Quantcast

Multi Measure: display slice time

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Multi Measure: display slice time

Fco. Javier Diez Guerra
Hello,

For FRAP time-lapsed stacks, I am using ROI Manager/Multi Measure and
then export data to .csv files. For analysis outside Fiji/ImageJ, I want
to include a time reference of each slice in the first column of the
Results file, but I do not know how to do that.

Since labels can be displayed in the Results window, I assigned a
time-stamp label to individual slices using this simple macro:

timestamp=0.0000
setSlice(1);
for (i=1; i<=nSlices; i++) {
     setMetadata("Label",timestamp);
     timestamp=timestamp+0.1667;
     run("Next Slice [>]");
        }

After running the macro, I can see the added label next to the slice
position in the image stack window. However ROI Manager/Multi Measure
sheets only display the title of the stack under the column tagged
"Label", which is obviously the same for all the slices.

I would appreciate any help.

Best


--

Fco. Javier Díez Guerra, PhD
Profesor Titular
Centro de Biología Molecular Severo Ochoa
C/ Nicolás Cabrera, 1
Universidad Autónoma
Ctra Colmenar Viejo Km 15
Cantoblanco, 28049 Madrid
SPAIN

phone:  +34 91 196 4612
e-mail: [hidden email]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Multi Measure: display slice time

Michael Schmid-3
Hi Javier,

assuming that you refer to the ROI Manager's Multi Measure:
If you do NOT enable 'One row per slice', you can enable 'Display Label'
in Analyze>Set Measurements.
Then you will get a label in the form:
   ImageName:RoiName:SliceLabel
In your case, the SliceLabel would be the time.

If you DO use the 'One row per slice' output, I fear that you can't have
it with the current version of ImageJ:
RoiManager.multiMeasure(ImagePlus, Roi[], boolean) writes only the image
title, not the slice label.

What you could do is adding a column by a macro after running 'Multi
Measure'. It will be the last, not the first column, however.

   if (nResults() != nSlices())
     exit("Error: not one Results row per stack slice");
   timestamp = 0;
   for (i=0; i<nSlices; i++) {
     setResult("SliceTime", i, timestamp);
     timestamp=timestamp+0.1667;
   }

Note that Results Table rows are numbered from 0 to nResults-1 (in
contrast to stack slices, which are numbered 1 to nSlices).

Michael
________________________________________________________________


On 2016-12-26 16:30, Fco. Javier Díez Guerra wrote:

> Hello,
>
> For FRAP time-lapsed stacks, I am using ROI Manager/Multi Measure and
> then export data to .csv files. For analysis outside Fiji/ImageJ, I
> want to include a time reference of each slice in the first column of
> the Results file, but I do not know how to do that.
>
> Since labels can be displayed in the Results window, I assigned a
> time-stamp label to individual slices using this simple macro:
>
> timestamp=0.0000
> setSlice(1);
> for (i=1; i<=nSlices; i++) {
>     setMetadata("Label",timestamp);
>     timestamp=timestamp+0.1667;
>     run("Next Slice [>]");
>        }
>
> After running the macro, I can see the added label next to the slice
> position in the image stack window. However ROI Manager/Multi Measure
> sheets only display the title of the stack under the column tagged
> "Label", which is obviously the same for all the slices.
>
> I would appreciate any help.
>
> Best
>
>
> --
>
> Fco. Javier Díez Guerra, PhD
> Profesor Titular
> Centro de Biología Molecular Severo Ochoa
> C/ Nicolás Cabrera, 1
> Universidad Autónoma
> Ctra Colmenar Viejo Km 15
> Cantoblanco, 28049 Madrid
> SPAIN
>
> phone:  +34 91 196 4612
> e-mail: [hidden email]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Multi Measure: display slice time

Michael Schmid-3
Hi Javier,

if I understand it correctly, you want to rename the headings of the
Results Table? I fear that this is not possible via the macro language.
It would be doable in javaScript:

   rt=ResultsTable.getResultsTable();
   rt.setHeading(1, "Bleach");
   rt.show("Results");


What you could do in the Macro Language is creating your own macro to
save the Results Table, e.g. using File.saveString(string, path).
You could first write the headings of your choice to the String, '\n',
and then read the Results Table line by line, and add its elements to
the String, with tabs ('\t') and linefeeds ('\n').
Not very elegant, however.

