Intensity information on spot detector

[thiba...@gmail.com]

Hello,

I’m using spot detector to count green (GFP) bodies in the nucleus. I created multiple ROI corresponding to cell nuclei using the DAPI channel and then counted the bodies in each nucleus.

I wanted to know if there was a way to obtain intensity informations for detected spots or at least a way to get the total intensity generated by spots in a given ROI.

Thank you very much for your help

Best regards

Thibaut Snollaerts

[Fabrice de Chaumont]

Hi Thibaut,

You have the intensity of each spot in the excel file automaticaly created in a 'save' folder created for you in the folder of the original image.
For each ROI, you will see a (long) list of detection providing x,y,z,c,t position and also min/mean/max intensity.

I think it's what you are looking for.

Also, if you wish to export the ROI intensity of you nucleus, you can go in the ROI tab, then select all the ROIS (Ctrl A) and click export. You can set .xls or .csv

Best,

Fabrice

[SB]

On Friday, January 24, 2014 4:31:21 PM UTC+1, Fabrice de Chaumont wrote:

Hi Thibaut,

You have the intensity of each spot in the excel file automaticaly created in a 'save' folder created for you in the folder of the original image.
For each ROI, you will see a (long) list of detection providing x,y,z,c,t position and also min/mean/max intensity.

I think it's what you are looking for.

Also, if you wish to export the ROI intensity of you nucleus, you can go in the ROI tab, then select all the ROIS (Ctrl A) and click export. You can set .xls or .csv

Best,

Fabrice

Hi Fabrice,

I am also interested in intensity in ROI, however, when I try to export the ROI tab in order to get the surface of the different ROI spots and the ROI of the nucleus, the Icy software blocks everything and it does not export anything. Do you know why?
I do this, because, I noticed that the file generated by the "start detection program" contains the ROI in pixels² while in the ROI tabs, it is in um². Would it be possible to add this surface area unit in the automated generated file?
thanks a lot for your help,

Sophie

[Stephane]

Hi Sophie,

When you export the ROI from the ROI tab you should see a windows asking you for the output filename. Do you see it ?
Then when you export, do you receive any error message (dialog or just in the output tab) ?
Normally the ROI excel export can take a bit of time but should generate an error message if something wrong happen.
Can you also give me the informations which appears in the output tab when the application start ? you should see something as :

<<
Java(TM) SE Runtime Environment 1.6.0_45-b06 (64 bit)
Running on Windows 7 6.1 (amd64)
Number of processors : 8
System total memory : 8180.2 MB
System available memory : 3754.8 MB
Max java memory : 3555.6 MB

VTK library successfully loaded...

Icy Version 1.6.0.1 started !
>>

It can help me in understanding what happen, i do know that on some linux JVM the JXL library can miss.

Best,

- Stephane

[X. Qin]

Hi all,

Where can I find the intensity information for a tracked trajectory? I know I can find the intensity for the detected spots in the save folder. However, I could not find the intensity information after I apply a spot tracking for the detected spots. I would like to produce a intensity vs time curve, to see how many photobleaching steps are there.

Does anybody know how to realize it on Icy?

Thank you!

Xianan Qin

[Stephane]

Hi Xianan,

When you do tracking you should obtain your tracks in the Track Manager plug-in, and once you are there you can add new track processors to visualize or quantify your tracks. The one you need it is "Track Processor Intensity Profile". If you don't find it in the list you can try to type his name in the main search bar to install the required plugin.

Best,

- Stephane

[X. Qin]

Thank you Stephane!!