Skip to main content

Command line interface for digital pathology tools.

Project description

pamly-lib

The pamly-lib originates from the initial pamly project for whole slide image conversion, upload and viewing. The pamly-lib contains the source code for the pamly rust crate which contains the converter tool of pamly as a CLI.

Installing and Compiling Openslide

It builds upon the C-library Openslide in order to convert the main propietary scanner formats to an accessible sqlite database. Thus, follow the installation and compilation instructions for Openslide as the pamly-lib depends on openslide to be properly installed. Mac users can also install via brew.

NOTE: If openslide is not found during cargo install it might be caused by your PATH, e.g. if you brew install on Mac run

export LIBRARY_PATH="/opt/homebrew/lib"

If you've installed and compiled via the git repo, add the path to the .dylib, so something like

export DYLD_LIBRARY_PATH="$HOME/.../openslide/builddir/src"

Installing the Converter Tool

In order to install the pamly CLI, including the converter tool, run

cargo install pamly --features convert

Without the flag --features convert you still get other features of pamly which do not depend on openslide, such as generating the types file (containing diagnoses, stains, labels, ...).

Run the Converter Tool

In order to convert a raw WSI scan into an .sqlite databse run

pamly convert <Slide Path>

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pamly-0.2.5.tar.gz (93.9 kB view hashes)

Uploaded Source

Built Distributions

pamly-0.2.5-pp310-pypy310_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.0 MB view hashes)

Uploaded PyPy manylinux: glibc 2.17+ x86-64

pamly-0.2.5-pp310-pypy310_pp73-manylinux_2_17_s390x.manylinux2014_s390x.whl (1.2 MB view hashes)

Uploaded PyPy manylinux: glibc 2.17+ s390x

pamly-0.2.5-pp310-pypy310_pp73-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl (1.2 MB view hashes)

Uploaded PyPy manylinux: glibc 2.17+ ppc64le

pamly-0.2.5-pp310-pypy310_pp73-manylinux_2_17_armv7l.manylinux2014_armv7l.whl (1.0 MB view hashes)

Uploaded PyPy manylinux: glibc 2.17+ ARMv7l

pamly-0.2.5-pp310-pypy310_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (1.0 MB view hashes)

Uploaded PyPy manylinux: glibc 2.17+ ARM64

pamly-0.2.5-pp310-pypy310_pp73-manylinux_2_5_i686.manylinux1_i686.whl (1.1 MB view hashes)

Uploaded PyPy manylinux: glibc 2.5+ i686

pamly-0.2.5-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.0 MB view hashes)

Uploaded PyPy manylinux: glibc 2.17+ x86-64

pamly-0.2.5-pp39-pypy39_pp73-manylinux_2_17_s390x.manylinux2014_s390x.whl (1.2 MB view hashes)

Uploaded PyPy manylinux: glibc 2.17+ s390x

pamly-0.2.5-pp39-pypy39_pp73-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl (1.2 MB view hashes)

Uploaded PyPy manylinux: glibc 2.17+ ppc64le

pamly-0.2.5-pp39-pypy39_pp73-manylinux_2_17_armv7l.manylinux2014_armv7l.whl (1.0 MB view hashes)

Uploaded PyPy manylinux: glibc 2.17+ ARMv7l

pamly-0.2.5-pp39-pypy39_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (1.0 MB view hashes)

Uploaded PyPy manylinux: glibc 2.17+ ARM64

pamly-0.2.5-pp39-pypy39_pp73-manylinux_2_5_i686.manylinux1_i686.whl (1.1 MB view hashes)

Uploaded PyPy manylinux: glibc 2.5+ i686

pamly-0.2.5-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.0 MB view hashes)

Uploaded PyPy manylinux: glibc 2.17+ x86-64

pamly-0.2.5-pp38-pypy38_pp73-manylinux_2_17_s390x.manylinux2014_s390x.whl (1.2 MB view hashes)

Uploaded PyPy manylinux: glibc 2.17+ s390x

pamly-0.2.5-pp38-pypy38_pp73-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl (1.1 MB view hashes)