Michael
________________________________________________________________
On 12/26/2016 08:39 PM, Fco. Javier Díez Guerra wrote:

> Hi Michael,
>
> Thanks for your quick and well-targeted reply. My goal is to automate as
> much as possible the data extraction process, which is done using Fiji,
> along with the data analysis of FRAP experiments, which is done using
> EasyFRAP/Matlab. This app is very appropriate for our FRAP analysis, but
> sometimes very sensitive to data input formats.
>
> I can still streamline and speed up the whole process using your
> suggestion of appending SliceTime as the last column of the Multi
> Measure Results array. I would need though to specify the identity of
> each column (Bleach, Reference, Background ROIs, and Time) when feeding
> the data into EasyFRAP.
>
> Thanks again.
>
> Javier
>
>
> El 26/12/2016 a las 19:46, Michael Schmid escribió:
>> Hi Javier,
>>
>> assuming that you refer to the ROI Manager's Multi Measure:
>> If you do NOT enable 'One row per slice', you can enable 'Display
>> Label' in Analyze>Set Measurements.
>> Then you will get a label in the form:
>>   ImageName:RoiName:SliceLabel
>> In your case, the SliceLabel would be the time.
>>
>> If you DO use the 'One row per slice' output, I fear that you can't
>> have it with the current version of ImageJ:
>> RoiManager.multiMeasure(ImagePlus, Roi[], boolean) writes only the
>> image title, not the slice label.
>>
>> What you could do is adding a column by a macro after running 'Multi
>> Measure'. It will be the last, not the first column, however.
>>
>>   if (nResults() != nSlices())
>>     exit("Error: not one Results row per stack slice");
>>   timestamp = 0;
>>   for (i=0; i<nSlices; i++) {
>>     setResult("SliceTime", i, timestamp);
>>     timestamp=timestamp+0.1667;
>>   }
>>
>> Note that Results Table rows are numbered from 0 to nResults-1 (in
>> contrast to stack slices, which are numbered 1 to nSlices).
>>
>> Michael
>> ________________________________________________________________
>>
>>
>> On 2016-12-26 16:30, Fco. Javier Díez Guerra wrote:
>>> Hello,
>>>
>>> For FRAP time-lapsed stacks, I am using ROI Manager/Multi Measure and
>>> then export data to .csv files. For analysis outside Fiji/ImageJ, I
>>> want to include a time reference of each slice in the first column of
>>> the Results file, but I do not know how to do that.
>>>
>>> Since labels can be displayed in the Results window, I assigned a
>>> time-stamp label to individual slices using this simple macro:
>>>
>>> timestamp=0.0000
>>> setSlice(1);
>>> for (i=1; i<=nSlices; i++) {
>>>     setMetadata("Label",timestamp);
>>>     timestamp=timestamp+0.1667;
>>>     run("Next Slice [>]");
>>>        }
>>>
>>> After running the macro, I can see the added label next to the slice
>>> position in the image stack window. However ROI Manager/Multi Measure
>>> sheets only display the title of the stack under the column tagged
>>> "Label", which is obviously the same for all the slices.
>>>
>>> I would appreciate any help.
>>>
>>> Best
>>>
>>>
>>> --
>>>
>>> Fco. Javier Díez Guerra, PhD
>>> Profesor Titular
>>> Centro de Biología Molecular Severo Ochoa
>>> C/ Nicolás Cabrera, 1
>>> Universidad Autónoma
>>> Ctra Colmenar Viejo Km 15
>>> Cantoblanco, 28049 Madrid
>>> SPAIN
>>>
>>> phone:  +34 91 196 4612
>>> e-mail: [hidden email]
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Multi Measure: display slice time

Fco. Javier Diez Guerra
Hi Michael,

Thanks for your email.

EasyFRAP/Matlab has the option to reassign the lists (columns) of data
in the Results Table to their corresponding parameters for the analysis
(SliceTime, and Bleach, Reference and Bkg intensities). So, no matter
whether SliceTime appears first or last in the Results Table, and no
need to rename the headings.

