Label images

[Robert Dougherty]

Dear List,

I often make color contour plots in which the vertical scale is  
frequency in Hz or kHz and the the horizontal scale is either channel  
number or x in inches. Axis labels and scales are needed.  I usually  
make the canvas larger to create white space and then use the text  
tool to create the labels outside the plot.  This is a bit  
laborious.  Macro recording does not seem to work, as text does not  
record.  Before I write a marco or plugin for external annotation/
axis labeling, does one already exist?

Bob

Robert Dougherty, Ph.D.
President, OptiNav, Inc.
10900 NE 8th St, Suite 900
Bellevue, WA 98004
Tel. [phone]
FAX [phone]
www.optinav.com
[hidden email]

[Michael Schmid]

Hi Robert,

maybe you could get some inspiration from the code in the
drawTicksEtc() method of ij.gui.Plot.

It contains the code needed for axis labels with "nice" numbers
(i.e. numbers such as 100, 200, ... and not 123.4 246.8, ...)

Michael
________________________________________________________________

On 22 Jan 2008, at 22:23, Robert Dougherty wrote:

> Dear List,
>
> I often make color contour plots in which the vertical scale is  
> frequency in Hz or kHz and the the horizontal scale is either  
> channel number or x in inches. Axis labels and scales are needed.  
> I usually make the canvas larger to create white space and then use  
> the text tool to create the labels outside the plot.  This is a bit  
> laborious.  Macro recording does not seem to work, as text does not  
> record.  Before I write a marco or plugin for external annotation/
> axis labeling, does one already exist?
>
> Bob
>
> Robert Dougherty, Ph.D.
> President, OptiNav, Inc.
> 10900 NE 8th St, Suite 900
> Bellevue, WA 98004
> Tel. [phone]
> FAX [phone]
> www.optinav.com
> [hidden email]

[Wayne Rasband]

The text tool is recorded in ImageJ 1.39q, which is due by the end of
this week.

-wayne

On Jan 22, 2008, at 4:23 PM, Robert Dougherty wrote:

> Dear List,
>
> I often make color contour plots in which the vertical scale is
> frequency in Hz or kHz and the the horizontal scale is either channel
> number or x in inches. Axis labels and scales are needed.  I usually
> make the canvas larger to create white space and then use the text
> tool to create the labels outside the plot.  This is a bit laborious.  
> Macro recording does not seem to work, as text does not record.  
> Before I write a marco or plugin for external annotation/axis
> labeling, does one already exist?
>
> Bob
>
> Robert Dougherty, Ph.D.
> President, OptiNav, Inc.
> 10900 NE 8th St, Suite 900
> Bellevue, WA 98004
> Tel. [phone]
> FAX [phone]
> www.optinav.com
> [hidden email]
>

[Robert Dougherty]

Michael,

Yes.  See http://www.optinav.com/Label-Image.htm.  Thanks.

Bob

On Jan 23, 2008, at 10:32 AM, Michael Schmid wrote:

> Hi Robert,
>
> maybe you could get some inspiration from the code in the
> drawTicksEtc() method of ij.gui.Plot.
>
> It contains the code needed for axis labels with "nice" numbers
> (i.e. numbers such as 100, 200, ... and not 123.4 246.8, ...)
>
> Michael
> ________________________________________________________________
>
> On 22 Jan 2008, at 22:23, Robert Dougherty wrote:
>
>> Dear List,
>>
>> I often make color contour plots in which the vertical scale is  
>> frequency in Hz or kHz and the the horizontal scale is either  
>> channel number or x in inches. Axis labels and scales are needed.  
>> I usually make the canvas larger to create white space and then  
>> use the text tool to create the labels outside the plot.  This is  
>> a bit laborious.  Macro recording does not seem to work, as text  
>> does not record.  Before I write a marco or plugin for external  
>> annotation/axis labeling, does one already exist?
>>
>> Bob
>>
>> Robert Dougherty, Ph.D.
>> President, OptiNav, Inc.
>> 10900 NE 8th St, Suite 900
>> Bellevue, WA 98004
>> Tel. [phone]
>> FAX [phone]
>> www.optinav.com
>> [hidden email]
>

[Gabriel Landini]

On Wednesday 30 January 2008 20:32:48 Robert Dougherty wrote:
> Yes.  See http://www.optinav.com/Label-Image.htm.  Thanks.
>

Bob,
This is quite a useful plugin.
Just a suggestion: is it possible to make this plugin create a white
background with black letters for those who have set the foreground as white
and the background as black?
A quick hack would be to Invert, draw the axes and labels and invert again.
Another way could be to allow for specifying whether background is 255 or 0.

