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import tif files

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import tif files

Postby glyn_nelson » Fri Dec 10, 2010 3:30 pm


I'm a new user, so please forgive any obvious mistake I'm making. I have images which I've post-processed in ImageJ and saved as .tifs. They are one channel (GFP) time series but when I import them with OMERO.importer, it automatically thinks they are an rgb tif z series. It creates a maxed out image for the red and blue channels and even though the image properties are set correctly in ImageJ, it sets it as a zed series rather than time.

So I'd like to know:
a: what am I doing wrong
b: how can I stop OMERO.importer thinking it is an rgb file and making up data (going to use a lot of disk space at this rate)
c: get it to import the metadata correctly? It doesn't just think it is a z series, it also sets the frame interval to 10 without a suffix (s, min, h?) and changes the pixel size from 0.22um to 2.2um.

Hopefully there is a simple answer to question a which will cover the other points!

Thanks, Glyn.
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Re: import tif files

Postby glyn_nelson » Mon Dec 13, 2010 9:29 am

I've updated loci_tools.jar and saved as ome.tiff files. This fixed the z instead of t issue, and the pixel size.

For the rgb problem;
ImageJ was pseudo-colouring my GFP channel green when I imported the orignial .lsm files- it is this that causes OMERO.importer to think that the file is an rgb apparently. If I go back to a greyscale LUT and save the tif, it imports as a single colour tif. Bit bizarre.

Playing around with ome.tiff saves, it seems it reads any time interval given in imagej as seconds, regardless of any suffix. Therefore if I make sure that is in seconds, Bob's your uncle. Now just need to figure out how you see that bit of data in OMERO.insight...
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Re: import tif files

Postby wmoore » Thu Jan 20, 2011 10:11 am


You can see exposure duration for each plane under the "Acquisition" tab on the right of Insight - Look under the specific Channel panel, at the bottom there is an "Exposure Time" table with the times for each frame.

You can see the exposure time-point for each frame at the bottom of the full image viewer window. The time (since the start of the movie) is displayed for each channel in the currently displayed timepoint.

Hope that helps,

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