Library

D.LAB Public Library

DECTRIS D.LAB · Public library

Everything here is ready to run.

The public library is a shared catalogue of scientific software environments and job templates, maintained by DECTRIS application scientists and by the D.LAB community. Nothing needs installing, compiling or version-matching — pick one, point it at your data, choose a node, and go. Every environment can be cloned and extended; every template can be adapted into a workflow of your own.

54Software environments

35Job templates

6Technique families

0Installation steps

Environments are containerised, versioned software stacks. Launch one as an interactive session, or use it as the basis for a job. Older versions stay available, so past work reruns unchanged.

Job templates are parameterised, ready-to-run workflows. Each is bound to a specific environment version, so a template you run today gives the same result a year from now.

cryo-EM & cryo-ET

13 environments · 8 job templates

Single-particle analysis, tomogram alignment, subtomogram averaging and membrane segmentation. The GPU-heavy stacks are already compiled and CUDA-matched.

Environments

AreTomo3

Fabian Eisenstein

cryo-ETOpen source

Base image: ubuntu:24.04

CCP-EM Doppio

Fabian Eisenstein

cryo-EMOpen source

Base image: ubuntu:24.04

cisTEM

Fabian Eisenstein

cryo-EMOpen source

Base image: ubuntu:24.04

CryoSPARC

Fabian Eisenstein

cryo-EMSPA

Base image: ubuntu:24.04

CryoSPARC Tutorial

Fabian Eisenstein

cryo-EMSPATutorial

Base image: ubuntu:24.04

IMOD

Fabian Eisenstein

cryo-ETOpen source

Base image: ubuntu:24.04

MemBrain

Fabian Eisenstein

cryo-ETSegmentationOpen source

Base image: ubuntu:24.04

MotionCor3

Fabian Eisenstein

cryo-EMOpen source

Base image: ubuntu:24.04

RELION-5.0

Fabian Eisenstein

cryo-EMSPAOpen source

Base image: ubuntu:24.04

RELION-5.0 --tomo

Fabian Eisenstein

cryo-ETSTAOpen source

Base image: ubuntu:24.04

Scipion 3

Fabian Eisenstein

cryo-EMcryo-ETOpen source

Base image: ubuntu:24.04

WarpM + RELION-4 + IMOD

Fabian Eisenstein

cryo-ETSTAOpen source

Base image: ubuntu:24.04

WarpM + RELION-5 + IMOD

Fabian Eisenstein

cryo-ETSTAOpen source

Base image: ubuntu:24.04

Job templates

AreTomo3

Fabian Eisenstein

cryo-ETTomogram alignment

Environment: AreTomo3 v0

Calculate Gain Reference

Fabian Eisenstein

cryo-EMPreprocessing

Environment: RELION-5.0 v3

CryoSPARC — Preprocessing

Fabian Eisenstein

cryo-EMSPA

Environment: CryoSPARC v5

CryoSPARC — Workflow with Reference

Fabian Eisenstein

cryo-EMSPA

Environment: CryoSPARC v5

MemBrain Segmentation

Fabian Eisenstein

cryo-ETSegmentationGPU

Environment: MemBrain v2

ModelAngelo

Fabian Eisenstein

cryo-EMModel buildingGPU

Environment: RELION-5.0 v0

ModelAngelo with Sequence

Fabian Eisenstein

cryo-EMModel buildingGPU

Environment: RELION-5.0 v2

RELION — Preprocessing

Fabian Eisenstein

cryo-EMPreprocessing

Environment: CCP-EM Doppio v1

Crystallography

11 environments · 14 job templates

Macromolecular, serial and small-molecule crystallography — indexing, integration, phasing, refinement and model building, in both GUI and command-line form.

