Image name in LoadData

I want to use LoadData to load a csv file with the name of image files on a multi-well plate, the drug that was administered to each well, and the concentration. I have checked the “Load images based on this data?” box, but I don’t understand how to give a name to the loaded images (like you can in the LoadImages module). The processing modules after the LoadData module expect me to indicate which image they will work on, based on the name (no names appear in the drop-down menu of the processing modules when using LoadData). If I try to fix this issue by putting a LoadImages module after LoadData, I get a warning about this not being in good form, and a “Failed to initialize the pipeline” error if I try running.

I’m totally stumped with this issue, so any help is greatly appreciated.

Thanks!

Hi,

The LoadData image name is set after the second underscore in the header column for the filename column. If you look in the LoadData Help, you’ll see this example:

[quote]Image_FileName_FITC, Image_PathName_FITC, Metadata_Plate, Titration_NaCl_uM
"04923_d1.tif", “2009-07-08”, “P-12345”, 750
"51265_d1.tif", “2009-07-09”, “P-12345”, 2750[/quote]

and so the image name will be “FITC” here. Is that what you mean?

Also, does the “View…” button in LoadData reproduce your input CSV? There may be a syntax error in the CSV and it might not be read correctly, so the View button is a quick check on this.

Let us know if this helps!
David

Thanks David.
I didn’t not understand that detail from the help at all. I thought that string after “Image_FileName_” was just extra annotation so I didn’t add it to my file. I can view the CSV just fine.

Thanks a lot!

Great!

I added the image name to the header of the FileName column, and the pipeline runs properly now. But some of the output is wrong. At the end of the pipeline I’m exporting to a spreadsheet the colony counts, image file name, drug name, and drug dose. The colony counts are correct, but the image file name and drug dose for all rows of the output are stuck to the values corresponding to the first image (i.e. all output rows have image file “A01.tif”, drug “Drug1”, and dose “2e-5”). Is this a bug?

When I was using LoadImages (no LoadData to get drug doses) the output file was correct, with the right file name on each row. Am I missing again something obvious?

Additionally, my dose response curves have an X axis that has nothing to do with my dose values (neither with the straight dose or the log(dose)). Below is part of my CSV file. In the CalculateStatistics module I selected "Titration"as dose category, and “M” and the measurement.

Image_FileName_imgRaw Metadata_Drug Titration_M Data_Control
A01.tif Drug1 0.00002 1
A02.tif Drug1 6.67E-06 0
A03.tif Drug1 2.22E-06 0
A04.tif Drug1 7.41E-07 0
A05.tif Drug1 2.47E-07 0
A06.tif Drug1 8.23E-08 0
A07.tif Drug1 2.74E-08 0
A08.tif Drug1 9.14E-09 0
A09.tif Drug1 3.05E-09 0
A10.tif Drug1 1.02E-09 0
A11.tif Drug1 3.39E-10 0
A12.tif Drug1 0 -1

Thanks!!!

Hi,

In ExportToSpreadsheet, did you do the following:

  • Make sure to specify “,” as the delimiter?
  • Do your output spreadsheet files actually end in “.csv”, as opposed to something else?

You can also post a sample csv in your response, if you’d like us to check it out.

Regards,
-Mark

Hello.
I’m specifying “,” as the delimiter in ExportToSpreadSheet, and the output file has the correct .csv file extension. I’m attaching here the input csv loaded by LoadData (CellProfiler-Help_Key.csv) and the output csv created by ExportToSpreadsheet (Image.csv). As you can see, the export of the image file name and the drug dose are incorrect (all rows have the values from the first image).

Thanks a lot!
Image.csv (2.88 KB)
CellProfiler-Help_Key.csv (2.44 KB)

Would you mind posting the pipeline plus a couple of sample images? Not all the images, of course, but one or two wells?
-Mark