Regards,

Gabriel

[Robert Dougherty]

Gabriel,

The use of toolbar foreground/background colors is an option now.  I  
think it will make for dramatic powerpoint slides, but black on white  
is probably more generally useful.

Bob

On Jan 31, 2008, at 2:58 AM, Gabriel Landini wrote:

> On Wednesday 30 January 2008 20:32:48 Robert Dougherty wrote:
>> Yes.  See http://www.optinav.com/Label-Image.htm.  Thanks.
>>
>
> Bob,
> This is quite a useful plugin.
> Just a suggestion: is it possible to make this plugin create a white
> background with black letters for those who have set the foreground  
> as white
> and the background as black?
> A quick hack would be to Invert, draw the axes and labels and  
> invert again.
> Another way could be to allow for specifying whether background is  
> 255 or 0.
>
> Regards,
>
> Gabriel
>

[Wolfgang Schechinger]

Dear ImageJ experts,

is there a way to do peak fitting within ImageJ? I habe obtained some chromatogram-like curves with the Crtl+1,2,3 sequence and would like to estimate if there is more than one signal hidden in one peak (i.e. if one peak may be expressed as the sum of two, partially conincidental, peaks).
Alternatively, is there a way to convert and save these curves as numbers in e.g. a csv or text file that one may process with some third party software (any recommendation for which software might be useful are highly appreciated as well)

Many thanks!

Wolfgang
--
Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen!
Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer

[David Hovis]

Wolfgang,

I'm not really familiar with the gel tools, but I think what you are  
asking is not trivial.  I use fityk (http://fityk.sf.net/) for general  
1-D peak fitting.  Fityk is free and comes in GUI, CLI, and library  
versions.  I've hacked a JNI interface with SWIG to use libfityk  
directly with my custom ImageJ plugins.  It is very fast, but it is  
decidedly non-trivial.

Often when there are overlapping peaks, you need to take care with  
your model to make sure that you get a physical result.  Oftentimes,  
closely spaced peaks can be fit reasonably well with a single wider  
peak.  If you know that there is some reasonable maximum width to your  
peaks, then there are ways of applying constraints in fityk to prevent  
the fitting algorithm from converging on non-physical results.

--David

----------------------------------------
David Hovis
Senior Research Associate
Department of Materials Science
Case Western Reserve University
[hidden email]

On Feb 3, 2008, at 8:55 AM, Wolfgang Schechinger wrote:

> Dear ImageJ experts,
>
> is there a way to do peak fitting within ImageJ? I habe obtained  
> some chromatogram-like curves with the Crtl+1,2,3 sequence and would  
> like to estimate if there is more than one signal hidden in one peak  
> (i.e. if one peak may be expressed as the sum of two, partially  
> conincidental, peaks).
> Alternatively, is there a way to convert and save these curves as  
> numbers in e.g. a csv or text file that one may process with some  
> third party software (any recommendation for which software might be  
> useful are highly appreciated as well)
>
> Many thanks!
>
> Wolfgang
> --
> Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen!
> Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer

[Robert Dougherty]

Wolfgang,

It might possible to try deconvolution software. There are some 2D and 3D
plugins on my site. I think they could be applied to 1-D problems by using
very thin images, but it would require some experimentation.  It would help
if you know the peak width so you can compute the Point Spread Function. As
David mentioned, it would be easy to get strange artifacts in the
reconstruction.

Bob

Robert P. Dougherty, Ph.D.
President, OptiNav, Inc.
Phone [phone]
Fax [phone]
www.optinav.com
 

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Wolfgang Schechinger
> Sent: Sunday, February 03, 2008 5:56 AM
> To: [hidden email]
> Subject: Peak fitting with ImageJ
>
> Dear ImageJ experts,
>
> is there a way to do peak fitting within ImageJ? I habe obtained some
> chromatogram-like curves with the Crtl+1,2,3 sequence and would like to
> estimate if there is more than one signal hidden in one peak (i.e. if one
> peak may be expressed as the sum of two, partially conincidental, peaks).
> Alternatively, is there a way to convert and save these curves as numbers
> in e.g. a csv or text file that one may process with some third party
> software (any recommendation for which software might be useful are highly
> appreciated as well)
>
> Many thanks!
>
> Wolfgang
> --
> Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen!
> Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer