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Yes, dramatically higher quality. Lightroom is fine, but if you import your raw images as an image sequence directly into AE you'll get an Adobe ACR window in AE. It will only work on the first image unfortunately and if your exposure or color temp changes during the sequence, (you should not be capturing in awb mode!), however if it does change you can re-import the footage in another layer and blend/dissolve to match footage and create amazingly consistent footage. I would imagine some would also create hdr sequences this way as well...
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There's at least one timelapse forum, search for "timescapes." Several After Effects users there but traffic is low.
In my opinion, your workflow shoudl not be designed based on your perceived need to maximize image quality. Instead it shoudl be based on your target output or your anticipated editing needs. For instance, bringing raw images form your Nikon or Canon into AE at full rez, say, 4k, is going to make editing sluggish on any machine. Even if your output is HD video at 1920x1080, you're still throwing away 75% of the pixels from the raw images. If you know you're going to be doing lots of zooming and panning, you may need to use larger images.
If you are trying to make a living with yoru timelapse work, you will want to explore or purchase scripts and actions for batch processing in Photoshop upstream of After Effects.
There are so many ways to move still images to a screen for display. You just want to know why you will be using one tool or another.
Thanks for that Jesse. So to understand this the first image of the raw sequence will dictate the setting for each image in the sequence? So if I make specific corrections in Lightroom to images in mid sequece they will be ignored by After Effects?
Could I achieve the same quality by exporting tiff files (instead of jpegs) from Lightroom to create the sequence in Premiere?
I have viewed some of the discussions on Timescapes that were very helpful. Thanks for suggesting that. My interest in this is not based entirely on quality. From the Timescape forum I've heard claims of better performance (over premiere) for slowing and speeding up footage among other things. Mainly trying to detemine if it's worth the time investment to learn the program. I have the After Effects product from the suite - seems like a waste just sitting on my hard drive.
That is correct, unfortunately we can't keyframe raw settings mid-sequence. However I've had very good results with using separate imports of the same sequence, using different raw settings, then blending/dissolving, (in AE), the sequences to achieve nice results. I don't use LR much, but that could work... not sure. Tiffs are unwieldly, at least that's been my experience. Work with your raws.
My belief is in digital realm, why not have as much quality as possible! You never know where your footage might find a home - AND don't forget, the 4k+ rez of dslr, well 5DmkII and the like, allows you to make zooms and pans within your sequence. As bogiesan mentions there are deflicker and other apps/scripts available, I guess I'm just more hands-on. I've deflickered footage using my above method with excellent results. Some might find it tedious, but it bloody works.
Delve deep in Timescapes.org, there gems there, and everything you need to know about time lapse.
Here's a recent effort of mine - actually my first, (after many tests, trials and tribulations) http://vimeo.com/23830325
I suppose I will just have to do some experimenting in After Effects. Really appreciate the help and insight. Enjoyed your movie too. Thanks.