_______ _____ _______  _____         _______
      |______   |   |  |  | |_____] |      |______
      ______| __|__ |  |  | |       |_____ |______  v3b1

SIMPLE

SIMPLE is a high‑performance, end‑to‑end cryo‑EM image processing and reconstruction platform.

It transforms raw electron microscopy data --- movies, micrographs, and particle images --- into scientifically meaningful outputs including:

• 2D class averages
• High-resolution 3D reconstructions
• Symmetry analysis
• Atomic-level structural models

SIMPLE supports interactive batch workflows and fully automated streaming pipelines, scaling seamlessly from single workstations to distributed HPC environments.

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🚀 Release

Stable release (v3.0.0):

https://github.com/hael/SIMPLE/releases/tag/v3.0.0

Public unit tests:

https://zenodo.org/records/18789533

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🧬 Features

• End-to-end cryo‑EM workflow
• Streaming data processing
• HPC scalability
• Modular architecture
• Test-driven development
• Production-ready scientific computing environment

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📦 Installation

System Requirements

• Linux (Ubuntu 16.04+ recommended)
• macOS 10.10+
• CMake ≥ 3.5
• GNU gcc & gfortran ≥ 14.2
• FFTW ≥ 3.3 (double + single + threaded builds)
• libTIFF ≥ 4 (optional, required for motion correction)
• jbigkit ≥ 2 (optional)
• Python ≥ 3.10

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Standard Build

1️⃣ Obtain source

Stable release:

gunzip SIMPLE-3.0.0.tar.gz
tar -xvf SIMPLE-3.0.0.tar
cd SIMPLE-3.0.0

Or clone:

git clone https://github.com/hael/SIMPLE.git
cd SIMPLE

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2️⃣ Build

mkdir build
cd build
cmake ..
make -j install

Disable TIFF support:

cmake -DUSE_LIBTIFF=OFF ..
make -j install

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3️⃣ Environment Setup

For bash:

cat add2.bashrc >> ~/.bashrc

For tcsh/csh:

cat add2.tcshrc >> ~/.tcshrc

Minimal manual setup:

Add to PATH:

<simple_path>/build/bin
<simple_path>/build/scripts

Define:

SIMPLE_PATH=<simple_path>

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⚙ Advanced Configuration

Custom install directory:

cmake -DCMAKE_INSTALL_PREFIX=<install_dir> ..
make -j install

Custom compiler / FFTW paths:

FC=<gfortran_path> CC=<gcc_path> FFTW_DIR=<fftw_path> cmake ..
make -j install

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🔁 Updating

cd ~/SIMPLE
git stash
git stash clear
git pull
cd build
make -j install
source add2.bashrc
nice_local

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📜 License

SIMPLE is distributed under the GNU General Public License v3 (GPLv3) or later.

This software is provided without warranty, including without implied warranty of merchantability or fitness for a particular purpose.

See the GNU General Public License for details.

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🧠 Philosophy

SIMPLE combines:

• High-performance numerical kernels
• Cryo‑EM domain abstractions
• Workflow orchestration
• Engineering discipline

into a scalable scientific application suite built for real experimental workflows.