Modifying font/cross size on ImageJ default plugins

[Jonni Virtanen]

Hey,

I'm working on a project where I have to analyze a lot of samples by using
a grid overlay with crosses (Grid plugin) and counting the different cell
types with the Cell counter plugin. The problem is that the crosses are
really small and hard to see and so are the points when using Cell counter.
Is there a way to modify the cross size on Grid plugin and the font size on
Cell Counter?

Thanks,

Jonni Virtanen

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[Rasband, Wayne (NIH/NIMH) [E]]

> On Oct 11, 2015, at 10:03 AM, Jonni Virtanen <[hidden email]> wrote:
>
> Hey,
>
> I'm working on a project where I have to analyze a lot of samples by using
> a grid overlay with crosses (Grid plugin) and counting the different cell
> types with the Cell counter plugin. The problem is that the crosses are
> really small and hard to see and so are the points when using Cell counter.
> Is there a way to modify the cross size on Grid plugin and the font size on
> Cell Counter?

You can easily make the crosses larger in the Grid plugin:

  1. Type “L” (Plugins>Utilities>Command Finder)
  2. Enter “grid” in the Search box
  2. Select the line with “Grid” in the “Command” column
  3. Click “Source” (opens Grid_.java in the editor)
  4. Type ctrl-f (Edit>Find)
  5. Enter “arm” in the search box
  6. Change “float arm=5” to “float arm=20”
  7. Type ctrl-r (File>Compile and Run)

The crosses will now be four times larger. On Macs, use the command key instead of the control key when using keyboard shortcuts in the editor.

You can change the size of points created by the multi-point tool, and, in the next version of ImageJ, the multi-point tool will support multiple counters.

-wayne


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[Jonni Virtanen]

Hey,

Thanks a lot, this will make my life easier. Any idea when the next version
will be released?



2015-10-12 2:53 GMT+02:00 Rasband, Wayne (NIH/NIMH) [E] <
[hidden email]>:

> > On Oct 11, 2015, at 10:03 AM, Jonni Virtanen <[hidden email]>
> wrote:
> >
> > Hey,
> >
> > I'm working on a project where I have to analyze a lot of samples by
> using
> > a grid overlay with crosses (Grid plugin) and counting the different cell
> > types with the Cell counter plugin. The problem is that the crosses are
> > really small and hard to see and so are the points when using Cell
> counter.
> > Is there a way to modify the cross size on Grid plugin and the font size
> on
> > Cell Counter?
>
> You can easily make the crosses larger in the Grid plugin:
>
>   1. Type “L” (Plugins>Utilities>Command Finder)
>   2. Enter “grid” in the Search box
>   2. Select the line with “Grid” in the “Command” column
>   3. Click “Source” (opens Grid_.java in the editor)
>   4. Type ctrl-f (Edit>Find)
>   5. Enter “arm” in the search box
>   6. Change “float arm=5” to “float arm=20”
>   7. Type ctrl-r (File>Compile and Run)
>
> The crosses will now be four times larger. On Macs, use the command key
> instead of the control key when using keyboard shortcuts in the editor.
>
> You can change the size of points created by the multi-point tool, and, in
> the next version of ImageJ, the multi-point tool will support multiple
> counters.
>
> -wayne
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[PEARSON Matthew]

Hi all,

I've created a number of action tool macros and when i select the more tools >> icon and select the action tool it gets added with an icon to the image toolbar.  I only had two icons originally which once installed always appear with a shortcut icon after restarting.  However i have now added a 3rd tool but when i restart imagej i always have to go to the more tools >> menu to create the shortcut icon for the 3rd action tool as if you cannot automatically have more than 2 additional tool bar icons but i assume this isn't the case?  The action tool in question is below.  It does work and the icon remains after restarting if i remove one of my other action tools from the Tools folder backing up the theory that only two can be on the toolbar at one time.

macro "Save Action Tool - C000D02D03D04D05D06D07D08D09D0aD0bD17D18D19D1aD1bD1cD28D29D2aD2bD2cD2dD38D39D3aD3bD3cD3dD3eD48D49D4aD58D59D5aD68D69D78D79D88D89D98D99Da8Da9Db8Db9Dc8Dc9Dd8Dd9DdaDe7De8De9DeaDebC000D11D12D13D14D15D16D4bDe1De2De3De4De5De6DecDedDeeDf2Df3Df4Df5Df6Df7Df8Df9DfaDfbDfcDfdC000D27D6aD7aD8aD9aDaaDbaDcaDd7C000D4fC000D0cD3fC000D37D47D4cD4dD4eD57D67D77D87D97Da7Db7Dc7C000D01D10De0DefDf1DfeC000D1dD2eC000C111C222D7dC222C333D7eC333DdbC333C444D7cC444D6dC444D5bC444D20Dd0DdfC555D5fC555D26D6eDd6C666D6cC666D7fC666D00Df0DffC666D6fC666C777D2fC777D0dC777D1eC777C888D24D8fDd4C888D22Dd2C888D30D40D50D60D70D80D90D9fDa0DafDb0DbfDc0DcfC888D7bC888D6bC888C999D21Dd1C999DdcC999D23Dd3C999D25Dd5DddDdeC999DcbC999D8bC999CaaaD9bDabDbbCaaaD5cCaaaD5dCaaaD5eCaaaCbbbD36D46D56D66D76D86D96Da6Db6Dc6CbbbCcccCdddD34D44D54D64D74D84D94Da4Db4Dc4CdddD32D42D52D62D72D82D92Da2Db2Dc2CdddD8dCeeeD8eCeeeD8cCeeeCfffD0eD1fCfffD31D41D51D61D71D81D91Da1Db1Dc1CfffD33D43D53D63D73D83D93Da3Db3Dc3CfffD0fD35D45D55D65D75D85D95D9cD9dD9eDa5DacDadDaeDb5DbcDbdDbeDc5DccDcdDce"{
run("Tiff...");
}

Thanks for the help,

Matt



--
Matt Pearson
Microscopy Facility
MRC Human Genetics Unit
IGMM
University of Edinburgh
Crewe Road
EH4 2XU



On 11 Oct 2015, at 15:03, Jonni Virtanen <[hidden email]> wrote:

> Hey,
>
> I'm working on a project where I have to analyze a lot of samples by using
> a grid overlay with crosses (Grid plugin) and counting the different cell
> types with the Cell counter plugin. The problem is that the crosses are
> really small and hard to see and so are the points when using Cell counter.
> Is there a way to modify the cross size on Grid plugin and the font size on
> Cell Counter?
>
> Thanks,
>
> Jonni Virtanen
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Rasband, Wayne (NIH/NIMH) [E]]

On Oct 14, 2015, at 8:43 AM, PEARSON Matthew <[hidden email]> wrote:
>
> Hi all,
>
> I've created a number of action tool macros and when i select the more tools >> icon and select the action tool it gets added with an icon to the image toolbar.  I only had two icons originally which once installed always appear with a shortcut icon after restarting.  However i have now added a 3rd tool but when i restart imagej i always have to go to the more tools >> menu to create the shortcut icon for the 3rd action tool as if you cannot automatically have more than 2 additional tool bar icons but i assume this isn't the case?  The action tool in question is below.  It does work and the icon remains after restarting if i remove one of my other action tools from the Tools folder backing up the theory that only two can be on the toolbar at one time.

The first seven custom tools are restored when ImageJ restarts. To install more, add the extra tools to the Edit>Options>Startup dialog. For example, to install your action tool, add

    run("Save Action Tool”);

to the Edit>Options>Startup dialog. This assumes that a tool named “Save_Action_Tool.ijm” is in the ImageJ/plugins/Tools folder.

-wayne

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[Rasband, Wayne (NIH/NIMH) [E]]

> On Oct 12, 2015, at 1:22 AM, Jonni Virtanen <[hidden email]> wrote:
>
> Hey,
>
> Thanks a lot, this will make my life easier. Any idea when the next version
> will be released?

The multi-point tool in the latest ImageJ daily build (1.50d14) supports multiple counters but you are limited to 10 counters and there is no way to save the counts. This will be fixed by next week.

