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User Guide 1.46 released

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Tiago Ferreira-2

User Guide 1.46 released

Hi everyone,

It's a pleasure to release the 4th version of the ImageJ Handbook:
<http://imagej.nih.gov/ij/docs/guide/index.html>

What is new:
- This is the second major revision, more based on the annotated IJ source code
- Updated for IJ 1.46p
- New sections on Overlays, 3D Volumes, Sub pixel selections, Curve fitting and
Interface customization
- Improved contents on Image Processing and "Noteworthy Notes"
- More visibility to Fiji (and IJ2), mentioned when pertinent
- More macro examples (with proper syntax highlighting, that can be selected by
double-click and copied directly into IJ)
- Better browsability (please note that the searchbox on the online version is
not yet working)

Your contributions on this forum are essential for the IJ documentation effort,
so thanks to you all,

-tiago

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Krs5

bugs in Merge Channels?

Dear Wayne and list,

While validating a macro I wrote, one of the problems we came across was that the measurements obtained with ImageJ did not agree with data obtained with an other program. Spending several days picking my macro apart I think I have found at least part of the problem.

During the analysis we merge some of the channels and it seems we lose in some cases the scale of the image. When I checked this further and wrote the little macro below to show the problem I also noticed that there is a difference in doing it manually (2 channels are merged) and running the macro (channels don't seem to merge). Strange thing is that in the macro we try to validate this does not seem to be a problem, the 2 channels are merged although we have an original grey channel in our merged image, what might explain the difference.
I see the same problem in FIJI and ImageJ (1.46p) running on Windows7.

dir1 = getDirectory("Choose directory to save results");
run("Confocal Series (2.2MB)");
run("RGB Color", "slices keep");
run("Split Channels");
run("Merge Channels...", "c1=[confocal-series-1.tif (red)] c4=[confocal-series-1.tif (green)] keep");
selectWindow("RGB");
saveAs("tif", dir1+"merge1");
run("Merge Channels...", "c3=[confocal-series-1.tif (red)] c4=[confocal-series-1.tif (green)]");
selectWindow("RGB");
saveAs("tif", dir1+"merge2");
run("Close All");

Best wishes

Kees

Dr Ir K.R. Straatman
Senior Experimental Officer
Centre for Core Biotechnology Services
University of Leicester
UK

Immunolabelling and fluorescence microscopy workshops 20-24 August: http://www.le.ac.uk/biochem/microscopy/workshop2012.html.
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David Webster

Re: User Guide 1.46 released

In reply to this post by Tiago Ferreira-2

I think there is an error in the section "Part IV. ImageJ User
Interface". The diagram, " *The ImageJ window (version 1.46j).* " implies
that the Freehand selection tool, the Straight line selection tool, and
the Segmented Line Selection
Tool<http://imagej.nih.gov/ij/docs/guide/146-19.html#sub:Segmented-Line-Selection>
are
grouped together at position 4. In fact the, Straight line selection
tool, and the Segmented Line Selection
Tool<http://imagej.nih.gov/ij/docs/guide/146-19.html#sub:Segmented-Line-Selection>
are
grouped together at position 5.

Thanx - David Webster

On Sat, Jun 9, 2012 at 6:19 AM, Tiago Ferreira <
[hidden email]> wrote:

> Hi everyone,
>
> It's a pleasure to release the 4th version of the ImageJ Handbook:
> <http://imagej.nih.gov/ij/docs/guide/index.html>
>
> What is new:
> - This is the second major revision, more based on the annotated IJ source
> code
> - Updated for IJ 1.46p
> - New sections on Overlays, 3D Volumes, Sub pixel selections, Curve
> fitting and
> Interface customization
> - Improved contents on Image Processing and "Noteworthy Notes"
> - More visibility to Fiji (and IJ2), mentioned when pertinent
> - More macro examples (with proper syntax highlighting, that can be
> selected by
> double-click and copied directly into IJ)
> - Better browsability (please note that the searchbox on the online
> version is
> not yet working)
>
> Your contributions on this forum are essential for the IJ documentation
> effort,
> so thanks to you all,
>
> -tiago
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

Rasband, Wayne (NIH/NIMH) [E]

Re: bugs in Merge Channels?