Environments

CCP4 Workshop — AsCA 2025

Ludmila Leroy

MXWorkshop

Base image: ubuntu:24.04

CCP4 & XDS & PyMOL — command line

Camilla Larsen

Base image: ubuntu:24.04

CCP4 & XDS & PyMOL — GUI

Ludmila Leroy

Base image: ubuntu:24.04

CrystFEL

Thomas White

v10

Serial crystallographyOpen source

Base image: ubuntu:24.04

crystfel-sx

Camilla Larsen

SXOpen source

Base image: ubuntu:22.04

DIALS

Camilla Larsen

MXOpen source

Base image: ubuntu:24.04

Fast DP — fast processing with XDS

Camilla Larsen

MXOpen source

Base image: ubuntu:24.04

Olex2

Fabian Eisenstein

v10

Small moleculeOpen source

Base image: ubuntu:22.04

Olex2 & DIALS

Oliver Harder

Small moleculeOpen source

Base image: ubuntu:24.04

WS ED

Oliver Harder

MXOpen source

Base image: ubuntu:24.04

XDS

Camilla Larsen

MXOpen source

Base image: ubuntu:24.04

Job templates

Coot script example

Camilla Larsen

MXModel building

Environment: CCP4 & XDS & PyMOL GUI v9

CrystFEL indexamajig

Camilla Larsen

Serial crystallographyIndexing

Environment: crystfel-sx v4

CrystFEL list_events

Camilla Larsen

Serial crystallography

Environment: crystfel-sx v4

DIALS example job

Camilla Larsen

MXIntegration

Environment: DIALS v1

DIALS Macro Molecule Tutorial

Ludmila Leroy

MXTutorial

Environment: DIALS v1

DIALS Small Molecule Tutorial

Ludmila Leroy

Small moleculeTutorial

Environment: DIALS v1

Fast DP job

Camilla Larsen

MXAutomated processing

Environment: Fast DP v1

Molecular Replacement MOLREP

Ludmila Leroy

MXPhasing

Environment: CCP4 & XDS & PyMOL CLI v3

PRETTY XDS

Ludmila Leroy

MXReporting

Environment: XDS v1

REFMAC5 example job

Camilla Larsen

MXRefinement

Environment: CCP4 & XDS & PyMOL CLI v5

Sequential MOLREP

Camilla Larsen

MXPhasingBatch

Environment: CCP4 & XDS & PyMOL CLI v5

Simple XDS_PAR

Camilla Larsen

MXIntegration

Environment: XDS v9

xds_par & generate_XDS.INP

Camilla Larsen

MXIntegration

Environment: XDS v9

xia2 example job

Camilla Larsen

MXAutomated processing

Environment: CCP4 & XDS & PyMOL CLI v5

Diffraction & 4D-STEM

6 environments · 3 job templates

Scanning diffraction, electron crystallography and powder XRD, including the DECTRIS 4D-STEM reconstruction stack.

Environments

4D-STEM DECTRIS

Ludmila Leroy

v11

4D-STEM

Base image: ubuntu:22.04

4D-STEM Python

Ludmila Leroy

4D-STEMOpen source

Base image: Python 3.10

DIOPTAS

Max Burian

XRD

Base image: ubuntu:22.04

GSAS-II

Camilla Larsen

XRDOpen source

Base image: ubuntu:24.04

Jana2020

Oliver Harder

Electron crystallographyOpen source

Base image: ubuntu:24.04

Novena (Wine)

Oliver Harder

4D-STEMOpen source

Base image: rockylinux:9

Job templates

4D-STEM reconstruction (CoM corrected)

Ludmila Leroy

4D-STEMReconstruction

Environment: 4D-STEM DECTRIS v11

4D-STEM Single Sideband Reconstruction

Oliver Harder

4D-STEMReconstruction

Environment: 4D-STEM DECTRIS v11

GSAS-II batch refinement battery

Camilla Larsen

XRDRietveld

Environment: GSAS-II v1

Imaging & visualization

6 environments · 1 job templates

Computed tomography, image analysis, 3D rendering and scientific visualization.

