libvips is much slower than OpenSlide's DeepZoomGenerator #4580

gracezheng9 · 2025-06-23T19:08:31Z

gracezheng9
Jun 23, 2025

I am running a Mirax wsi that is 137 MB. I ran

time vips dzsave x.mrxs x.dzi --suffix .avif --tile-size 1022 --overlap 1

real    17m51.538s
user    192m44.949s
sys     2m4.679s

and this took 17 minutes to complete, where in comparison using OpenSlide's DeepZoomGenerator with the exact same settings, this only took 2 minutes.

real    2m3.251s
user    19m56.297s
sys     0m38.814s

I tried with a bunch of mrxs and svs slides and had the same result, libvips is always much slower than DeepZoomGenerator... but everywhere I read says that it's supposed to be much faster?

As another example, e.g. the CMU-2.svs (about 372 MB) from OpenSlide's demo: https://openslide.org/demo/

10 minutes using libvips

time vips dzsave tests/test_slides/CMU-2.svs CMU-2.dzi --suffix .avif --tile-size 1022 --overlap 1

real    10m6.539s
user    111m9.601s
sys     0m38.031s

but only 3 minutes with DeepZoom

real    3m21.407s
user    32m3.182s
sys     0m44.734s

I am running in a Debian docker container, on a MacBook Pro, Apple M3 Pro.

Is there something I am missing?

lovell · 2025-06-23T20:10:11Z

lovell
Jun 23, 2025
Maintainer

where in comparison using OpenSlide's DeepZoomGenerator with the exact same settings

Are you able to share the command line options being used? Does DeepZoomGenerator support AVIF tile output? If not, that would explain the timing difference as the AV1 encoding you're using with libvips/libheif will be much, much slower than JPEG or PNG.

5 replies

gracezheng9 Jun 23, 2025
Author

Thanks for the quick response!

My code is basically the same as OpenSlide's example DZI tilling: https://github.com/openslide/openslide-python/blob/main/examples/deepzoom/deepzoom_tile.py#L134

except where they call tile.save, I call it like

tile.save(
      <output>.avif,
      quality=50,
      codec="aom",
      speed=6,
  )

From my understanding this uses libaom to encode the output.

gracezheng9 Jun 23, 2025
Author

I tried encoding with jpg, you are right, libvips is much faster:

time vips dzsave tests/test_slides/CMU-2.svs CMU-2.dzi --suffix .jpg --tile-size 1022 --overlap 1

real    0m13.567s
user    1m2.660s
sys     0m9.730s

whereas DeepZoomGenerator was:

real    1m4.960s
user    5m14.648s
sys     0m35.036s

Is there any way to improve the performance of libvips when using avif encoding? Why is it so much slower than using pillow-avif-plugin with DeepZoomGenerator?

lovell Jun 23, 2025
Maintainer

Thanks, are you using the latest version of both libvips and libheif? If not, you might have run into #2983

It's probably also worth adjusting the effort flag to control CPU time e.g. --suffix .avif[effort=2]

gracezheng9 Jun 25, 2025
Author

Thank you, I built and installed the latest version of openslide, libvips and libheif from source, but am still getting a really long processing time. Is there a way to see the version of libheif that libvips is using to make sure it's using the right version? Is there something else that could be causing this slowdown?

