Video

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Supported File Types

After Effects supports a wide variety of different still and video formats - and because it supports quicktime it can use any format supported by quicktime (which is a lot). However, in practical use there are a few formats you will probably find yourself using most often.

Still Image formats

You'll often be using still images or graphics which you will then add motion to in your AE compositions. Still images can be either bitmaps, meaning they are pixel-based and have a fixed resolution, or vector, meaning they are composed of mathematically-described curves which can scale to any resolution. Which type you choose will depend on both the nature of your graphics and what you plan to do with them in AE.

Bitmaps

Bitmaps break an image down into a large number of individual picture elements, or "pixels", each of which is assigned a color. These are well suited to photographs or complex images with a lot of detail and color gradations. The primary drawback of bitmap images is their fixed resolution; this means if you want to scale an image up (i.e. zoom into it) in AE you need a high enough resolution so that you never end up scaling the individual pixels beyond 100%. Bitmap images also tend to have larger file sizes than vectors, especially when working at high resolutions. Some common bitmap formats you'll work with are:
PICT, TIFF, Targa (.pct, .tif, and .tga)
All of these are high quality, 24bit color (meaning photographic quality with over 16 million possible colors), uncompressed (usually) formats which also support an additional 8bit channel of transparency called an "Alpha Channel" (for more info on alpha channels see my notes on using Photoshop with AE). These are usually your best choice because their quality is so high.
Photoshop (.psd)
Photoshop is another high quality, uncompressed, 24bit image format, but it also supports multiple layers of image elements which can be imported individually, as a single flattened image, or as a new composition which maintains the layers on AE's timeline. For more info on these options see my notes on using Photoshop with AE). If you are working in Photoshop to prepare your images for AE there is no need to export copies to another format - just use the native PS files.
JPEG (.jpg)
Jpeg is a 24bit, photographic-quality image format that has been compressed to reduce the file size. The compression process requires some image info to be thrown out, which results in "artifacts", or visual errors, when the image is decompressed. This makes JPEG a less desireable format to use, although the quality loss is highly dependent on the amount of compression used. JPEG is also the most commonly used format online, which means if you found your images on the web they are probably already compressed. If the compression is low they may be suitable for your AE work, but if it's high you may be better off looking for an alternative image source - it's really a judgement call you have to make. An additional limitation of JPEG is that it does not support an alpha channel so your image will not contain any transparency information.
GIF (.gif)
GIF is another commonly used image format for the web, however it is not well suited to AE work. It is only 8bit, meaning it has a maximum of 256 possible colors in the image, and it supports only 1bit transparency, meaning a pixel is either fully visible or fully transparent but never anywhere in between. This results in pictures which are often speckled with color("dithering") or have color bands in gradients, and the transparency often has a color fring around the edges of the transparent area. Though they are commonly found on the web I would highly recommend staying away from them as AE source material.

Vectors

Vector-based images describe the image elements mathematically using lines, fills and curves. While this is a very efficient way of storing visual images it's not well suited to photographic images. Hoever, it works very well for text, line art, graphics with solid shapes or large gradients, and graphics without a lot of fine detail. Besides small file sizes you have the additional advantage of being able to scale vector graphics up to any resolution without a loss of visual quality. Commonly encountered formats include:
Adobe Illustrator and EPS (.ai or .art, .eps)
These are the most commonly used vector formats for AE projects. Quality on both is the same; the main advantage to using the native illustrator format over EPS is the ability to create your graphics as layers and import those layers seperately or as a composition withe the layers on the timeline (this works in almost exactly the same way as with layered Photoshop files, see my Photoshop with AE notes for more info on the process).
PDF (.pdf)
PDF is most commonly used as a way to distribute electronic documents online while maintaining ther printed format. It can contain a mixture of vector text and graphics along with embedded bitmaps (usually jpegs). It's not a format you will probably need to use often unless you are trying to incorporate a printed document as a visual element in your video compositions.

Motion Formats

You may want to bring in video or animations created in another program and there are several formats you can use depending on the source of the video:

Image Sequences

Image sequences are a special type of still image - it is essentially a video in which each frame has been saved as an individual numbered file. This is frequently used for animation created in a #D animation program. The individual files can be any of the bitmapped formats above, but they must contain numbers in their filenames which indicate the order they are to be played in (i.e. image001.tif, image002.tiff, image003.tif, etc).

Quicktime (.mov) or Video for Windows (.avi or .wmv, Windows only)

Both of these are video formats and can contain compressed or uncompressed video - the quality of the video in either format will depend heavily on the type and amount of compression used. Whether you are capturing video from a DV camcorder, importing it from a CDROM, or downloading from the web, it is likely you will use one of these formats. For best results you want to use video that is either uncompressed or a high quality compressed format like DV or Motion-JPEG. For more info on compression formats check out my notes on Digital Video Compression.

Flash (.swf)

Flash is a popular animation format for the web, and it uses vectors for most of it's graphics. AE supports flash through a quicktime conversion, which means you can bring it in but it gets rasterized as a bitmap at whatever resolution the original flash file was created at. This just means that if you zoom in on it it will become pizelated rather than staying clean like a true vector graphic would.

This should give you a good idea of the types of files you'll be using most commonly in AE. Thanks to it's support for quicktime there are dozens of other still and motion formats which it supports, but you are not likely to be using them frequently. If you have a file of a type you are unsure about, try importing it into AE - it may be supported. If not, it simply won't bring it into your project and you'll need to find an alternate file or a program to convert it into a supported type.