AV1R

AV1 video encoding for biological microscopy data.

AV1R is an R package for biologists that converts legacy microscopy video formats (H.264/H.265, AVI/MJPEG, TIFF stacks) to the modern AV1 codec with minimal quality loss.

Why AV1R?

Compress large TIFF stacks from confocal microscopy, time-lapse, and EBImage workflows from hundreds of gigabytes to manageable sizes — without noticeable loss of information.
Re-encode MP4 files exported from CellProfiler, ImageJ/Fiji, and microscope software with ~2x better compression at the same visual quality.
Standardise legacy recordings — convert old AVI (MJPEG) and H.265 files to a single patent-free format suited for long-term archival.

GPU acceleration

AV1R automatically selects the best available backend:

Priority	Backend	How
1	Vulkan	`VK_KHR_VIDEO_ENCODE_AV1` — native GPU encode
2	CPU	`libsvtav1` or `libaom-av1` via FFmpeg

Tested hardware

GPU	Driver	Status
AMD Radeon RX 9070 (RDNA4)	Mesa RADV (GFX1201)	Working

Vulkan AV1 encode headers are bundled in src/vk_video/, so no SDK upgrade is needed at build time. Builds with any Vulkan SDK >= 1.3.275. Runtime support depends on GPU driver.

Quick Start

library(AV1R)

# Convert microscopy recording
convert_to_av1("recording.mp4", "recording_av1.mp4")

# TIFF stack with custom settings
convert_to_av1("stack.tif", "stack.mp4", av1r_options(crf = 20))

# Batch convert entire experiment folder
convert_folder("experiment/", "compressed/")

# Check what backend will be used
detect_backend()

GPU encoding

# Check GPU availability
vulkan_available()
vulkan_devices()

# Force GPU backend
convert_to_av1("input.mp4", "output.mp4", av1r_options(backend = "vulkan"))

# Force CPU backend
convert_to_av1("input.mp4", "output.mp4", av1r_options(backend = "cpu"))

GPU encoding uses CQP (constant quantizer) rate control. The crf parameter (0–63) is mapped nonlinearly to AV1 quantizer index (0–255), approximating aomenc --cq-level behaviour. Frames smaller than the hardware minimum coded extent are automatically scaled up. Audio from the original file is preserved automatically.

Supported Input Formats

Format	Extension
H.264 / MP4	`.mp4`, `.mkv`, `.mov`
H.265 / HEVC	`.mp4`, `.mkv`
AVI / MJPEG	`.avi`
TIFF stack	`.tif`, `.tiff`
TIFF sequence	`frame%04d.tif`

System Requirements

FFmpeg >= 4.4 with libsvtav1 or libaom-av1 (required for CPU encoding)
libvulkan-dev (optional, for GPU encoding on Linux)

# Ubuntu 22.04+
sudo apt install ffmpeg libvulkan-dev

Options

av1r_options(
  crf     = 28,    # quality: 0 (best) - 63 (worst)
  preset  = 8,     # speed: 0 (slow/best) - 13 (fast/worst), CPU only
  threads = 0,     # 0 = auto, CPU only
  backend = "auto" # "auto", "cpu", or "vulkan"
)

License

MIT

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