root@3421f2ff59be:/app# 
root@3421f2ff59be:/app# pkg-config vips --modversion
8.17.0
root@3421f2ff59be:/app# pkg-config libheif --modversion
1.19.8
root@3421f2ff59be:/app# pkg-config openslide --modversion
4.0.0
root@3421f2ff59be:/app# vips --vips-config
enable debug: false
enable deprecated: true
enable modules: true
enable C++ binding: true
enable RAD load/save: true
enable Analyze7 load: true
enable PPM load/save: true
enable GIF load: true
FFTs with fftw: false
SIMD support with libhwy or liborc: false
ICC profile support with lcms2: true
deflate compression with zlib: true
text rendering with pangocairo: false
font file support with fontconfig: false
EXIF metadata support with libexif: true
JPEG load/save with libjpeg: true
JXL load/save with libjxl: false (dynamic module: false)
JPEG2000 load/save with libopenjp2: true
PNG load/save with libpng: true
image quantisation with imagequant or quantizr: false
TIFF load/save with libtiff-4: true
image pyramid save with libarchive: true
HEIC/AVIF load/save with libheif: true (dynamic module: true)
WebP load/save with libwebp: true
PDF load with PDFium or Poppler: false (dynamic module: false)
SVG load with librsvg-2.0: true
EXR load with OpenEXR: false
WSI load with openslide: true (dynamic module: true)
Matlab load with Matio: false
NIfTI load/save with libnifti: false
FITS load/save with cfitsio: false
GIF save with cgif: false
Magick load/save with MagickCore: false (dynamic module: false)
root@3421f2ff59be:/app# time vips dzsave CMU-2.svs CMU-2 --suffix .avif --tile-size 1022 --overlap 1

real    9m51.849s
user    73m38.034s
sys     0m19.746s

Setting effort=2 seems to have helped, but this did not increase the file size as I was expecting since compression is not as hard, why is this the case? How does this effort flag compare with the speed flag in pillow?

root@3421f2ff59be:/app# time vips dzsave CMU-2.svs CMU-2-low-effort --suffix .avif[effort=2] --tile-size 1022 --overlap 1

real    1m36.265s
user    9m51.102s
sys     0m11.459s

gracezheng9 Jun 26, 2025
Author

@lovell Hi,

I think that I am running the newest version of both libheif and libvips including the fix, I checked /usr/local/src/vips-8.17.0/build/meson-info/intro-dependencies.json and see this (this is the libheif.so that I built):

{"name": "libheif", "version": "1.19.8", "compile_args": ["-I/usr/local/include"], "link_args": ["/usr/local/lib/libheif.so"]}

but when I run VIPS_INFO=1 vips I see that it is loading from /usr/local/lib/vips-modules-8.17/, is this expected?

root@54eddd13c39f:/usr/local/src/vips-8.17.0/build# VIPS_INFO=1 vips
VIPS-INFO: 20:11:44.977: found /usr/local/lib/vips-modules-8.17
VIPS-INFO: 20:11:44.978: using configure-time prefix
VIPS-INFO: 20:11:44.978: VIPS_PREFIX = /usr/local
VIPS-INFO: 20:11:44.978: VIPS_LIBDIR = /usr/local/lib
VIPS-INFO: 20:11:44.978: prefix = /usr/local
VIPS-INFO: 20:11:44.978: libdir = /usr/local/lib
VIPS-INFO: 20:11:44.981: searching "/usr/local/lib/vips-modules-8.17"
VIPS-INFO: 20:11:44.981: loading "/usr/local/lib/vips-modules-8.17/vips-heif.so"
VIPS-INFO: 20:11:44.983: loading "/usr/local/lib/vips-modules-8.17/vips-openslide.so"
VIPS-INFO: 20:11:44.990: searching "/usr/local/lib/vips-plugins-8.17"
VIPS-INFO: 20:11:44.990: im_load_plugins: searching "/usr/local/lib/vips-8.17"
VIPS-INFO: 20:11:44.990: im_load_plugins: searching "/usr/local/lib"

I'm building this using the Debian bookworm docker image, like so:

RUN apt-get update && apt-get install -y \
    build-essential \
    software-properties-common \
    cmake \
    ninja-build \
    meson \
    pkg-config \
    wget

WORKDIR /usr/local/src
ENV LD_LIBRARY_PATH=/usr/local/lib
ENV PKG_CONFIG_PATH=/usr/local/lib/pkgconfig

# Build OpenSlide from source so that libvips can find it
# needed for DICOM WSI in openslide
ARG DICOM_VERSION=1.2.0
ARG DICOM_URL=https://github.com/ImagingDataCommons/libdicom/releases/download