Uploaded PyPy manylinux: glibc 2.17+ ppc64le

pamly-0.2.5-pp38-pypy38_pp73-manylinux_2_17_armv7l.manylinux2014_armv7l.whl (1.0 MB view hashes)

Uploaded PyPy manylinux: glibc 2.17+ ARMv7l

pamly-0.2.5-pp38-pypy38_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (1.0 MB view hashes)

Uploaded PyPy manylinux: glibc 2.17+ ARM64

pamly-0.2.5-pp38-pypy38_pp73-manylinux_2_5_i686.manylinux1_i686.whl (1.1 MB view hashes)

Uploaded PyPy manylinux: glibc 2.5+ i686

pamly-0.2.5-cp312-none-win_amd64.whl (144.0 kB view hashes)

Uploaded CPython 3.12 Windows x86-64

pamly-0.2.5-cp312-none-win32.whl (138.2 kB view hashes)

Uploaded CPython 3.12 Windows x86

pamly-0.2.5-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.0 MB view hashes)

Uploaded CPython 3.12 manylinux: glibc 2.17+ x86-64

pamly-0.2.5-cp312-cp312-manylinux_2_17_s390x.manylinux2014_s390x.whl (1.2 MB view hashes)

Uploaded CPython 3.12 manylinux: glibc 2.17+ s390x

pamly-0.2.5-cp312-cp312-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl (1.2 MB view hashes)

Uploaded CPython 3.12 manylinux: glibc 2.17+ ppc64le

pamly-0.2.5-cp312-cp312-manylinux_2_17_armv7l.manylinux2014_armv7l.whl (1.0 MB view hashes)

Uploaded CPython 3.12 manylinux: glibc 2.17+ ARMv7l

pamly-0.2.5-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (1.0 MB view hashes)

Uploaded CPython 3.12 manylinux: glibc 2.17+ ARM64

pamly-0.2.5-cp312-cp312-manylinux_2_5_i686.manylinux1_i686.whl (1.1 MB view hashes)

Uploaded CPython 3.12 manylinux: glibc 2.5+ i686

pamly-0.2.5-cp312-cp312-macosx_11_0_arm64.whl (260.6 kB view hashes)

Uploaded CPython 3.12 macOS 11.0+ ARM64

pamly-0.2.5-cp312-cp312-macosx_10_12_x86_64.whl (265.3 kB view hashes)

Uploaded CPython 3.12 macOS 10.12+ x86-64

pamly-0.2.5-cp311-none-win_amd64.whl (146.2 kB view hashes)

Uploaded CPython 3.11 Windows x86-64

pamly-0.2.5-cp311-none-win32.whl (140.0 kB view hashes)

Uploaded CPython 3.11 Windows x86

pamly-0.2.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.0 MB view hashes)

Uploaded CPython 3.11 manylinux: glibc 2.17+ x86-64

pamly-0.2.5-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl (1.2 MB view hashes)

Uploaded CPython 3.11 manylinux: glibc 2.17+ s390x

pamly-0.2.5-cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl (1.1 MB view hashes)

Uploaded CPython 3.11 manylinux: glibc 2.17+ ppc64le

pamly-0.2.5-cp311-cp311-manylinux_2_17_armv7l.manylinux2014_armv7l.whl (1.0 MB view hashes)

Uploaded CPython 3.11 manylinux: glibc 2.17+ ARMv7l

pamly-0.2.5-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (1.0 MB view hashes)

Uploaded CPython 3.11 manylinux: glibc 2.17+ ARM64

pamly-0.2.5-cp311-cp311-manylinux_2_5_i686.manylinux1_i686.whl (1.1 MB view hashes)

Uploaded CPython 3.11 manylinux: glibc 2.5+ i686

pamly-0.2.5-cp311-cp311-macosx_11_0_arm64.whl (264.1 kB view hashes)

Uploaded CPython 3.11 macOS 11.0+ ARM64

pamly-0.2.5-cp311-cp311-macosx_10_12_x86_64.whl (269.2 kB view hashes)

Uploaded CPython 3.11 macOS 10.12+ x86-64

pamly-0.2.5-cp310-none-win_amd64.whl (146.2 kB view hashes)

