses. I’ve tried ObjectJ
(created by Norbert Visscher who did Object-Image) but so far I’m unable to
perform what I need.

Kind regards,
HT

[Michael Schmid]

Hi Håkan,

if it is good enough to have numbers, the built-in point
selection tool could help.

Double-click it and check "Label points".

You can get a point selection manually, in a macro (makePoint
command) or as a result of Process>Binary>Find Maxima.

Michael
________________________________________________________________

On 25 Aug 2008, at 17:34, Håkan Toresson wrote:

> My group does work on dynamic changes within dendritic spines. We thus
> analyse at least two channels; one for the spine and one or more  
> for an
> organelle or protein of interest.  The analysis is done manually  
> over time
> (from three time-points and up) by evaluating, spine by spine, the  
> content
> of different markers. Typically a stack will contain a few hundred  
> markers.
>
> For a long time we have been using Object-Image for these analyses.  
> As the
> number of MacOS9 computers go down this becomes a less convenient  
> solution
> though...
>
> The requirements for the software we need are some key features of  
> Object-Image.
> 1. That non-destructive labels can be added to time stacks (and  
> sometimes
> z-stacks) to mark the position of different classes of spines and,
> evidently, that the program records the number and position of the  
> different
> labels.
> 2. That a label set in one of the slices can be seen in all other  
> slices.
> This is important because we set one label for a feature observed  
> in one
> channel (e.g. stubby spine) and then another feature at a later  
> time-point
> (e.g. the presence of GFP-labelled CamKII).
>
> I’m new to ImageJ and would very much appreciate if anyone could  
> let me know
> of a suitable plugin for ImageJ to perform such analyses. I’ve  
> tried ObjectJ
> (created by Norbert Visscher who did Object-Image) but so far I’m  
> unable to
> perform what I need.
>
> Kind regards,
> HT

[Bill Mohler]

I have been recently using the Cell Counter plugin written by Kurt de
Vos.  A very useful utility.

As I'm working with densely populated 3D stacks, it would actually be
useful if I could toggle the display such that every cell marker is
displayed (and not only those that are in the current section).
Being able to interchangeably see all markers in the volume or only
those in the current section would enhance my ability to account for
objects that extend through several sections.

I haven't seen the option in the plugin dialog/control panel, and I
wonder if it already exists or could be easily added.  Let me know if
this request is unclear, and I can explain further.

Bill
--
-----------------
William A. Mohler
Associate Professor
Dept. of Genetics and Developmental Biology
University of Connecticut Health Center
MC-3301
263 Farmington Ave.
Farmington, CT   06030-3301

[hidden email]
Mobile: [phone]

Office: [phone], room E2056
Lab: [phone], room E2052
Fax: [phone]

G&DB dept. ofc.: [phone]
G&DB dept. fax : [phone]
http://genetics.uchc.edu/Faculty/Mohler/Mohler.html

[Bill Mohler]

I think I've found the line(s) of code that would need to be changed
to allow this toggle behavior:  In File CellCntrImageCanvas.java,
within class imageWithMarkers, is an "if
(m.getZ()==img.getCurrentSlice()){" statement.  It seems the logic of
that statement and the following lines of code that govern display
would be all that need to be changed to effect the toggling
display-all/display-in-slice behavior.

Bill

>I have been recently using the Cell Counter plugin written by Kurt
>de Vos.  A very useful utility.
>
>As I'm working with densely populated 3D stacks, it would actually
>be useful if I could toggle the display such that every cell marker
>is displayed (and not only those that are in the current section).
>Being able to interchangeably see all markers in the volume or only
>those in the current section would enhance my ability to account for
>objects that extend through several sections.
>
>I haven't seen the option in the plugin dialog/control panel, and I
>wonder if it already exists or could be easily added.  Let me know
>if this request is unclear, and I can explain further.
>
>Bill
>--
>-----------------
>William A. Mohler
>Associate Professor
>Dept. of Genetics and Developmental Biology
>University of Connecticut Health Center
>MC-3301
>263 Farmington Ave.
>Farmington, CT   06030-3301
>
>[hidden email]
>Mobile: [phone]
>
>Office: [phone], room E2056
>Lab: [phone], room E2052
>Fax: [phone]
>
>G&DB dept. ofc.: [phone]
>G&DB dept. fax : [phone]
>http://genetics.uchc.edu/Faculty/Mohler/Mohler.html

[H=?ISO-8859-1?Q?=E5kan?= Toresson]

This modification would be excellent for my purposes (I just posted a  
question titled Object-Image successor...). I'm not a programmer so  
if this modification works I'd appreciate if it was made available.  
Many thanks!//HT


25 aug 2008 kl. 21.26 skrev Bill Mohler:

> I think I've found the line(s) of code that would need to be  
> changed to allow this toggle behavior:  In File  
> CellCntrImageCanvas.java, within class imageWithMarkers, is an "if  
> (m.getZ()==img.getCurrentSlice()){" statement.  It seems the logic  
> of that statement and the following lines of code that govern  
> display would be all that need to be changed to effect the toggling  
> display-all/display-in-slice behavior.
>
> Bill
>
>> I have been recently using the Cell Counter plugin written by Kurt  
>> de Vos.  A very useful utility.
>>
>> As I'm working with densely populated 3D stacks, it would actually  
>> be useful if I could toggle the display such that every cell  
>> marker is displayed (and not only those that are in the current  
>> section). Being able to interchangeably see all markers in the  
>> volume or only those in the current section would enhance my  
>> ability to account for objects that extend through several sections.
>>
>> I haven't seen the option in the plugin dialog/control panel, and  
>> I wonder if it already exists or could be easily added.  Let me  
>> know if this request is unclear, and I can explain further.
>>
>> Bill
>> --
>> -----------------
>> William A. Mohler
>> Associate Professor
>> Dept. of Genetics and Developmental Biology
>> University of Connecticut Health Center
>> MC-3301
>> 263 Farmington Ave.
>> Farmington, CT   06030-3301
>>
>> [hidden email]
>> Mobile: [phone]
>>
>> Office: [phone], room E2056
>> Lab: [phone], room E2052
>> Fax: [phone]
>>
>> G&DB dept. ofc.: [phone]
>> G&DB dept. fax : [phone]
>> http://genetics.uchc.edu/Faculty/Mohler/Mohler.html

[Wayne Rasband]

On Aug 25, 2008, at 3:26 PM, Bill Mohler wrote:

> I think I've found the line(s) of code that would need to be changed
> to allow this toggle behavior:  In File CellCntrImageCanvas.java,
> within class imageWithMarkers, is an "if
> (m.getZ()==img.getCurrentSlice()){" statement.  It seems the logic of
> that statement and the following lines of code that govern display
> would be all that need to be changed to effect the toggling
> display-all/display-in-slice behavior.

There is a new version of the Cell Counter at

     http://rsbweb.nih.gov/ij/plugins/cell-counter.html

that adds a "Show All" checkbox. This version also works with
hyperstacks and composite color images.

-wayne

> Bill
>
>> I have been recently using the Cell Counter plugin written by Kurt de
>> Vos.  A very useful utility.
>>
>> As I'm working with densely populated 3D stacks, it would actually be
>> useful if I could toggle the display such that every cell marker is
>> displayed (and not only those that are in the current section). Being
>> able to interchangeably see all markers in the volume or only those
>> in the current section would enhance my ability to account for
>> objects that extend through several sections.
>>
>> I haven't seen the option in the plugin dialog/control panel, and I
>> wonder if it already exists or could be easily added.  Let me know if
>> this request is unclear, and I can explain further.
>>
>> Bill
>> --
>> -----------------
>> William A. Mohler
>> Associate Professor
>> Dept. of Genetics and Developmental Biology
>> University of Connecticut Health Center
>> MC-3301
>> 263 Farmington Ave.
>> Farmington, CT   06030-3301
>>
>> [hidden email]
>> Mobile: [phone]
>>
>> Office: [phone], room E2056
>> Lab: [phone], room E2052
>> Fax: [phone]
>>
>> G&DB dept. ofc.: [phone]
>> G&DB dept. fax : [phone]
>> http://genetics.uchc.edu/Faculty/Mohler/Mohler.html
>

[H=?ISO-8859-1?Q?=E5kan?= Toresson]

Thanks Wayne, this makes the cell counter more useful for my  
purposes.//Hakan


27 aug 2008 kl. 18.10 skrev Wayne Rasband:

> On Aug 25, 2008, at 3:26 PM, Bill Mohler wrote:
>
>> I think I've found the line(s) of code that would need to be  
>> changed to allow this toggle behavior:  In File  
>> CellCntrImageCanvas.java, within class imageWithMarkers, is an "if  
>> (m.getZ()==img.getCurrentSlice()){" statement.  It seems the logic  
>> of that statement and the following lines of code that govern  
>> display would be all that need to be changed to effect the  
>> toggling display-all/display-in-slice behavior.
>
> There is a new version of the Cell Counter at
>
>     http://rsbweb.nih.gov/ij/plugins/cell-counter.html
>
> that adds a "Show All" checkbox. This version also works with  
> hyperstacks and composite color images.
>
> -wayne
>
>> Bill
>>
>>> I have been recently using the Cell Counter plugin written by  
>>> Kurt de Vos.  A very useful utility.
>>>
>>> As I'm working with densely populated 3D stacks, it would  
>>> actually be useful if I could toggle the display such that every  
>>> cell marker is displayed (and not only those that are in the  
>>> current section). Being able to interchangeably see all markers  
>>> in the volume or only those in the current section would enhance  
>>> my ability to account for objects that extend through several  
>>> sections.
>>>
>>> I haven't seen the option in the plugin dialog/control panel, and  
>>> I wonder if it already exists or could be easily added.  Let me  
>>> know if this request is unclear, and I can explain further.
>>>
>>> Bill
>>> --
>>> -----------------
>>> William A. Mohler
>>> Associate Professor
>>> Dept. of Genetics and Developmental Biology
>>> University of Connecticut Health Center
>>> MC-3301
>>> 263 Farmington Ave.
>>> Farmington, CT   06030-3301
>>>
>>> [hidden email]
>>> Mobile: [phone]
>>>
>>> Office: [phone], room E2056
>>> Lab: [phone], room E2052
>>> Fax: [phone]
>>>
>>> G&DB dept. ofc.: [phone]
>>> G&DB dept. fax : [phone]
>>> http://genetics.uchc.edu/Faculty/Mohler/Mohler.html
>>