AV1R: 'AV1' Video Encoding for Biological Microscopy Data

Description

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.

Author(s)

Maintainer: Yuri Baramykov lbsbmsu@mail.ru

See Also

Useful links:

• https://github.com/Zabis13/AV1R

• Report bugs at https://github.com/Zabis13/AV1R/issues

AV1R encoding options

Description

AV1R encoding options

Usage

av1r_options(
  crf = 28L,
  preset = 8L,
  threads = 0L,
  bitrate = NULL,
  tiff_crf = 5L,
  tiff_scale = NULL,
  verbose = TRUE,
  backend = "auto"
)

Arguments

Value

A named list of encoding parameters.

Examples

# Default options (auto-detect backend and bitrate)
av1r_options()

# High-quality lossless-ish for publication figures
av1r_options(crf = 15, preset = 4)

# Explicit bitrate (GPU VAAPI)
av1r_options(bitrate = 2000, backend = "vaapi")

# Fast batch conversion of large TIFF stacks
av1r_options(crf = 32, preset = 12, threads = 16)

Show AV1R backend status

Description

Prints the active encoding backend and available GPU/CPU capabilities.

Usage

av1r_status()

Value

Invisibly returns the active backend string.

Convert all videos in a folder to AV1

Description

Finds all supported video files in input_dir and converts them to AV1. Output files are written to output_dir with the same base name and .mp4 extension.

Usage

convert_folder(
  input_dir,
  output_dir = input_dir,
  options = av1r_options(),
  ext = c("mp4", "avi", "mkv", "mov", "flv", "mpg", "mpeg", "webm", "tif", "tiff"),
  skip_existing = TRUE,
  recursive = FALSE,
  max_depth = 5L
)

Arguments

Details

When a folder contains only single-page TIFF images (e.g. a microscopy image sequence), they are automatically combined into a single video named after the input folder.

When recursive = TRUE, subfolders (up to max_depth levels) are scanned. Each subfolder containing only TIFF images is combined into a single video named after the subfolder. Subfolders with video files are processed file-by-file. All output is written flat into output_dir, with subfolder names used as prefixes to avoid collisions.

Value

Invisibly returns a data.frame with columns input, output, input_size (bytes), status ("ok", "skipped", or "error"), and message.

Examples

## Not run: 
# Requires FFmpeg installed
convert_folder("~/data/microscopy", file.path(tempdir(), "av1_output"))

# Recursive: each subfolder with TIFFs becomes a separate video
convert_folder("~/data/plates", "~/av1_output", recursive = TRUE)

## End(Not run)

Convert video to AV1

Description

Converts biological microscopy video files (MP4/H.264, H.265, AVI/MJPEG) or TIFF stacks to AV1 format. Automatically selects the best available backend: Vulkan GPU (VK_KHR_VIDEO_ENCODE_AV1) when a compatible device is found, otherwise CPU via FFmpeg (libsvtav1).

Usage

convert_to_av1(input, output, options = av1r_options())

Arguments

Value

Invisibly returns 0L on success. Stops with an error on failure.

Examples

# List available options
str(av1r_options())

## Not run: 
# Requires FFmpeg installed
convert_to_av1("recording.mp4", file.path(tempdir(), "recording_av1.mp4"))

## End(Not run)

Detect best available encoding backend

Description

Priority order: "vaapi" (VAAPI AV1 GPU via ffmpeg, best speed/quality ratio) > "vulkan" (Vulkan AV1 GPU, fastest but CQP only) > "cpu" (SVT-AV1 via ffmpeg).

Usage

detect_backend(prefer = "auto")

Arguments

Value

Character string: "vaapi", "vulkan", or "cpu".

Measure SSIM quality score between two video files

Description

Compares encoded video against the original using SSIM. Values close to 1.0 indicate high similarity.

Usage

measure_ssim(original, encoded, duration = NULL)

Arguments

Value

Numeric SSIM score (0-1), or NA on failure.

Read a TIFF stack and return basic metadata

Description

Does not load pixel data into R – only inspects the file. Useful for checking frame count and dimensions before encoding.

Usage

read_tiff_stack(path)

Arguments

Value

A list with elements: path, n_frames, width, height, size_mb.

Examples

# Create a small temporary TIFF and inspect it
tmp <- tempfile(fileext = ".tif")
writeBin(raw(1024), tmp)
info <- read_tiff_stack(tmp)
str(info)
unlink(tmp)

Check Vulkan AV1 availability

Description

Check Vulkan AV1 availability

Usage

vulkan_available()

Value

TRUE if the package was compiled with Vulkan AV1 encode support.

List Vulkan-capable GPU devices

Description

List Vulkan-capable GPU devices

Usage

vulkan_devices()

Value

Character vector of device names. Devices supporting VK_KHR_VIDEO_ENCODE_AV1 are marked with [AV1].