-wayne

> 2015-10-12 2:53 GMT+02:00 Rasband, Wayne (NIH/NIMH) [E] <
> [hidden email]>:
>
>>> On Oct 11, 2015, at 10:03 AM, Jonni Virtanen <[hidden email]>
>> wrote:
>>>
>>> Hey,
>>>
>>> I'm working on a project where I have to analyze a lot of samples by
>> using
>>> a grid overlay with crosses (Grid plugin) and counting the different cell
>>> types with the Cell counter plugin. The problem is that the crosses are
>>> really small and hard to see and so are the points when using Cell
>> counter.
>>> Is there a way to modify the cross size on Grid plugin and the font size
>> on
>>> Cell Counter?
>>
>> You can easily make the crosses larger in the Grid plugin:
>>
>>  1. Type “L” (Plugins>Utilities>Command Finder)
>>  2. Enter “grid” in the Search box
>>  2. Select the line with “Grid” in the “Command” column
>>  3. Click “Source” (opens Grid_.java in the editor)
>>  4. Type ctrl-f (Edit>Find)
>>  5. Enter “arm” in the search box
>>  6. Change “float arm=5” to “float arm=20”
>>  7. Type ctrl-r (File>Compile and Run)
>>
>> The crosses will now be four times larger. On Macs, use the command key
>> instead of the control key when using keyboard shortcuts in the editor.
>>
>> You can change the size of points created by the multi-point tool, and, in
>> the next version of ImageJ, the multi-point tool will support multiple
>> counters.
>>
>> -wayne

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Gabriel Landini]

On Friday 16 Oct 2015 18:22:35 you wrote:
> The multi-point tool in the latest ImageJ daily build (1.50d14) supports
> multiple counters but you are limited to 10 counters and there is no way to
> save the counts. This will be fixed by next week.

Hi Wayne,
Unfortunately double clicking on the "mutiple point tool" button brings up an
empty dialog with a "0", and freezes ImageJ (linux with oracle 1.6, 1.7 or 1.8
as well as openjdk 1.7).

Just selecting the multiple point or single point mode via right clicking
works fine (and calling the dialog of the single point tool by double clicking
on the button works too), it is bringing up the dialog of the "multiple" that
causes the issue).
Cheers

Gabriel

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[Rasband, Wayne (NIH/NIMH) [E]]

> On Oct 17, 2015, at 4:41 AM, Gabriel Landini <[hidden email]> wrote:
>
> On Friday 16 Oct 2015 18:22:35 you wrote:
>> The multi-point tool in the latest ImageJ daily build (1.50d14) supports
>> multiple counters but you are limited to 10 counters and there is no way to
>> save the counts. This will be fixed by next week.
>
> Hi Wayne,
> Unfortunately double clicking on the "mutiple point tool" button brings up an
> empty dialog with a "0", and freezes ImageJ (linux with oracle 1.6, 1.7 or 1.8
> as well as openjdk 1.7).

This bug should be fixed in the latest ImageJ daily build (1.50d19). While testing on Linux, I noticed that alt-clicking on a point to delete it did not work, so the daily build allows you to also control-click to delete points. And you can now press ‘y’ (Edit>Selection>Properties) to display the counters in a results table and the counters in the table are updated as you add and delete points.

-wayne

> Just selecting the multiple point or single point mode via right clicking
> works fine (and calling the dialog of the single point tool by double clicking
> on the button works too), it is bringing up the dialog of the "multiple" that
> causes the issue).
> Cheers
>
> Gabriel

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[Gabriel Landini]

On Sunday 18 Oct 2015 00:32:32 Rasband, Wayne  [E] wrote:
> This bug should be fixed in the latest ImageJ daily build (1.50d19). While
> testing on Linux, I noticed that alt-clicking on a point to delete it did
> not work, so the daily build allows you to also control-click to delete
> points. And you can now press ‘y’ (Edit>Selection>Properties) to display
> the counters in a results table and the counters in the table are updated
> as you add and delete points.

Thanks Wayne. The "Alt" key issue might be related at least in KDE due to the
keys default assignment.  This can be changed.
In KDE System Settings, Window Behaviour category go to :

Window Behaviour (again)>Window Actions then change the "Modifier key" from
"Alt" to "Meta".
Now KDE uses the "Windows key" as modifier and leaves the "Alt key" available
to ImageJ.

Cheers

Gabriel

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