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Type: Package
Title: 'AV1' Video Encoding for Biological Microscopy Data
Version: 0.1.2
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' (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'. Audio tracks are preserved automatically. Provides a simple R API for batch conversion of entire experiment folders.
Depends: R (≥ 4.1.0)
License: MIT + file LICENSE
URL: https://github.com/Zabis13/AV1R
BugReports: https://github.com/Zabis13/AV1R/issues
Encoding: UTF-8
SystemRequirements: C++17, GNU make, FFmpeg (>= 4.4) with libavcodec/libavformat, libvulkan-dev (optional, for GPU encoding on Linux), Vulkan SDK (optional, for GPU encoding on Windows)
Suggests: magick, testthat (≥ 3.0.0)
RoxygenNote: 7.3.3
Config/testthat/edition: 3
NeedsCompilation: yes
Packaged: 2026-02-28 21:42:21 UTC; yuri
Author: Yuri Baramykov [aut, cre]
Maintainer: Yuri Baramykov <lbsbmsu@mail.ru>
Repository: CRAN
Date/Publication: 2026-03-05 10:40:18 UTC

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' (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'. 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:

AV1R encoding options

Description

AV1R encoding options

Usage

av1r_options(
  crf = 28L,
  preset = 8L,
  threads = 0L,
  bitrate = NULL,
  backend = "auto"
)

Arguments

crf

Constant Rate Factor: 0 (lossless) to 63 (worst). Default 28. Lower = better quality, larger file. Used as fallback when bitrate is NULL and input bitrate cannot be detected.

preset

Encoding speed preset: 0 (slowest/best) to 13 (fastest). Default 8 (good balance for microscopy batch jobs).

threads

Number of CPU threads. 0 = auto-detect.

bitrate

Target video bitrate in kbps (e.g. 3000 for 3 Mbps). NULL (default) = auto-detect from input (55% of source bitrate for VAAPI, CRF for CPU).

backend

"auto" (best GPU if available, else CPU), "vulkan" (Vulkan AV1), "vaapi" (VAAPI AV1, AMD/Intel), or "cpu".

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", "tif", "tiff"),
  skip_existing = TRUE
)

Arguments

input_dir

Path to folder with input files.

output_dir

Path to folder for output files. Created if it does not exist. Defaults to input_dir.

options

An av1r_options list. Defaults to av1r_options().

ext

Character vector of input extensions to process. Default: c("mp4","avi","mkv","mov","tif","tiff").

skip_existing

If TRUE (default), skip files where the output already exists.

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.

Value

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

Examples

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

## 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 or libaom-av1).

Usage

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

Arguments

input

Path to input file. Supported: .mp4, .avi, .mkv, .mov, .tif/.tiff (multi-page), or printf pattern like "frame%04d.tif".

output

Path to output file (.mp4 or .mkv).

options

An av1r_options list. Defaults to av1r_options(). Use backend = "cpu" or backend = "vulkan" to force a backend.

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: "vulkan" (Vulkan AV1 GPU) > "vaapi" (VAAPI AV1 GPU via ffmpeg, AMD/Intel) > "cpu" (libsvtav1/libaom-av1 via ffmpeg).

Usage

detect_backend(prefer = "auto")

Arguments

prefer

"auto" (default), "vulkan", "vaapi", or "cpu".

Value

Character string: "vulkan", "vaapi", 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

original

Path to original video file.

encoded

Path to encoded video file.

duration

Seconds to compare. NULL = full video.

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

path

Path to a multi-page TIFF file or printf-pattern (e.g. "frame%04d.tif").

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].

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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