How to calculate with my formula

[Ken]

Hi everybody,

I am developing a protocol to measure spot intensity.
I was able to output the each spot intensity and display the number of cell (ROI) on the screen with ICY.
However, I have no idea how to sum intensity of all spots and how to divide it by the number of cells.
I can do it manually but I would like to automate it using ICY because I'll input a ton of data.

Is there any way to do this?
Please see the attached image for details.

Thank you in advance.

Ken

[Stephane]

Hi Ken,

Of course we understand you prefer to fully automatize the process :)
It's possible to do that but still the excel export require using javascript a bit :
- merge your spot ROIs using the "Merge ROI" with OR operation
- use "Get ROI Descriptor Value" to retrieve the sum intensity of your merged ROI
- use "List Size" block to get the number of ROI from ROI list
- use "Math operation binary" to divide the global sum intensity by the number of ROI
- use "javascript" block to build your customized excel output (you can type "ROI export to Excel" to get an example script for excel file generation).

Hope that helps :)

Best,

- Stephane

[Ken]

Hi Stephane,

Thanks to your help, I was able to calculate the total spot intensity and output the number of ROI, but there are some problems.

1) Total spot intensity
When I use Merge ROI -> ROI statics -> Workbook to file, the correct value is output.
However, using Merge ROI -> Get ROI descriptor value -> Math operation binary, "NaN" is output.
What is the cause of this?

2) The number of ROI
Is there any way to link "the number of ROI" to a "workbook to file" block?
I would like to merge sheets for batch analysis but I can not write Javascript to do that.

For details, please see the attached file.
I appreciate your cooperation.

Best,

- Ken

2017年9月7日木曜日 0時37分03秒 UTC+9 Stephane:

[Ken]

Hi,

I attached my protocol file and I uploaded the tif file to the following link.

https://drive.google.com/open?id=0BwSQjr0XAK3wWWkxNEQ5bVRBTzQ

I would be grateful if you could help me.

Best,
- Ken

2017年9月12日火曜日 11時18分45秒 UTC+9 Ken:

[Stephane]

Hi Ken,

Thanks for sharing the protocol, it's better for us as we can directly modify it. It would be even better if you can provide us a sample image to test it, is it possible ? thanks !

Best,

- Stephane

[Ken]

Hi Stephane,

Thanks for your reply.

I pasted the link for downloading a sample image file in the previous post. ( I was not able to attach it here because of the large file size. )

https://drive.google.com/open?id=0BwSQjr0XAK3wWWkxNEQ5bVRBTzQ

Please let me know if you can not download.

I am very grateful to your cooperation.

Best,

- Ken

2017年9月14日木曜日 18時24分00秒 UTC+9 Stephane:

[Stephane]

Hi Ken,

Perfect i was able to download it and make some tests.
In fact you just need an extra block to make the ROI descriptor working.
I can explain why, by default the ROI position apply on all channel, because of the the ROI descriptor which return a single value doesn't know which channel sum intensity to compute and return Nan, to avoid that just set manually the ROI channel position to 0 (as we have only a single channel image here) before using the ROI Descriptor block.

I attached you the modified protocol.

About the ROI number inside an excel file, in fact it looks like you were able to do it by yourself :)
Let me know if you still have issue.

Best,

- Stephane

Le mercredi 6 septembre 2017 09:40:04 UTC+2, Ken a écrit :

[Ken]

Hi Stephane,

Thank you for modifying my protocol.

After all, I decided to take the nuclei fluorescence intensity instead of the number of nuclei (ROI). This is because it is difficult to export output the number of nuclei continuously and automatically in batch analysis.

I was able to easily export output the nuclei intensity using "Workbook to file" block and the both results were almost the same.

Anyway, thanks to you, it looks like this work will go well.
Thank you very much.

I'll let you know if I have any questions.

Best,

- Ken

2017年9月15日金曜日 22時05分33秒 UTC+9 Stephane: