Mac OS Lion and ImageJ

[Chris_Leonard]

Greetings.  Has anyone tried imageJ on Mac OS 10.7 (Lion) yet?
Anything broken that we should watch out for before upgrading?
Thanks
-Chris Leonard

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

On Jul 20, 2011, at 12:20 AM, Chris_Leonard wrote:

> Greetings.  Has anyone tried imageJ on Mac OS 10.7 (Lion) yet?
> Anything broken that we should watch out for before upgrading?
> Thanks
> -Chris Leonard

I tried ImageJ on Lion today and noticed one little problem: scrollbars are missing the unit increment and decrement buttons (see attached screenshot). This is not a problem with the channel/slice/frame scrollbars used with stacks and hyperstacks since they have keyboard shortcuts. It is a problem with other scrollbars, such as the ones in the "B&C" and "Threshold" windows, which currently lack keyboard shortcuts.

-wayne

[cid:[hidden email]]

[Bill Mohler]

I got to test OS 10.7 today.  Some good news:

1.  I can still launch ImageJ in 32-bit mode if I want.
2. (dependent on 1.) I can still run plugins/classes that depend on
QTJava (32-bit only).
3.  Everything other than scrollbars seems pretty normal.

As Wayne mentioned, the scrollbars in Lion have lost their arrows in all
contexts, including Java and ImageJ windows.  There is no OS level
preference that allows you to bring them back.  This is clearly a pain
for any window with more than one scrollbar!  I wonder if that is a
different component that might substitute for awt.gui.Scrollbar and have
arrows?  It would be a minor pain to need to recode a
ij.gui.ScrollbarWithArrowsOnMacOS10_7.java just for this special case.  
Might be worth waiting on for Apple updates first, to see if they might
bring them back as an option.  There seems to be a certain amount of web
screaming going on already about the lack of the arrows on scrollbars in
general:
http://www.google.com/#hl=en&sugexp=bvie&cp=23&gs_id=3e&xhr=t&q=os+10.7+scrollbar+arrow


I also found this older command-line tip.  Might it give us some control
over the scrollbar arrows in 10.7?  I haven't tried yet.
defaults write "Apple Global Domain" AppleScrollBarVariant DoubleBoth
http://lifehacker.com/5040043/add-double-scroll-arrows-to-both-ends-of-the-scroll-bar

...although this option seems not to even work in 10.6.8...  so maybe
not much hope there in 10.7

Clearly it would help if the look-and-feel of Java on the Mac were not
so tied to the L&F of the OS itself.

Bill

On 7/20/11 4:49 PM, Rasband, Wayne (NIH/NIMH) [E] wrote:

> On Jul 20, 2011, at 12:20 AM, Chris_Leonard wrote:
>
>> Greetings.  Has anyone tried imageJ on Mac OS 10.7 (Lion) yet?
>> Anything broken that we should watch out for before upgrading?
>> Thanks
>> -Chris Leonard
> I tried ImageJ on Lion today and noticed one little problem: scrollbars are missing the unit increment and decrement buttons (see attached screenshot). This is not a problem with the channel/slice/frame scrollbars used with stacks and hyperstacks since they have keyboard shortcuts. It is a problem with other scrollbars, such as the ones in the "B&C" and "Threshold" windows, which currently lack keyboard shortcuts.
>
> -wayne
>
> [cid:[hidden email]]

--

William A. Mohler

Associate Professor
Dept. of Genetics and Developmental Biology
University of Connecticut Health Center

*Physical Address:***

Room R1159

Cell and Genome Sciences Building

400 Farmington Ave.

Farmington, CT

*Mail Address:*

MC-6403

263 Farmington Ave.

Farmington, CT06030-6403

[hidden email] <mailto:[hidden email]>
*Mobile: [phone]*

skype: wmohler
Office: [phone], room R1159
Lab: [phone], room R1265
Fax: [phone]

http://genetics.uchc.edu/Faculty/assoc_professors/mohler.html
PThink before you print

[Olivier Burri]

Hello,

I've experienced the missing arrows issue and would like to potentially report another one involving the mouse listener.

