Job Template Index
Explore official DECTRIS workflows and pre-configured templates for common scientific applications.
General Programming & Visualization
Simple python examples, Machine Learning, and 3D rendering.
- 1D Data Fitting: Fit polynomial, exponential, and power curves to 1D data sets.
- Double Moons - ML example: A Job Template that uses Python's sklearn to tackle the classification problem on the Double Moon problem framework.
- Fourier Fun: Generates the Fourier transform of an image and enhances it visually.
- Render Molecule: Use Blender and MolecularNodes to generate a beautiful render of your protein structure!
- Simple Python Example: Example showing how to run your own python script via a bash-styled job template.
Macromolecular Crystallography (MX)
Single-crystal diffraction data processing, phasing, and refinement.
- Coot script example: Use coot to visualize PDB and MTZ files and generate zoomed-in views of the regions with the largest density differences.
- DIALS example job: An example job for running a DIALS processing pipeline.
- Fast DP job: Run fast_dp command for fast data processing with XDS. Generates visual output and monitors resource usage of the node.
- Molecular Replacement MOLREP: Executes molecular replacement utilizing MOLREP. Usage requires one input model from the PDB and a reflection file
- PRETTY XDS: Runs XDS in a dataset from a given XDS.INP file and plots the results of the last CORRECT.LP table.
- Simple XDS_PAR: Run XDS_PAR with a given XDS.INP file. The path to the data can be overwritten with a path from the file browser.
- REFMAC5 example job: Structural refinement with REFMAC5.
- xia2 example job:
Cryo-Electron Microscopy (Cryo-EM)
Biological imaging, single-particle analysis, and tomography.
- AreTomo3: Automatically reconstruct your cryo electron tomograms from raw tilt series movies using AreTomo3 and judge data quality by plotted metrics.
- Calculate Gain Reference: Estimate the gain reference from all movies using RELION's relion_estimate_gain.
- CryoSPARC - Preprocessing: Imports raw movie frames, corrects for beam-induced sample motion, and estimates the CTF.
- CryoSPARC - Workflow with Reference: Automates the main processing steps of cryoEM data using CryoSPARC given a reference from the EMDB. The result will be a 3D map, that can be further refined manually.
- EMPIAR Download: Download a raw EM dataset from EMPIAR. ⚠️ Note: Check hot storage limits.
- MemBrain Segmentation: MemBrain v2 is a deep learning-enabled program aimed at the efficient analysis of membranes in cryo-electron tomography (cryo-ET). It provides automated membrane segmentation using a general pretrained model.
- ModelAngelo with Sequence: ModelAngelo is an automatic atomic model building program for cryoEM maps.
4D-STEM & Materials EM
Scanning Transmission Electron Microscopy for materials science.
- 4D-STEM reconstruction (CoM corr): 4D-STEM reconstruction with Center of Mass correction using py4DSTEM.
- 4D-STEM Single Sideband Reconstruction: Single Sideband (SSB) reconstruction for 4D STEM datasets. More robust to defocus and better for lower doses.
X-ray Diffraction & Coherent Imaging
Powder diffraction and phase retrieval workflows.
- GSAS-II batch refinement battery: Example job showing how to batch process XRD profiles from an XRD-CT scan using GSAS-II.
- Ptycho simulate: A small script for simulating a ptychography dataset.
Utilities & Miscellany
File management tools, event-based challenges, and more
- Unpack: Unpacks file archives.
- Formosa CLOUD Challenge: For the participants of the 2025 AsCA DECTRIS CLOUD workshop.
- Ultimate Question: The answer to Life, the Universe, and Everything.