RUN wget ${DICOM_URL}/v${DICOM_VERSION}/libdicom-${DICOM_VERSION}.tar.xz

RUN tar xJf libdicom-${DICOM_VERSION}.tar.xz \
        && cd libdicom-${DICOM_VERSION} \
        && meson setup --libdir=lib --buildtype=release builddir \
        && meson compile -C builddir \
        && meson install -C builddir

# openslide dependencies
RUN apt-get install -y \
        glib-2.0-dev \
        libcairo2-dev \
        libgdk-pixbuf-2.0-dev \
        libjpeg-dev \
        libopenjp2-7-dev \
        zlib1g-dev \
        libtiff-dev \
        libxml2-dev \
        libpng-dev \
        libsqlite3-dev

ARG OPENSLIDE_VERSION=4.0.0
ARG OPENSLIDE_URL=https://github.com/openslide/openslide/releases/download

RUN wget ${OPENSLIDE_URL}/v${OPENSLIDE_VERSION}/openslide-${OPENSLIDE_VERSION}.tar.xz

RUN tar xJf openslide-${OPENSLIDE_VERSION}.tar.xz \
        && cd openslide-${OPENSLIDE_VERSION} \
        && meson setup --libdir=lib --buildtype=release builddir \
        && meson compile -C builddir \
        && meson install -C builddir


# Build libheif from source to get the latest version (1.19.8)
RUN apt-get install -y \
    libaom-dev \
    libdav1d-dev \
    libde265-dev \
    libgdk-pixbuf2.0-dev \
    libjpeg-dev \
    libpng-dev \
    libx265-dev

ARG HEIF_VERSION=1.19.8
ARG HEIF_URL=https://github.com/strukturag/libheif/releases/download

RUN wget ${HEIF_URL}/v${HEIF_VERSION}/libheif-${HEIF_VERSION}.tar.gz \
    && tar xf libheif-${HEIF_VERSION}.tar.gz \
    && cd libheif-${HEIF_VERSION} \
    && mkdir build \
    && cd build \
    && cmake -DCMAKE_INSTALL_LIBDIR=${LD_LIBRARY_PATH} --preset=release .. \
    && make \
    && make install


# Build libvips from source to get the latest version (8.17.0)
RUN apt-get install -y \
    libglib2.0-dev \
    libexpat1-dev \
    libarchive-dev

ARG VIPS_VERSION=8.17.0
ARG VIPS_URL=https://github.com/libvips/libvips/releases/download

RUN wget ${VIPS_URL}/v${VIPS_VERSION}/vips-${VIPS_VERSION}.tar.xz \
	&& tar xJf vips-${VIPS_VERSION}.tar.xz \
	&& cd vips-${VIPS_VERSION} \
	&& meson setup build --buildtype=release --libdir=lib \
	&& cd build \
	&& meson compile \
        && meson install

What am I missing?

Uh oh!

libvips is much slower than OpenSlide's DeepZoomGenerator #4580

Uh oh!

Uh oh!

gracezheng9 Jun 23, 2025

Replies: 1 comment · 5 replies

Uh oh!

lovell Jun 23, 2025 Maintainer

Uh oh!

gracezheng9 Jun 23, 2025 Author

Uh oh!

gracezheng9 Jun 23, 2025 Author

Uh oh!

lovell Jun 23, 2025 Maintainer

Uh oh!

Uh oh!

gracezheng9 Jun 25, 2025 Author

Uh oh!

Uh oh!

gracezheng9 Jun 26, 2025 Author

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gracezheng9
Jun 23, 2025

Replies: 1 comment 5 replies

lovell
Jun 23, 2025
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gracezheng9 Jun 23, 2025
Author

gracezheng9 Jun 23, 2025
Author

lovell Jun 23, 2025
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gracezheng9 Jun 25, 2025
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gracezheng9 Jun 26, 2025
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