Operetta images - metadata extraction regulare expressions

Hi
I am trying to process some images generated on the Operetta system from Perkin Elmer to eventually put into FCS Express 4 and generate picture and heatmaps with it. I have the pipeline running ok for the segmentation but my problem lies in extracting the row and column information from the file using regular expressions. I must admit regular expressions are alittle beyond me, even with the tutorials, although I do get it to work with the BD pathway so I I live in hope. :smile:
I was wondering if anyone could shed any light on how I would extract the row and column data from these types of images and I have attached one just so you can see the image name. I am wondering if perhaps I have to rename the images ?
Any tips would be greatly appreciated.
Thanks Everyone.

Hi,
I’m not terribly familiar with the Operetta nomenclature. Can you describe where the row/column information is contained in the filename, e.g, in the example you uploaded, 007001-4-001001002.tif?
Regards,
-Mark

Hello,

I am also looking to use CellProfiler and CellProfiler Analyst to analyze data generated with the Operetta HCS.
Here is what I was able to figure out from the image identification:

007001-4-001001002.tif
007 = row
001 = column
4 = “site” (image number in the well)
last number is the channel number
(not figured out what the other numbers were yet…)

I have been able to use the current regular expression with CellProfiler:
^(?P[0-9]{3})(?P[0-9]{3})-(?P[0-9]{1,2}) (tested)
Now I hope to figure out how to upload the layout with relation to the wells… :wink:
Claudia

Hey Guy~
My HCS device is also Operetta system from Perkin Elmer, but My filename is like this:
r02c02f01p01rc1-ch1sk1fk1fl1.tiff
thanks for the help from clolalan7, now I can extract the metadata from this filename by using regulare expressions. like this
^r(?P[0-9]{2})c(?P[0-9]{2})f(?P[0-9]{2})p(?P[0-9]{2})rc(?P[0-9])

[quote=“BlueALH”]Hi
I am trying to process some images generated on the Operetta system from Perkin Elmer to eventually put into FCS Express 4 and generate picture and heatmaps with it. I have the pipeline running ok for the segmentation but my problem lies in extracting the row and column information from the file using regular expressions. I must admit regular expressions are alittle beyond me, even with the tutorials, although I do get it to work with the BD pathway so I I live in hope. :smile:
I was wondering if anyone could shed any light on how I would extract the row and column data from these types of images and I have attached one just so you can see the image name. I am wondering if perhaps I have to rename the images ?
Any tips would be greatly appreciated.
Thanks Everyone.[/quote]

Hi,

I also use operetta from Perkin Elemer to do HCS, the file name in my device is like this:

r02c02f01p01rc1-ch1sk1fk1fl1.tiff

Now, I have been able to extract metadata from file name by using regular expressions with Cellprofiler, like this:

^r(?P[0-9]{2})c(?P[0-9]{2})f(?P[0-9]{2})p(?P[0-9]{2})rc(?P[0-9])

Although, the file names lack dose data in this test experiments, In fact, the dose data can also be extracted by using regular expressions. Another convenient way to extract metadata is by importing a .csv file which can be quickly got by transforming Harmony’s .xml