Names&Types; Matching by order error

I am uisng the illumination pipeline provided to correct some images I have taken, all of one well at different sites with five wavelengths at each site.

I have dragged my images into the Images input module and added the metadata, which correctly identifies the well, site and wavelength values for each image. However, when I assign names and/or an image matching method I recieve an error message that there is an error in some of my image set and a warning that I have no valid images configured (nothing appears in the “update” check box at the bottom of the screen either). As far as I can see my metadata in the metadata input module matches that I am using to name the channels.

I attach screenshots of each stage I have done so far, any help would be really appreciated!

Hi! I’m looking at your screen shots on my phone, so take this advice with a grain of salt: it seems you are only inputting four channels but then in the last screen shot you are attempting to match meta data for five channels. Can you figure out how to adjust that?

The other thing that jumps out at me is that if you are matching by meta data, you don’t want to match by order also. So you’d want to remove that selection.

Thank you. I noticed the number of input channels just after I had uploaded the photos! Even with the correct number I still get the same error. I have tried with both order by order and metadata and neither are working I’m afraid.

Bummer. Next step is to attach your pipeline! Please also attach the log that’s mentioned in the error windows. I’m sure it’s something simple and we can get you fixed up in no time.

I also note you are attempting to match by “Plate” but it doesn’t seem that information is extracted as Metadata in the Metadata module?

Okay! Here is the pipeline file

Carpenter_Illum_Pipeline_Cardiac_Testrun.cpproj (141.0 KB)

I’m afriad the log file doesn’t add anything to it when the error message comes up.

Thanks for your help

Hm, I changed NamesAndTypes to only match Site (deleted UserStem, Well, Plate) and it worked… can you try that on your small test set and then maybe we can build from there?

If I try to click update after making that change I still get the same error message, but if I just run the analysis it works! Thank you. May I also ask, in order to get the output as a speadsheet rather than a matlab file, do I just export as spreadsheet? As when I do this I get an error message (below) which may be linked to the first error message?

Thanks for all your help!

Super. You might be able to now add back the other metadata one by one.

Indeed, you will want to add the ExportToSpreadsheet module.

Unfortunately, I am not familiar with that error. It might help others to diagnose it if you can clarify exactly when it appears and if it’s associated w processing a particular module?

Once I have run the illumination pipeline I try to export the output .MAT files to spreadsheet. I selected datatools; export to spreadsheet and then selected a .MAT file. On doing this I receive this error:

Ah, instead of using the ExportToSpreadsheet data tool, can you instead use ExportToSpreadsheet as a module in the pipeline? The module generally works more reliably than doing it after processing completes.

Thank you for all your help Anne! It is all working perfectly now and will hopefully have some exicting data out of the assay soon!

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