'AV1' Video Encoding for Biological Microscopy Data

Converts legacy microscopy video formats (H.264/H.265, AVI/MJPEG, TIFF stacks) to the modern 'AV1' codec with minimal quality loss. Typical use cases include compressing large TIFF stacks from confocal microscopy and time-lapse experiments from hundreds of gigabytes to manageable sizes, re-encoding MP4 files exported from 'CellProfiler', 'ImageJ'/'Fiji', and microscope software with approximately 2x better compression at the same visual quality, and converting legacy AVI (MJPEG) and H.265 recordings to a single patent-free format suited for long-term archival. Automatically selects the best available backend: GPU hardware acceleration via 'Vulkan' 'VK_KHR_VIDEO_ENCODE_AV1' or 'VAAPI' (tested on AMD RDNA4; bundled headers, builds with any 'Vulkan' SDK >= 1.3.275), with automatic fallback to CPU encoding through 'FFmpeg' and 'SVT-AV1'. User controls quality via a single CRF parameter; each backend adapts automatically (CPU and Vulkan use CRF directly, VAAPI targets 55 percent of input bitrate). TIFF stacks use near-lossless CRF 5 by default, with optional proportional scaling via tiff_scale (multiplier or bounding box, aspect ratio always preserved). Small frames are automatically scaled up to meet hardware encoder minimums. Audio tracks are preserved automatically. Provides a simple R API for batch conversion of entire experiment folders.

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:

Tested hardware

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.

Benchmark (30 s clip, 1920x1080, CRF 28, AMD RX 9070)

Compression = input clip size / encoded size. SSIM >= 0.97 visually transparent. vs CPU = CPU time / backend time (higher = faster).

Reproduce: Rscript inst/examples/benchmark_backends.R

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"))

Each backend uses the quality control approach best suited to its rate control:

Frames smaller than the hardware minimum coded extent are automatically scaled up proportionally (no distortion). Audio from the original file is preserved automatically.

CRF equivalence across backends (TIFF, mitosis.tif, 510 frames)

CRF is a unified quality parameter (0 = best, 63 = worst). Since each backend uses a different internal quantizer scale, AV1R maps CRF automatically. The table below shows equivalent settings calibrated by file size:

Reproduce: Rscript inst/examples/calibrate_vaapi_cqp.R

Note: Vulkan uses CQP (constant quantizer) rate control — the only mode currently working on RADV. CQP does not adapt to scene complexity, so Vulkan produces slightly lower SSIM (~0.93) compared to CPU/VAAPI (~0.96). This is a driver limitation; VBR/CRF support will improve quality when RADV implements it.

Supported Input Formats

System Requirements

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

# Ubuntu 22.04+
sudo apt install ffmpeg libvulkan-dev

TIFF stacks

TIFF stacks use near-lossless CRF 5 by default (tiff_crf). Output resolution can be controlled via tiff_scale.

Note for quantitative microscopy: AV1 is a lossy codec even at CRF 1. If your workflow relies on pixel intensity measurements (fluorescence quantification, ratiometric imaging, colocalization analysis), lossy compression will alter the data. For such use cases, keep the original TIFF/PNG files for analysis and use AV1R only for visualization, sharing, and archival of preview copies. Lossless alternatives: TIFF, PNG, FFV1.

# 2x magnification (proportional, no distortion)
convert_to_av1("stack.tif", "stack.mp4", av1r_options(tiff_scale = 2))

# Fit into 1920x1080 bounding box (proportional)
convert_to_av1("stack.tif", "stack.mp4", av1r_options(tiff_scale = c(1920, 1080)))

See inst/examples/tiff_scale.R for more examples.

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
  tiff_crf   = 5,     # CRF for TIFF input (near-lossless)
  tiff_scale = NULL,  # NULL, multiplier (e.g. 2), or c(width, height)
  verbose    = TRUE,  # informational messages
  backend    = "auto" # "auto", "cpu", "vaapi", or "vulkan"
)

License

MIT

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