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cylindra

cylindra is a GUI-integrated cryo-ET image analysis tool for cylindric periodic structures such as microtubules.

→ Documentation

Installation

  • Use pip
pip install cylindra[recommended] -U
  • From source

If you install from the source, you'll need Rust to compile a part of the code.

git clone https://github.com/hanjinliu/cylindra.git
cd cylindra
pip install -e .

Usage

Launch GUI

  • From shell

    cylindra
    
  • From a Python interpreter

    from cylindra import start
    
    # launch a napari viewer with a cylindra dock widget.
    ui = start()
    

Command line interface

cylindra is implemented with some basic command line interface (CLI).

cylindra --help

Implemented Functions

  • Automatic/manual fitting of splines to cylindrical structures in 3D.
  • Analyze lattice structures (such as lattice spacing and skew angle) using Cylindric Fourier transformation.
  • Automatic determination of polarity, protofilament number etc.
  • Monomer mapping along splines for subtomogram averaging and alignment.
  • Microtubule seam search with or without binding proteins.
  • Subtomogram alignment with 2D constraint.
  • Tomogram simulation of cylindric structures.
  • Efficient manual picking along cylindrical structures.

Prerequisite and Recommendations

  • Python ≥ 3.11. This project follows spec-0000.
  • Sufficient memory size. Most of the intense calculations are done out-of-core using dask, so that you can even run on 8-GB memory PC in many cases. However, larger memory size will make parallel processing more efficient. ≥32 GB is recommended.
  • Images should be loaded from SSD. Raw image stacks are loaded lazily in most of the processes. Loading from HDD will slow down many analyses as well. In the latest version, you can use "Cache image on SSD" option to directly analyze tomograms stored in HDD.

Issues

If you encountered any bugs or have any requests, feel free to report an issue. (We'll appreciate if you find some methods are over-fitted to microtubules and do not work well on other cylindric structures)

For better reproducibility, please copy your environments from Others > cylindra info and the recorded macro from Others > Macro > Show macro.

Citation

If you find cylindra useful in your work, please consider citing our paper.

Heterogeneous local structures of the microtubule lattice revealed by cryo-ET and non-averaging analysis
Hanjin Liu, Hiroshi Yamaguchi, Masahide Kikkawa, Tomohiro Shima
bioRxiv 2024.04.30.591984; doi: https://doi.org/10.1101/2024.04.30.591984

Release files for cylindra 1.2.0

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

Source distribution (sdist)

Source distribution for cylindra 1.2.0
File Size Uploaded
cylindra-1.2.0.tar.gz 14.8 MB Details

Built distributions (wheels)