Run the following macro
macro "Test Wait" {
newImage("Untitled", "8-bit White", 400, 400, 1);
waitForUser;
// Try to draw something using the pencil tool before clicking on OK
IJ.log("I'm done");
}

In my case, drawing with the pencil causes the waitForUser to complete, which is rather troublesome. Anyone able to replicate that and eventually offer a way to solve this?

Thanks!

Oli

[Michael Schmid]

Hi Olivier,

you might try the old external Wait_For_User plugin,
   http://imagejdocu.tudor.lu/doku.php?
id=plugin:utilities:wait_for_user:start

It is similar code, but does not have the setAlwaysOnTop() feature.

I could imagine some stupid problem with the OS closing the 'always  
on top' window in case of some operation in a window behind.

Michael
________________________________________________________________

On 28 Jul 2011, at 17:11, Olivier Burri wrote:

> Hello,
>
> I've experienced the missing arrows issue and would like to  
> potentially
> report another one involving the mouse listener.
>
> Run the following macro
> macro "Test Wait" {
> newImage("Untitled", "8-bit White", 400, 400, 1);
> waitForUser;
> // Try to draw something using the pencil tool before clicking on OK
> IJ.log("I'm done");
> }
>
> In my case, drawing with the pencil causes the waitForUser to  
> complete,
> which is rather troublesome. Anyone able to replicate that and  
> eventually
> offer a way to solve this?
>
> Thanks!
>
> Oli
>
> --
> View this message in context: http://imagej.588099.n2.nabble.com/ 
> Mac-OS-Lion-and-ImageJ-tp6601294p6630184.html
> Sent from the ImageJ mailing list archive at Nabble.com.

[ayo raheem]

DearAll,
Can someone teach me the protocol of setting the positive and the negative colouration on image j for the purpose of  digitally quantification of  IHC staining
Thanks
Ayo


________________________________
From: Michael Schmid &lt;[hidden email]&gt;
To: [hidden email]
Sent: Thursday, July 28, 2011 4:53 PM
Subject: Re: Mac OS Lion and ImageJ

Hi Olivier,

you might try the old external Wait_For_User plugin,
  http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:wait_for_user:start

It is similar code, but does not have the setAlwaysOnTop() feature.

I could imagine some stupid problem with the OS closing the &#39;always on top&#39; window in case of some operation in a window behind.

Michael
________________________________________________________________

On 28 Jul 2011, at 17:11, Olivier Burri wrote:

&gt; Hello,
&gt;
&gt; I&#39;ve experienced the missing arrows issue and would like to potentially
&gt; report another one involving the mouse listener.
&gt;
&gt; Run the following macro
&gt; macro &quot;Test Wait&quot; {
&gt; newImage(&quot;Untitled&quot;, &quot;8-bit White&quot;, 400, 400, 1);
&gt; waitForUser;
&gt; // Try to draw something using the pencil tool before clicking on OK
&gt; IJ.log(&quot;I&#39;m done&quot;);
&gt; }
&gt;
&gt; In my case, drawing with the pencil causes the waitForUser to complete,
&gt; which is rather troublesome. Anyone able to replicate that and eventually
&gt; offer a way to solve this?
&gt;
&gt; Thanks!
&gt;
&gt; Oli
&gt;
&gt; --
&gt; View this message in context: http://imagej.588099.n2.nabble.com/Mac-OS-Lion-and-ImageJ-tp6601294p6630184.html
&gt; Sent from the ImageJ mailing list archive at Nabble.com.

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

On Jul 28, 2011, at 11:11 AM, Olivier Burri wrote:

> Hello,
>
> I've experienced the missing arrows issue and would like to potentially
> report another one involving the mouse listener.
>
> Run the following macro
> macro "Test Wait" {
> newImage("Untitled", "8-bit White", 400, 400, 1);
> waitForUser;
> // Try to draw something using the pencil tool before clicking on OK
> IJ.log("I'm done");
> }
>
> In my case, drawing with the pencil causes the waitForUser to complete,
> which is rather troublesome. Anyone able to replicate that and eventually
> offer a way to solve this?

According to the release notes (http://imagej.nih.gov/ij/notes.html), this bug was fixed in ImageJ 1.45c.

   1.45c 10 March 2011
      * Fixed a bug the caused the waitForUser() macro function
        to not work with the brush and pencil tools.

-wayne