Focus 1.1

Focus 1.0 was the first version released for the users and is in beta stage. The current minor release version is 1.1.0.

Introductory and Tutorial Movies

A number of movies is available that demonstrate installation, setup, and running FOCUS. The full playlist can be found at https://www.youtube.com/watch?v=mYsz33A5tmM&list=PLteVxMX-rlQspNczCoWrLyamWHgrhTMGv

Movie 1: Required hardware, download of FOCUS: https://youtu.be/mYsz33A5tmM

Movie 2: Compilation of FOCUS: https://youtu.be/zGIyn84taIE

Movie 3: Manual processing of one movie in FOCUS: https://youtu.be/_YDTIAYbgZ8

Movie 4: Batch processing of several movies in FOCUS: https://youtu.be/MTIXFTUZjts

Movie 5: Further batch processing in FOCUS: https://youtu.be/r8nteKYxxXg

Movie 6: Pruning the library of TRASH images in FOCUS: https://youtu.be/r8nteKYxxXg

Movie 7: Exporting all movies for external further processing: https://youtu.be/Yl5ltFtOALc


Movie 8: 2D crystal images (TIFF and MRC files, not movies) are imported into FOCUS, and processed: https://youtu.be/zITHQT1OCUA

Hardware recommendations

FOCUS requires C++, gfortran, Qt, tcsh and Python. It uses several third-party programs in the background. Several of these don't run under Microsoft Windows. For these reasons, FOCUS only works on LINUX or OS X machines. If you plan to use MotionCor2 or gCTF or other NVIDIA-GPU-enabled programs in the background, then you have to stay with LINUX, since Apple doesn't support NVIDIA GPUs unfortunately. However, if you plan to work with 2D crystals or only third-party programs that don't require NVIDIA GPUs, then OS X is also a suitable platform, provided you have at least 8 GB RAM.

==== For a LINUX installation, we recommend UBUNTU and the following hardware: ====

For all configurations, we recommend a large 4k monitor. This can on the UBUNTU machines be directly connected to one of the GPUs.

For online-processing per hour of up to 120 movies of 8k x 8k x 50 frames with MotionCor2, CTFFIND4 or gCTF and subsequent programs:

  • 2×14-core CPU (hyperthreading disabled)
  • >50 TB HD
  • 768 GB RAM (of which 384 GB mounted as RAM disk, used as FASTDISK)
  • at least 4x NVIDIA Titan Xp GPU
  • 10 Gb Ethernet

For online-processing per hour of up to 60 movies of 4k x 4k x 40 frames with MotionCor2, gCTF and subsequent programs:

  • 2×12-core CPU (hyperthreading disabled)
  • >50 TB HD
  • 256 GB RAM
  • 1 TB SSD (used as FASTDISK)
  • 2x NVIDIA GTX 1080 GPU

For offline processing of movies with MotionCor2, gCTF and subsequent programs:

  • 2×12-core CPU (hyperthreading disabled)
  • >50 TB HD
  • 64 GB RAM
  • NVIDIA GTX 1080 GPU

==== For an OS X installation, we recommend the following hardware: ====

OS X computer for offline processing of 2D crystal images or movies:

  • MacBook Pro (Quadcore) or Mac Pro
  • 250 GB free space on HD
  • 16 GB RAM or more
  • OSX 10.11 or higher

Installation and setup

Focus depends on Qt5 for deploying a GUI. Other EM Suites are used wherever required. Find information on how to download, install and setup Focus software for the first time.

Download the software

Installation from source code

Setting up external software tools

Default installation directories

Getting started

Once Focus is installed it can be easily launched using the Command line or Desktop utilities provided with Focus. Following links give more information on launching Focus, adding a project, configuring global user settings and brief introduction of the GUI.

Launching Focus

Adding a new project

Introduction to GUI

Configuring user settings

Basic Usage

The links below would help you to start using Focus. The first things to do in any project is to import images and later once imported process them and manage them. Processing depends on the type of EM method used and is detailed in later sections.

Import images and movies

Managing Images using Project Library

Processing Images

Focus allows to process images via the precompiled scripts. Each script calls a few executables (external or internal) and fetches parameters associated with the project or the image from the configuration files as required. Processing can be either done manually for each image allowing to tune-in the parameters and later a bunch of images can be processed in parallel.

Manually processing an image

Parallel Processing

Remote Monitoring

Remote monitoring allows to see the status of the processing in Focus from a website that can be accessed remotely. This in turn helps to check the recording status of the microscope.

Setting up the server

Configuring Focus for remote monitoring

Collecting data in Focus

Setting up apps on Android and iOS

2D Crystal Processing

Focus includes scripts prebuilt to carry out complete 2D crystallographic image processing. Following pages describe how to start from images/movies, create final 2D maps, merge the data to produce 3D and finally refine the reconstruction to minimise the effects of missing cone.

Image Processing of 2D Crystal Images

2D Merging

3D Merging

Refining Merged Map

Exporting the data

Once the images have been processed they can be exported. The export function in Focus organizes the image files and metadata in the arrangement required by the target package. For example, if the target package is RELION, the data will be reorganized so that all aligned average images and a single metadata STAR file are created in a single subfolder. On the other hand, if the target package is IMOD, the electron tomography data will be reorganized so that there is one MRC stack for each specimen location, containing the entire tilt series ordered by tilt angle, irrespective of the recording order (e.g., if they were acquired using the Hagen scheme).

Single Particle/Drift Correction mode

Electron Tomography mode

FAQs

A list of FAQ is available in the following page:

Frequently Asked Questions

Previous Versions

No previous versions available