I'm trying to capture pixel data from an AVCaptureStillImageOutput and noticed that upon cropping the image to a CGImage, it becomes re-oriented. To test this, I output a temporary image to the photo library. Now I've noticed that even before the image is cropped, it's thumbnail is rotated while the full image is not. (This later becomes a problem when I pass the UIImage to my custom pixelDataManager that requires proper dimensions of the image.)
Setting captureVideoPreviewLayer.orientation = AVCaptureVideoOrientationPortrait; and [videoConnection setVideoOrientation:AVCaptureVideoOrientationPortrait]; did not seem to change anything.
Any thoughts??? I'll break it up into sections...
1) Setting up the session, input, and output:
    // Create a capture session
    AVCaptureSession *session = [[AVCaptureSession alloc] init];
    session.sessionPreset = AVCaptureSessionPresetMedium;
    AVCaptureVideoPreviewLayer *captureVideoPreviewLayer = [[AVCaptureVideoPreviewLayer alloc] initWithSession:session];
    // Add capture layer to visible view    
    captureVideoPreviewLayer.videoGravity = AVLayerVideoGravityResize;
    captureVideoPreviewLayer.frame = screenBounds;
    captureVideoPreviewLayer.bounds = screenBounds;
    captureVideoPreviewLayer.orientation = AVCaptureVideoOrientationPortrait;
    [self.vImagePreview.layer addSublayer:captureVideoPreviewLayer];
    AVCaptureDevice *device = [AVCaptureDevice defaultDeviceWithMediaType:AVMediaTypeVideo];
    // Setup error handling
    NSError *error = nil;
    AVCaptureDeviceInput *input = [AVCaptureDeviceInput deviceInputWithDevice:device error:&error];
    if (!input) {
        // Handle the error appropriately.
        NSLog(@"ERROR: trying to open camera: %@", error);
    }
    [session addInput:input];
    // Start session
    [session startRunning];
    // Output image data 
    stillImageOutput = [[AVCaptureStillImageOutput alloc] init];
    NSDictionary *outputSettings = [[NSDictionary alloc] initWithObjectsAndKeys: AVVideoCodecJPEG, AVVideoCodecKey, nil];
    [stillImageOutput setOutputSettings:outputSettings];
    [session addOutput:stillImageOutput];
2) Setting up the video connection:
AVCaptureConnection *videoConnection = nil;
for (AVCaptureConnection *connection in stillImageOutput.connections)
{
    for (AVCaptureInputPort *port in [connection inputPorts])
    {
        if ([[port mediaType] isEqual:AVMediaTypeVideo] )
        {
            videoConnection = connection;
            break;
        }
    }
    if (videoConnection) { break; }
}
if ([videoConnection isVideoOrientationSupported])
{
    [videoConnection setVideoOrientation:AVCaptureVideoOrientationPortrait];
}
3) Output the captured image:
NSLog(@"about to request a capture from: %@", stillImageOutput);
[stillImageOutput captureStillImageAsynchronouslyFromConnection:videoConnection completionHandler: ^(CMSampleBufferRef imageSampleBuffer, NSError *error)
{         
    NSData *imageData = [AVCaptureStillImageOutput jpegStillImageNSDataRepresentation:imageSampleBuffer];
    UIImage *image = [[UIImage alloc] initWithData:imageData];
    UIImageWriteToSavedPhotosAlbum(image, nil, nil, nil);
    //......
}