Uploaded CPython 3.10 Windows x86-64

pamly-0.2.5-cp310-none-win32.whl (140.0 kB view hashes)

Uploaded CPython 3.10 Windows x86

pamly-0.2.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.0 MB view hashes)

Uploaded CPython 3.10 manylinux: glibc 2.17+ x86-64

pamly-0.2.5-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl (1.2 MB view hashes)

Uploaded CPython 3.10 manylinux: glibc 2.17+ s390x

pamly-0.2.5-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl (1.1 MB view hashes)

Uploaded CPython 3.10 manylinux: glibc 2.17+ ppc64le

pamly-0.2.5-cp310-cp310-manylinux_2_17_armv7l.manylinux2014_armv7l.whl (1.0 MB view hashes)

Uploaded CPython 3.10 manylinux: glibc 2.17+ ARMv7l

pamly-0.2.5-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (1.0 MB view hashes)

Uploaded CPython 3.10 manylinux: glibc 2.17+ ARM64

pamly-0.2.5-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.whl (1.1 MB view hashes)

Uploaded CPython 3.10 manylinux: glibc 2.5+ i686

pamly-0.2.5-cp310-cp310-macosx_11_0_arm64.whl (264.1 kB view hashes)

Uploaded CPython 3.10 macOS 11.0+ ARM64

pamly-0.2.5-cp310-cp310-macosx_10_12_x86_64.whl (269.2 kB view hashes)

Uploaded CPython 3.10 macOS 10.12+ x86-64

pamly-0.2.5-cp39-none-win_amd64.whl (146.5 kB view hashes)

Uploaded CPython 3.9 Windows x86-64

pamly-0.2.5-cp39-none-win32.whl (140.2 kB view hashes)

Uploaded CPython 3.9 Windows x86

pamly-0.2.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.0 MB view hashes)

Uploaded CPython 3.9 manylinux: glibc 2.17+ x86-64

pamly-0.2.5-cp39-cp39-manylinux_2_17_s390x.manylinux2014_s390x.whl (1.2 MB view hashes)

Uploaded CPython 3.9 manylinux: glibc 2.17+ s390x

pamly-0.2.5-cp39-cp39-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl (1.1 MB view hashes)

Uploaded CPython 3.9 manylinux: glibc 2.17+ ppc64le

pamly-0.2.5-cp39-cp39-manylinux_2_17_armv7l.manylinux2014_armv7l.whl (1.0 MB view hashes)

Uploaded CPython 3.9 manylinux: glibc 2.17+ ARMv7l

pamly-0.2.5-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (1.0 MB view hashes)

Uploaded CPython 3.9 manylinux: glibc 2.17+ ARM64

pamly-0.2.5-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.whl (1.1 MB view hashes)

Uploaded CPython 3.9 manylinux: glibc 2.5+ i686

pamly-0.2.5-cp38-none-win_amd64.whl (146.5 kB view hashes)

Uploaded CPython 3.8 Windows x86-64

pamly-0.2.5-cp38-none-win32.whl (140.1 kB view hashes)

Uploaded CPython 3.8 Windows x86

pamly-0.2.5-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.0 MB view hashes)

Uploaded CPython 3.8 manylinux: glibc 2.17+ x86-64

pamly-0.2.5-cp38-cp38-manylinux_2_17_s390x.manylinux2014_s390x.whl (1.2 MB view hashes)

Uploaded CPython 3.8 manylinux: glibc 2.17+ s390x

pamly-0.2.5-cp38-cp38-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl (1.2 MB view hashes)

Uploaded CPython 3.8 manylinux: glibc 2.17+ ppc64le

pamly-0.2.5-cp38-cp38-manylinux_2_17_armv7l.manylinux2014_armv7l.whl (1.0 MB view hashes)

Uploaded CPython 3.8 manylinux: glibc 2.17+ ARMv7l

pamly-0.2.5-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (1.0 MB view hashes)

Uploaded CPython 3.8 manylinux: glibc 2.17+ ARM64

pamly-0.2.5-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.whl (1.1 MB view hashes)

Uploaded CPython 3.8 manylinux: glibc 2.5+ i686

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page