How to export multiple ROI statistics to excel

[Jake Howden]

Hi everyone

I'm currently doing batch processing of images with different ROI created for each image. I would like to export the statistics of each ROI to an excel spreadsheet, such as the area of the ROI. I'm currently using ROI statistics and workbook to file block but when I click run it exports the ROI data and then replaces it with the next set of data. 

Also, once exported does 'interior' mean area of the ROI? 

Cheers

Jake

[Stephane]

Hi Jake,

You can look on this example to see how to generate a different excel file from the original image file name :
http://icy.bioimageanalysis.org/protocol/Intensity_threshold_to_ROI_%28batch%29

You can even directly get it in Icy by taping 'intensity threshold' in the Icy search bar.
Currently, if you want to separate image result in different spreadsheet, you have to use a script bloc as there is not yet block to allow spreadsheet appending operation.

The 'interior' field is indeed the area of the ROI but in number of pixel.

Best,

- Stephane

[Jake Howden]

Hi Stephane

Ah excellent that really helps. The values that appear in the excel spreadsheet, are they just the intensity values of the image within the boundaries of the ROI? e.g:

Regards

Jake

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[Stephane]

Hi Jake,

Yeah basically those values are the calculations made for the ROI, you can find min / mean / max intensity value per channel along others informations.

Best,

[Jake Howden]

Hi Stephane

Thanks. Another quick query. How do I add folder loop to a protocol? It doesn't appear in the protocol search, but something called FolderLoop appears on the global search and it says installed. 

Along a similar line I am having trouble with the protocol search. Sometimes it doesn't find a block that I know is there. For example typing 'file' shows a number of options including 'file batch' and typing 'batch' also brings up 'file batch' but typing 'file batch' brings back nothing. I also encounter this problem on a variety of blocks.

Cheers

Jake

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[Stephane]

Hi Jake,

The protocol search feature can be improved indeed, i faced similar problems as well... i don't really understand how it work but i guess the author of the plugin is aware of the problem ;)
For the folder loop, you can find it in the "Loop / Batch" section, also if you want to embed your workflow into a folder loop you need to use just "Embed" button in the toolbar :)

Cheers,

- Stephane

Le jeudi 8 janvier 2015 14:34:47 UTC+1, Jake Howden a écrit :

Hi Stephane

[Alexandre Dufour]

Hi Jake (and Stephane),

The block search bar wasn’t too happy with spaces until now, but at least that was easy to fix.

Let me know if you have other such issues after updating.

Alexandre

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[Jake Howden]

Hi guys

I've come back to my protocol and found that when I generate workbooks they wont open with excel and excel says that they are corrupt.

I don't think it's anything that I am doing wrong. Any advice?

Cheers

Jake

 

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[Alexandre Dufour]

Hi Jake,

This is perhaps due to a synchronisation problem between Icy and the operating system while writing the file to disk.

I’ve just pushed an update to “Workbooks” that hopefully will fix this. Could you please double check?

Cheers

Alexandre

On 04 Mar 2015, at 13:12, Jake Howden <jak...@gmail.com> wrote:

Hi guys

I've come back to my protocol and found that when I generate workbooks they wont open with excel and excel says that they are corrupt.

I don't think it's anything that I am doing wrong. Any advice?

Cheers

Jake

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[Jake Howden]

Hi Alexandre

Thanks for getting back to me. I installed the update but it still is saying that the file is corrupt.

Cheers

Jake

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[Alexandre Dufour]

Hmm, running out of ideas…

Out of curiosity (and my far away memory), when you indicate the name of the file to export, are you indicate the extension as “.xls” or “.xlsx”? It should be the former and not the latter (this is to allow even old versions of Excel to open the exported files. Using the latter may result in such an error.

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[Jake Howden]

Ah I had just forgotten to link the add ROI to sequence to ROI statistics. That's fixed the problem. My bad! Cheers for your help.

Jake

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