ion movie?

[ebmonroe]

Is there any way to export/create a movie or extract the 4th dimension (m/z) data? I am looking for interesting images manually at this point by clicking on the "N+" button. I’m also plotting images from the mass spectra and rois but thought it would be nice to have a movie or pull out all the images in a batch method to make one elsewhere. This could be particularly helpful when I’m looking at low level compounds that are present in only a few spectra…as is my goal.

I have ~16000 parameters in the m/z dimension in one file but if it were in a movie format, for instance, scanning the data set would be rather easy (that and, I know, I can rebin the data to make fewer data levels in that dimension.)

any help or direction would be greatly appreciated. Thanks in advance. Eric

[ebmonroe]

After fiddling around some, I figured out how to get a jpeg image stack to output but am limited to 999 "frames" it seems and any tiff stack output is failing as only one layer is included in the file. The export to AVI throws an error about missing a avi.dll file in a folder that doesn’t exist and is in an invalid folder structure anyway. Any ideas?

Also, is there a way to set the scale to autoscale for each image automatically? Or do I need to continue to do it manually (by adjusting or using the autoscale command)?

[Markus Stoeckli]

I finally had some time to look at the code and fix the issues you pointed. Check out BioMap version 3.7.4 and let me know how it works. Here’s what I changed:
[ul]
[li]Export of data without saving it to the database[/li]
[li]Tiff export with LZW compression, no limitation in image numbers (might take a while, though)[/li]
[li]Animated gif export[/li]
[li]Export as movie. A dll was missing, which is now part of the package. Play around with the codecs installed on your computer, some of them give strange results. Full frame for example results in a movie which plays just fine when watched with QuickTime Movie Player or ImageReady, but not on the Windows Media Player. MPEG-4 worked best for me.[/li][/ul]

markus

[ebmonroe]

thanks. I can get the uncompressed to work and image stacks but any suggestions on the mpeg4 encoder? What one did you have success with/how to get it installed?

I have QuicktimePro but the encoder does not seem to be recognized by BioMap.

I seem to have the best luck exporting it as a gif stack, opening in quicktime, and saving that as a quicktime movie. An alright work around but if I am just missing something easy, then direct from BioMap would be ideal.

Thanks for everything,
Eric

Post edited by: ebmonroe, at: 2007/01/04 18:47

[Markus Stoeckli]

The dll we use for this function is from a third party and therefore we have no control on the codecs being listed 🙁 . I successfully use the Microsoft MPEG-4 codec.

markus

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