Environments

Blender + MolecularNodes

Fabian Eisenstein

VisualizationOpen source

Base image: ubuntu:24.04

Fiji (ImageJ)

Camilla Larsen

Image analysisOpen source

Base image: ubuntu:22.04

nDTomo

Camilla Larsen

CTOpen source

Base image: ubuntu:22.04

nDTomo Jupyter

Camilla Larsen

CTJupyterOpen source

Base image: Python 3.11

ParaView

Camilla Larsen

VisualizationOpen source

Base image: ubuntu:24.04

Tomviz

Camilla Larsen

CTVisualizationOpen source

Base image: ubuntu:24.04

Job templates

Render Molecule

Fabian Eisenstein

VisualizationRendering

Environment: Blender + MolecularNodes v2

Coherent imaging

3 environments · 1 job templates

Ptychography and Bragg coherent diffractive imaging, including the environments used for community workshops.

Environments

Cohere4.5

Ross Harder

BCDIOpen source

Base image: Python 3.13

coherence_ptycho_workshop

Steven Henke

PtychographyWorkshop

Base image: ubuntu:24.04

ptycho-workshop

Ming Du

PtychographyWorkshop

Base image: ubuntu:24.04

Job templates

Ptycho simulate

Camilla Larsen

PtychographySimulation

Environment: Python Basics Ubuntu v3

Computing & general

15 environments · 8 job templates

Base images, desktops, Python and Jupyter stacks, GPU runtimes, data transfer and quantum-chemistry tooling — the starting points for your own environments.

Environments

CUDA-12.8

Fabian Eisenstein

GPUOpen source

Base image: ubuntu:24.04

environment-modules

Sagar Khavnekar

GeneralOpen source

Base image: rockylinux:9

Formosa Challenge Environment

Ludmila Leroy

GeneralOpen source

Base image: ubuntu:24.04

Globus Data Transfer

Fabian Eisenstein

Data transferOpen source

Base image: ubuntu:24.04

GNU Octave

Tom Stoops

Data analysisOpen source

Base image: ubuntu:22.04

orca-setup

Community

DFTOpen source

Base image: ubuntu:24.04

Python Basics

Ludmila Leroy

GeneralOpen source

Base image: Python 3.10

Python Basics Ubuntu

Camilla Larsen

GeneralOpen source

Base image: ubuntu:24.04

Python Ubuntu Template

Fabian Eisenstein

GeneralOpen source

Base image: ubuntu:24.04

Rocky Linux 9 Desktop

Daphne van Dijken

Desktop

Base image: rockylinux:9

rockylinux_modules

Sagar Khavnekar

cryo-ETOpen source

Base image: rockylinux:9

Ubuntu 22 Desktop

Daphne van Dijken

Desktop

Base image: ubuntu:22.04

Ubuntu 22 + WineHQ

Ludmila Leroy

DesktopWindows apps

Base image: ubuntu:22.04

Ubuntu 24.04 Utilities

Fabian Eisenstein

UtilitiesOpen source

Base image: ubuntu:24.04

Ubuntu 24 Desktop

Pascal Störzbach

Desktop

Base image: ubuntu:24.04

Job templates

1D Data Fitting

Camilla Larsen

FittingPython

Environment: Python Basics Ubuntu v3

Double Moons — ML example

Ludmila Leroy

Machine learningTutorial

Environment: Python Basics Ubuntu v2

EMPIAR Download

Fabian Eisenstein

Data transfer

Environment: Ubuntu 24.04 Utilities v2

Formosa CLOUD Challenge

Ludmila Leroy

Challenge

Environment: Formosa Challenge Environment v0

Fourier Fun

Fabian Eisenstein

TeachingPython

Environment: Python Basics Ubuntu v3

Simple python example

Camilla Larsen

PythonGetting started

Environment: Python Basics Ubuntu v0

Ultimate Question

Ludmila Leroy

v19

Getting started

Environment: Ubuntu 22 Desktop v3

Unpack

Fabian Eisenstein

Utilities

Environment: Ubuntu 24.04 Utilities v1

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