Re: problem with conversion to RGB - IJ 1.51k18 java 1.6.0_20

Posted by Cammer, Michael on Feb 26, 2017; 3:23pm
URL: http://imagej.273.s1.nabble.com/problem-with-conversion-to-RGB-IJ-1-51k18-java-1-6-0-20-tp5018189p5018199.html

Thank you!!!


_________________________________________
Michael Cammer, Optical Microscopy Specialist
http://ocs.med.nyu.edu/microscopy
http://microscopynotes.com/
Cell: [phone]

________________________________________
From: Wayne Rasband [[hidden email]]
Sent: Saturday, February 25, 2017 8:03 PM
To: [hidden email]
Subject: Re: problem with conversion to RGB - IJ 1.51k18 java 1.6.0_20

> On Feb 24, 2017, at 4:26 PM, Cammer, Michael <[hidden email]> wrote:
>
> We are having a problem converting hyperstacks to RGB in a macro.  Approximately one out of five times we run the macro, it does not work.  We tried adding a wait(200) step, but don't know if this really helps or not.

Hi Michael,

The latest ImageJ daily build (1.51k21) fixes a bug in the 3D Project… command that was causing your macro to fail. The 200 ms wait is not needed.

-wayne

> The error is that ImageJ cannot find image with id2.
>
> [cid:[e-mail]7A15E0]
>
> Any help appreciated.  The problem is with the second macro.  Included the first macro to show what types of files we are using (2 or 3 channel Z series confocal).
>
> macro "Set up images [q]" {
>  //run("Channels Tool...");
>  Stack.setDisplayMode("composite");
>  //run("Brightness/Contrast...");
>  Stack.getDimensions(width, height, channels, slices, frames) ;
>  for (n=1; n<=channels; n++) {
>    Stack.setChannel(n);
>    setMinAndMax(0, 65535);
>  }
>  Stack.setSlice(floor(slices / 3)) ;
> }
>
> /*  Draw a box around an area to be 3D projected.
>     Run this macro.
> */
> macro "Do 3D projections [F2]" {
>   run("Duplicate...", "duplicate");
>   id1 = getImageID();
>   // change to get scale for each sample if Z different than 0.3 um
>   run("3D Project...", "projection=[Brightest Point] axis=X-Axis slice=0.30 initial=0 total=360 rotation=10 lower=1 upper=255 opacity=0 surface=50 interior=25 interpolate");
>   //run("RGB Color", "frames");  // buggy
>   wait(200);   // appears the projection command needs this to hand off the image properly
>   id2 = getImageID();
>   run("RGB Color", "frames keep");
>   selectImage(id1); close(); selectImage(id2); close();
> }
>
>
>
>
>
>
>
>
> =*===========================================================*=
> Michael Cammer, DART Microscopy Laboratory, NYU Langone Medical Center
>    Cell:  914-309-3270     Office: Skirball 2nd Floor main office, back right
>      http://ocs.med.nyu.edu/microscopy & https://urldefense.proofpoint.com/v2/url?u=http-3A__microscopynotes.com_&d=DQIFaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=zMi2MImiqqSoL2uyrKtI4I5bqy1bpH_THjn82Cx3bKY&s=JmZUD6MpOIBQIL0gfrGQIvQToAvee28w5IMwhZQLfDM&e=
>
>
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