Metamorph .nd file timestamps
Posted: Fri Jul 21, 2017 6:31 pmHi all,
I've been writing an ImageJ macro to pull timestamps from multichannel z-stack timelapse data acquired using Metamorph's multi-dimensional acquisition tool, and I've discovered a discrepancy between the timestamps in images I acquire in Metamorph when viewed in Metamorph vs. when viewed in Fiji with BioFormats.
In Metamorph, every image is timestamped individually when it is acquired, even when two or more channels are acquired at every timepoint. If I view the metadata in Metamorph, the timestamp for slice 1, timepoint 1, channel 1 is different from the timestamp for slice 1, timepoint 1, channel 2 - as it should be. However, when I open either a .tif from the time series or the .nd file in Fiji using BioFormats, the timestamps that show up in the OME-XML metadata are identical for both channels. At each z position, the timestamp of channel 1 is duplicated for channel 2.
I'm working on a set of macros that I'll be using to monitor microscope performance and diagnose problems, so it's important for me to be able to access accurate timestamps for each channel that reflect when each image was acquired. Is there any way I can configure BioFormats to do this? I've started to explore other options for extracting the timestamp, and of course I can access the timestamps in Metamorph, but it would be great to be able to continue to use BioFormats.
Best,
Anna
I've been writing an ImageJ macro to pull timestamps from multichannel z-stack timelapse data acquired using Metamorph's multi-dimensional acquisition tool, and I've discovered a discrepancy between the timestamps in images I acquire in Metamorph when viewed in Metamorph vs. when viewed in Fiji with BioFormats.
In Metamorph, every image is timestamped individually when it is acquired, even when two or more channels are acquired at every timepoint. If I view the metadata in Metamorph, the timestamp for slice 1, timepoint 1, channel 1 is different from the timestamp for slice 1, timepoint 1, channel 2 - as it should be. However, when I open either a .tif from the time series or the .nd file in Fiji using BioFormats, the timestamps that show up in the OME-XML metadata are identical for both channels. At each z position, the timestamp of channel 1 is duplicated for channel 2.
I'm working on a set of macros that I'll be using to monitor microscope performance and diagnose problems, so it's important for me to be able to access accurate timestamps for each channel that reflect when each image was acquired. Is there any way I can configure BioFormats to do this? I've started to explore other options for extracting the timestamp, and of course I can access the timestamps in Metamorph, but it would be great to be able to continue to use BioFormats.
Best,
Anna