Best

Javier


El 27/12/2016 a las 11:57, Michael Schmid escribió:

> Hi Javier,
>
> if I understand it correctly, you want to rename the headings of the
> Results Table? I fear that this is not possible via the macro language.
> It would be doable in javaScript:
>
>   rt=ResultsTable.getResultsTable();
>   rt.setHeading(1, "Bleach");
>   rt.show("Results");
>
>
> What you could do in the Macro Language is creating your own macro to
> save the Results Table, e.g. using File.saveString(string, path).
> You could first write the headings of your choice to the String, '\n',
> and then read the Results Table line by line, and add its elements to
> the String, with tabs ('\t') and linefeeds ('\n').
> Not very elegant, however.
>
> Michael
> ________________________________________________________________
> On 12/26/2016 08:39 PM, Fco. Javier Díez Guerra wrote:
>> Hi Michael,
>>
>> Thanks for your quick and well-targeted reply. My goal is to automate as
>> much as possible the data extraction process, which is done using Fiji,
>> along with the data analysis of FRAP experiments, which is done using
>> EasyFRAP/Matlab. This app is very appropriate for our FRAP analysis, but
>> sometimes very sensitive to data input formats.
>>
>> I can still streamline and speed up the whole process using your
>> suggestion of appending SliceTime as the last column of the Multi
>> Measure Results array. I would need though to specify the identity of
>> each column (Bleach, Reference, Background ROIs, and Time) when feeding
>> the data into EasyFRAP.
>>
>> Thanks again.
>>
>> Javier
>>
>>
>> El 26/12/2016 a las 19:46, Michael Schmid escribió:
>>> Hi Javier,
>>>
>>> assuming that you refer to the ROI Manager's Multi Measure:
>>> If you do NOT enable 'One row per slice', you can enable 'Display
>>> Label' in Analyze>Set Measurements.
>>> Then you will get a label in the form:
>>>   ImageName:RoiName:SliceLabel
>>> In your case, the SliceLabel would be the time.
>>>
>>> If you DO use the 'One row per slice' output, I fear that you can't
>>> have it with the current version of ImageJ:
>>> RoiManager.multiMeasure(ImagePlus, Roi[], boolean) writes only the
>>> image title, not the slice label.
>>>
>>> What you could do is adding a column by a macro after running 'Multi
>>> Measure'. It will be the last, not the first column, however.
>>>
>>>   if (nResults() != nSlices())
>>>     exit("Error: not one Results row per stack slice");
>>>   timestamp = 0;
>>>   for (i=0; i<nSlices; i++) {
>>>     setResult("SliceTime", i, timestamp);
>>>     timestamp=timestamp+0.1667;
>>>   }
>>>
>>> Note that Results Table rows are numbered from 0 to nResults-1 (in
>>> contrast to stack slices, which are numbered 1 to nSlices).
>>>
>>> Michael
>>> ________________________________________________________________
>>>
>>>
>>> On 2016-12-26 16:30, Fco. Javier Díez Guerra wrote:
>>>> Hello,
>>>>
>>>> For FRAP time-lapsed stacks, I am using ROI Manager/Multi Measure and
>>>> then export data to .csv files. For analysis outside Fiji/ImageJ, I
>>>> want to include a time reference of each slice in the first column of
>>>> the Results file, but I do not know how to do that.
>>>>
>>>> Since labels can be displayed in the Results window, I assigned a
>>>> time-stamp label to individual slices using this simple macro:
>>>>
>>>> timestamp=0.0000
>>>> setSlice(1);
>>>> for (i=1; i<=nSlices; i++) {
>>>>     setMetadata("Label",timestamp);
>>>>     timestamp=timestamp+0.1667;
>>>>     run("Next Slice [>]");
>>>>        }
>>>>
>>>> After running the macro, I can see the added label next to the slice
>>>> position in the image stack window. However ROI Manager/Multi Measure
>>>> sheets only display the title of the stack under the column tagged
>>>> "Label", which is obviously the same for all the slices.
>>>>
>>>> I would appreciate any help.
>>>>
>>>> Best
>>>>
>>>>
>>>> --
>>>>
>>>> Fco. Javier Díez Guerra, PhD
>>>> Profesor Titular
>>>> Centro de Biología Molecular Severo Ochoa
>>>> C/ Nicolás Cabrera, 1
>>>> Universidad Autónoma
>>>> Ctra Colmenar Viejo Km 15
>>>> Cantoblanco, 28049 Madrid
>>>> SPAIN
>>>>
>>>> phone:  +34 91 196 4612
>>>> e-mail: [hidden email]
>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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