ffmpeg prores alpha channel not present when colormatrix and colorspace operations are performed So I've figured out how to convert images to prores with no colorspace shifts using either:

-vf colormatrix=bt601:bt709 filter for 8bit material

and

-vf colorspace=all=bt709:range=pc:format=yuv444p10:iall='bt601-6-625':irange=pc filter for 8bit or 10bit material.

However, whenever I use colormatrix or colorspace filters the output file contains no alpha channel.  As soon as I remove these filters the alpha channel is present but now I've got a color shift.

#this generates no alpha
ffmpeg -f image2 -r 24.0 -i tif_w_alpha.%3d.tif -c:v prores_ks -profile:v 5 -pix_fmt yuva444p10le -vf colorspace=all=bt709:range=pc:format=yuv444p10:iall='bt601-6-625':irange=pc -alpha_bits 16 this_has_no_alpha_channel.mov

#this has alpha but also a color shift
ffmpeg -f image2 -r 24.0 -i tif_w_alpha.%3d.tif -c:v prores_ks -profile:v 5 -pix_fmt yuva444p10le -alpha_bits 16 this_has_alpha.mov


This behavior is the same in both -profile:v 4 and 5 which are the only 2 that support alpha.  How can I get the color filter to work without losing the alpha channel?
The colorspace and colormatrix filters don't handle alpha pixel formats, so those get stripped off. The workaround is to extract the alpha and then reattach it.

ffmpeg -f image2 -framerate 24.0 -i tif_w_alpha.%3d.tif -filter_complex "[0]colorspace=all=bt709:range=pc:format=yuv444p10:iall='bt601-6-625':irange=pc[main];[0]alphaextract,format=gray10le[alpha];[main][alpha]alphamerge" -c:v prores_ks -profile:v 5 -pix_fmt yuva444p10le -alpha_bits 16 this_has_no_alpha_channel.mov

BTW, The Quicktime specification doesn't accommodate output range pc. Consumers should expect to treat range as always tv. If your software allows to override that, nice, but other software may not.