openTSNE

openTSNE is a modular Python implementation of t-Distributed Stochasitc Neighbor Embedding (t-SNE) [1], a popular dimensionality-reduction algorithm for visualizing high-dimensional data sets. openTSNE incorporates the latest improvements to the t-SNE algorithm, including the ability to add new data points to existing embeddings [2], massive speed improvements [3] [4] [5], enabling t-SNE to scale to millions of data points and various tricks to improve global alignment of the resulting visualizations [6].

Macosko 2015 mouse retina t-SNE embedding — A visualization of 44,808 single cell transcriptomes obtained from the mouse retina [7] embedded using the multiscale kernel trick to better preserve the global aligment of the clusters.

Documentation
User Guide and Tutorial
Examples: basic, advanced, preserving global alignment, embedding large data sets
Speed benchmarks

Installation

openTSNE can be installed on all supported versions of Python.

Conda

openTSNE can be easily installed from conda-forge with

conda install --channel conda-forge opentsne

Conda package

PyPi

openTSNE is also available through pip and can be installed with

pip install opentsne

PyPi package

Installing from source

If you wish to install openTSNE from source, please run

pip install .

in the root directory to install the appropriate dependencies and compile the necessary binary files.

Please note that openTSNE requires a C/C++ compiler to be available on the system.

In order for openTSNE to utilize multiple threads, the C/C++ compiler must support OpenMP. In practice, almost all compilers implement this with the exception of older version of clang on OSX systems.

To squeeze the most out of openTSNE, you may also consider installing FFTW3 prior to installation. FFTW3 implements the Fast Fourier Transform, which is heavily used in openTSNE. If FFTW3 is not available, openTSNE will use numpy’s implementation of the FFT, which is slightly slower than FFTW. The difference is only noticeable with large data sets containing millions of data points.

A hello world example

Getting started with openTSNE is very simple. First, we’ll load up some data using scikit-learn

from sklearn import datasets

iris = datasets.load_iris()
x, y = iris["data"], iris["target"]

then, we’ll import and run

from openTSNE import TSNE

embedding = TSNE().fit(x)

Citation

If you make use of openTSNE for your work we would appreciate it if you would cite the paper

@article{Policar2024,
    title={openTSNE: A Modular Python Library for t-SNE Dimensionality Reduction and Embedding},
    author={Poli{\v c}ar, Pavlin G. and Stra{\v z}ar, Martin and Zupan, Bla{\v z}},
    journal={Journal of Statistical Software},
    year={2024},
    volume={109},
    number={3},
    pages={1–30},
    doi={10.18637/jss.v109.i03},
    url={https://www.jstatsoft.org/index.php/jss/article/view/v109i03}
}

openTSNE implements two efficient algorithms for t-SNE. Please consider citing the original authors of the algorithm that you use. If you use FIt-SNE (default), then the citation is [5] below, but if you use Barnes-Hut the citations are [3] and [4].

References

Release files for openTSNE 1.0.4

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for openTSNE 1.0.4
File	Size	Uploaded
opentsne-1.0.4.tar.gz	252.5 kB	Oct 27, 2025	Details

Built distributions (wheels)

Table of built distributions (wheels) for openTSNE 1.0.4
File	Interpreter	ABI	Platform	Reset
opentsne-1.0.4-cp314-cp314-win_amd64.whl 448.7 kB Oct 27, 2025	CPython 3.14	CPython 3.14	Windows x86-64	Details
opentsne-1.0.4-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 3.4 MB Oct 27, 2025	CPython 3.14	CPython 3.14	Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64	Details
opentsne-1.0.4-cp314-cp314-macosx_10_15_universal2.whl 976.1 kB Oct 27, 2025	CPython 3.14	CPython 3.14	macOS 10.15+ universal2 (ARM64, x86-64)	Details
opentsne-1.0.4-cp313-cp313-win_amd64.whl 437.5 kB Oct 27, 2025	CPython 3.13	CPython 3.13	Windows x86-64	Details
opentsne-1.0.4-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 3.5 MB Oct 27, 2025	CPython 3.13	CPython 3.13	Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64	Details
opentsne-1.0.4-cp313-cp313-macosx_10_13_universal2.whl 974.3 kB Oct 27, 2025	CPython 3.13	CPython 3.13	macOS 10.13+ universal2 (ARM64, x86-64)	Details
opentsne-1.0.4-cp312-cp312-win_amd64.whl 438.3 kB Oct 27, 2025	CPython 3.12	CPython 3.12	Windows x86-64	Details
opentsne-1.0.4-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 3.5 MB Oct 27, 2025	CPython 3.12	CPython 3.12	Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64	Details
opentsne-1.0.4-cp312-cp312-macosx_10_13_universal2.whl 982.3 kB Oct 27, 2025	CPython 3.12	CPython 3.12	macOS 10.13+ universal2 (ARM64, x86-64)	Details
opentsne-1.0.4-cp311-cp311-win_amd64.whl 437.8 kB Oct 27, 2025	CPython 3.11	CPython 3.11	Windows x86-64	Details
opentsne-1.0.4-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 3.5 MB Oct 27, 2025	CPython 3.11	CPython 3.11	Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64	Details
opentsne-1.0.4-cp311-cp311-macosx_10_12_universal2.whl 977.2 kB Oct 27, 2025	CPython 3.11	CPython 3.11	macOS 10.12+ universal2 (ARM64, x86-64)	Details
opentsne-1.0.4-cp310-cp310-win_amd64.whl 438.8 kB Oct 27, 2025	CPython 3.10	CPython 3.10	Windows x86-64	Details
opentsne-1.0.4-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 3.3 MB Oct 27, 2025	CPython 3.10	CPython 3.10	Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64	Details
opentsne-1.0.4-cp310-cp310-macosx_10_12_universal2.whl 977.7 kB Oct 27, 2025	CPython 3.10	CPython 3.10	macOS 10.12+ universal2 (ARM64, x86-64)	Details

Total release size: 24.5 MB

Release files / opentsne-1.0.4.tar.gz

Download URL	opentsne-1.0.4.tar.gz
Size	252.5 kB
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Release files / opentsne-1.0.4-cp314-cp314-win_amd64.whl

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Size	448.7 kB
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Download URL	opentsne-1.0.4-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
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Release files / opentsne-1.0.4-cp314-cp314-macosx_10_15_universal2.whl

Download URL	opentsne-1.0.4-cp314-cp314-macosx_10_15_universal2.whl
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Download URL	opentsne-1.0.4-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
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Release files / opentsne-1.0.4-cp313-cp313-macosx_10_13_universal2.whl

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Release files / opentsne-1.0.4-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl

Download URL	opentsne-1.0.4-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
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Release files / opentsne-1.0.4-cp312-cp312-macosx_10_13_universal2.whl

Download URL	opentsne-1.0.4-cp312-cp312-macosx_10_13_universal2.whl
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Release files / opentsne-1.0.4-cp311-cp311-win_amd64.whl

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Release history Release notifications | RSS feed

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openTSNE 1.0.4