In reply to this post by Krs5

On Jun 9, 2012, at 10:41 AM, Straatman, Kees R. (Dr.) wrote:

> Dear Wayne and list,
>
> While validating a macro I wrote, one of the problems we came across was that the measurements obtained with ImageJ did not agree with data obtained with an other program. Spending several days picking my macro apart I think I have found at least part of the problem.
>
> During the analysis we merge some of the channels and it seems we lose in some cases the scale of the image. When I checked this further and wrote the little macro below to show the problem I also noticed that there is a difference in doing it manually (2 channels are merged) and running the macro (channels don't seem to merge). Strange thing is that in the macro we try to validate this does not seem to be a problem, the 2 channels are merged although we have an original grey channel in our merged image, what might explain the difference.
> I see the same problem in FIJI and ImageJ (1.46p) running on Windows7.

These bugs are fixed in the ImageJ 1.46q daily build.

-wayne

> dir1 = getDirectory("Choose directory to save results");
> run("Confocal Series (2.2MB)");
> run("RGB Color", "slices keep");
> run("Split Channels");
> run("Merge Channels...", "c1=[confocal-series-1.tif (red)] c4=[confocal-series-1.tif (green)] keep");
> selectWindow("RGB");
> saveAs("tif", dir1+"merge1");
> run("Merge Channels...", "c3=[confocal-series-1.tif (red)] c4=[confocal-series-1.tif (green)]");
> selectWindow("RGB");
> saveAs("tif", dir1+"merge2");
> run("Close All");
>
> Best wishes
>
> Kees
>
> Dr Ir K.R. Straatman
> Senior Experimental Officer
> Centre for Core Biotechnology Services
> University of Leicester
> UK
>
> Immunolabelling and fluorescence microscopy workshops 20-24 August: http://www.le.ac.uk/biochem/microscopy/workshop2012.html.
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

Krs5

Re: bugs in Merge Channels?

Dear Wayne,

Thanks for the quick replay.The problem with the scaling is solved.

However, it seems to have caused some other problems. Running the little code below will give a Java exception.

run("Confocal Series (2.2MB)");
run("Split Channels");
run("Merge Channels...", "c1=C1-confocal-series.tif c4=C2-confocal-series.tif keep");
selectWindow("RGB");
run("Split Channels");

Best wishes

Kees

Immunolabelling and fluorescence microscopy workshops, Leicester, UK, 20-24 August: http://www.le.ac.uk/biochem/microscopy/workshop2012.html.
________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of Rasband, Wayne (NIH/NIMH) [E] [[hidden email]]
Sent: 10 June 2012 04:54
To: [hidden email]
Subject: Re: bugs in Merge Channels?

On Jun 9, 2012, at 10:41 AM, Straatman, Kees R. (Dr.) wrote:

> Dear Wayne and list,
>
> While validating a macro I wrote, one of the problems we came across was that the measurements obtained with ImageJ did not agree with data obtained with an other program. Spending several days picking my macro apart I think I have found at least part of the problem.
>
> During the analysis we merge some of the channels and it seems we lose in some cases the scale of the image. When I checked this further and wrote the little macro below to show the problem I also noticed that there is a difference in doing it manually (2 channels are merged) and running the macro (channels don't seem to merge). Strange thing is that in the macro we try to validate this does not seem to be a problem, the 2 channels are merged although we have an original grey channel in our merged image, what might explain the difference.
> I see the same problem in FIJI and ImageJ (1.46p) running on Windows7.

These bugs are fixed in the ImageJ 1.46q daily build.

-wayne

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

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ctrueden

Re: User Guide 1.46 released

In reply to this post by Tiago Ferreira-2

Hi Tiago,

I just wanted to say thanks very much for doing this. I know how much work
it is to write documentation, especially of the thoroughness and caliber of
your guide. It is much appreciated!

-Curtis

On Sat, Jun 9, 2012 at 8:19 AM, Tiago Ferreira <
[hidden email]> wrote:

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Francis Burton-3

Re: User Guide 1.46 released

It is indeed appreciated - a superb resource! Thank you, Tiago.

Francis

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On
> Behalf Of Curtis Rueden
> Sent: 12 June 2012 22:30
> To: [hidden email]
> Subject: Re: User Guide 1.46 released
>
> Hi Tiago,
>
> I just wanted to say thanks very much for doing this. I know
> how much work
> it is to write documentation, especially of the thoroughness
> and caliber of
> your guide. It is much appreciated!
>
> -Curtis

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