Table of built distributions (wheels) for cylindra 1.2.0
File
cylindra-1.2.0-pp311-pypy311_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ x86-64 Details
cylindra-1.2.0-pp311-pypy311_pp73-manylinux_2_17_s390x.manylinux2014_s390x.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ IBM System/390x Details
cylindra-1.2.0-pp311-pypy311_pp73-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ PowerPC 64-le Details
cylindra-1.2.0-pp311-pypy311_pp73-manylinux_2_17_armv7l.manylinux2014_armv7l.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ ARMv7l Details
cylindra-1.2.0-pp311-pypy311_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ ARM64 Details
cylindra-1.2.0-pp311-pypy311_pp73-manylinux_2_5_i686.manylinux1_i686.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.5+ x86-32 Details
cylindra-1.2.0-cp315-cp315t-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.15 CPython 3.15 free-threading Linux glibc 2.17+ x86-64 Details
cylindra-1.2.0-cp315-cp315t-manylinux_2_5_i686.manylinux1_i686.whl CPython 3.15 CPython 3.15 free-threading Linux glibc 2.5+ x86-32 Details
cylindra-1.2.0-cp315-cp315-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.15 CPython 3.15 Linux glibc 2.17+ x86-64 Details
cylindra-1.2.0-cp315-cp315-manylinux_2_5_i686.manylinux1_i686.whl CPython 3.15 CPython 3.15 Linux glibc 2.5+ x86-32 Details
cylindra-1.2.0-cp314-cp314t-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.14 CPython 3.14 free-threading Linux glibc 2.17+ x86-64 Details
cylindra-1.2.0-cp314-cp314t-manylinux_2_17_s390x.manylinux2014_s390x.whl CPython 3.14 CPython 3.14 free-threading Linux glibc 2.17+ IBM System/390x Details
cylindra-1.2.0-cp314-cp314t-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl CPython 3.14 CPython 3.14 free-threading Linux glibc 2.17+ PowerPC 64-le Details
cylindra-1.2.0-cp314-cp314t-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.14 CPython 3.14 free-threading Linux glibc 2.17+ ARMv7l Details
cylindra-1.2.0-cp314-cp314t-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.14 CPython 3.14 free-threading Linux glibc 2.17+ ARM64 Details
cylindra-1.2.0-cp314-cp314t-manylinux_2_5_i686.manylinux1_i686.whl CPython 3.14 CPython 3.14 free-threading Linux glibc 2.5+ x86-32 Details
cylindra-1.2.0-cp314-cp314-win_amd64.whl CPython 3.14 CPython 3.14 Windows x86-64 Details
cylindra-1.2.0-cp314-cp314-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ x86-64 Details
cylindra-1.2.0-cp314-cp314-manylinux_2_17_s390x.manylinux2014_s390x.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ IBM System/390x Details
cylindra-1.2.0-cp314-cp314-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ PowerPC 64-le Details
cylindra-1.2.0-cp314-cp314-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ ARMv7l Details
cylindra-1.2.0-cp314-cp314-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ ARM64 Details
cylindra-1.2.0-cp314-cp314-manylinux_2_5_i686.manylinux1_i686.whl CPython 3.14 CPython 3.14 Linux glibc 2.5+ x86-32 Details
cylindra-1.2.0-cp314-cp314-macosx_11_0_arm64.whl CPython 3.14 CPython 3.14 macOS 11.0+ ARM64 Details
cylindra-1.2.0-cp314-cp314-macosx_10_12_x86_64.whl CPython 3.14 CPython 3.14 macOS 10.12+ x86-64 Details
cylindra-1.2.0-cp313-cp313-win_amd64.whl CPython 3.13 CPython 3.13 Windows x86-64 Details
cylindra-1.2.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ x86-64 Details
cylindra-1.2.0-cp313-cp313-manylinux_2_17_s390x.manylinux2014_s390x.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ IBM System/390x Details
cylindra-1.2.0-cp313-cp313-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ PowerPC 64-le Details
cylindra-1.2.0-cp313-cp313-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ ARMv7l Details
cylindra-1.2.0-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ ARM64 Details
cylindra-1.2.0-cp313-cp313-manylinux_2_5_i686.manylinux1_i686.whl CPython 3.13 CPython 3.13 Linux glibc 2.5+ x86-32 Details
cylindra-1.2.0-cp313-cp313-macosx_11_0_arm64.whl CPython 3.13 CPython 3.13 macOS 11.0+ ARM64 Details
cylindra-1.2.0-cp313-cp313-macosx_10_12_x86_64.whl CPython 3.13 CPython 3.13 macOS 10.12+ x86-64 Details
cylindra-1.2.0-cp312-cp312-win_amd64.whl CPython 3.12 CPython 3.12 Windows x86-64 Details
cylindra-1.2.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ x86-64 Details
cylindra-1.2.0-cp312-cp312-manylinux_2_17_s390x.manylinux2014_s390x.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ IBM System/390x Details
cylindra-1.2.0-cp312-cp312-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ PowerPC 64-le Details
cylindra-1.2.0-cp312-cp312-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ ARMv7l Details
cylindra-1.2.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ ARM64 Details
cylindra-1.2.0-cp312-cp312-manylinux_2_5_i686.manylinux1_i686.whl CPython 3.12 CPython 3.12 Linux glibc 2.5+ x86-32 Details
cylindra-1.2.0-cp312-cp312-macosx_11_0_arm64.whl CPython 3.12 CPython 3.12 macOS 11.0+ ARM64 Details
cylindra-1.2.0-cp312-cp312-macosx_10_12_x86_64.whl CPython 3.12 CPython 3.12 macOS 10.12+ x86-64 Details
cylindra-1.2.0-cp311-cp311-win_amd64.whl CPython 3.11 CPython 3.11 Windows x86-64 Details
cylindra-1.2.0-cp311-cp311-win32.whl CPython 3.11 CPython 3.11 Windows x86-32 Details
cylindra-1.2.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ x86-64 Details
cylindra-1.2.0-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ IBM System/390x Details
cylindra-1.2.0-cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ PowerPC 64-le Details
cylindra-1.2.0-cp311-cp311-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ ARMv7l Details
cylindra-1.2.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ ARM64 Details
cylindra-1.2.0-cp311-cp311-manylinux_2_5_i686.manylinux1_i686.whl CPython 3.11 CPython 3.11 Linux glibc 2.5+ x86-32 Details
cylindra-1.2.0-cp311-cp311-macosx_11_0_arm64.whl CPython 3.11 CPython 3.11 macOS 11.0+ ARM64 Details
cylindra-1.2.0-cp311-cp311-macosx_10_12_x86_64.whl CPython 3.11 CPython 3.11 macOS 10.12+ x86-64 Details

Total release size: 71.8 MB

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Release files / cylindra-1.2.0-cp313-cp313-win_amd64.whl

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Release files / cylindra-1.2.0-cp312-cp312-win_amd64.whl

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Release files / cylindra-1.2.0-cp312-cp312-manylinux_2_5_i686.manylinux1_i686.whl

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Release files / cylindra-1.2.0-cp312-cp312-macosx_11_0_arm64.whl

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Release files / cylindra-1.2.0-cp312-cp312-macosx_10_12_x86_64.whl

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Release files / cylindra-1.2.0-cp311-cp311-win_amd64.whl

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Release files / cylindra-1.2.0-cp311-cp311-win32.whl

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Release files / cylindra-1.2.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

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Release files / cylindra-1.2.0-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl

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Release files / cylindra-1.2.0-cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl

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Release files / cylindra-1.2.0-cp311-cp311-manylinux_2_17_armv7l.manylinux2014_armv7l.whl

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Release files / cylindra-1.2.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl

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Release files / cylindra-1.2.0-cp311-cp311-manylinux_2_5_i686.manylinux1_i686.whl

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Release files / cylindra-1.2.0-cp311-cp311-macosx_11_0_arm64.whl

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Size 1.0 MB
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Release files / cylindra-1.2.0-cp311-cp311-macosx_10_12_x86_64.whl

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Size 1.0 MB
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