[ome-users] associating png import into time series

[David Schreiner]

I posted this on the OME forum already, but in case that was the wrong place:

https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=8086

I am trying to import png files from a time series experiment using insight 5.1 but cannot accomplish the basic task of associating files at the same position with different time points into the same file set, i.e. generating some metadata about these pngs. The result is that viewing a file after import always shows T: 1/1, i.e. no ability to step through the frames of the "movie" that the png files describe.

The original naming of the files was like this:

p0001/t0001_Brightfield.png
p0001/t0001_Red.png
p0001/t0002_Brightfield.png
p0001/t0003_Brightfield.png
p0001/t0003_Cyan.png
p0001/t0004_Brightfield.png
etc.

i.e. position folder, timepoints per wavelength within. N.B. some wavelengths are only present at certain time points due to phototoxicity.

I also tried changing the wavelength strings to the pattern "c0", "c1", etc. to no avail.

Finally, I read about setting a up a pattern file to instruct the importer what to do, and created a directory called "test" with the following contents:

import.pattern
t0001_c0.png
t0002_c0.png
t0003_c0.png
t0003_c1.png
t0004_c0.png
t0005_c0.png
t0006_c0.png
t0007_c0.png
t0008_c0.png
t0008_c1.png
t0009_c0.png

where import.pattern contains:
t<0000-9999>_c<0-9>.png

in the insight client i tried importing this whole test directory, only the import.pattern file, only the first time point of each wavelength, all the files within the dir, and the pattern file + the first file of each wavelength. in each case only exactly those files are imported (except the pattern file, which isn't a valid image) with no association between wavelength sets.

since this is a very basic aspect of the import process, i assume i am missing something that should be obvious. any help would be much appreciated!

-david

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