Olympus Scan^R metadata

[s_watson1 (Watsons)]

We are using the Olympus Scan^R for high content screening of 96 well and 384 well plates, and I’d like to import the images into CellProfiler for analysis. The acquisition log produced by the Olympus software doesn’t seem to be compatible for deriving well position information from. For the sake of flexibility I would like to parse out the metadata from the file name, but am having trouble with the correct regular expression. Here is an example of the file names:

A1–W00001–P00001–Z00000–T00000–Alexa 488

The most important features are the well (A1), the image position within the well (P00001), and the Channel (Alexa 488). The channel is an alphanumeric variable, typically one of four for each position in each well, but is always at the end of the file name. Any help would be greatly appreciated.

Thanks!

[David_Logan]

Hi,

Try this out in the Metadata regular expression field:

^(?P<Well>[A-Z][0-9])--(?P<W_Field>[A-Z][0-9].*)--(?P<Position>[A-Z][0-9].*)--(?P<Z_Field>[A-Z][0-9].*)--(?P<T_Field>[A-Z][0-9].*)--(?P<Channel>.*).[tT][iI][fF]
It assumes a few things, including:
(1) The filename starts with a two character letter/number combination
(2) Each field always has two dashes as a separator
(3) The Channel field just grabs all the characters until the dot of the extension, which I assume there is one (though note that it may be hidden by your file viewer)
(4) the image type is tif (or TIF – I added case-insensitivity to the file extension just to be safe). Change this depending on the file type/extension.

It works for my mocked up file based on your text, with “.tif” added as an extension (see attached screenshot). If you don’t want all the fields, just replace any parenthetical with “.*” (not including quotes) and it should work.

Cheers,
David

[s_watson1 (Watsons)]

That’s great, thanks so much. Really appreciate the help.