Image Processing

Commercial Image Processing Software
Logo of Huygens Huygens Deconvolution
Application

  Huygens performs image restoration, background reduction, interactive analysis and volume visualization in 2D, 3D, multi-channel and time. The package includes many image processing modules, for all types of fluorescence microscopy images. Additional high performance cluster (HPC) and GPU involvement ensure maximization speed and multi-user environment.

Deconvolution modules
  • Widefield fluorescence images
  • Point-scanning confocal images
  • Spinning-disc confocal images
  • Airy-scan super-resolution images (purchase planned)
  • STED super-resolution images (purchase planned)
  • Multiphoton images (purchase planned)
General Information
  • Host workstation: ITS HPC facility
  • User induction required
  • Booking: not required
  • Software manual: Huygens User Manuals
  • Level of support: software induction and troubleshooting
  • Maintenance: SVI software maitenance contract, - June 2021
Accessibility
  • Register HPC user only
  • Access remotely from all office computers and workstations
  • Path to Huygens Core
  • Instruction to access Huygens Professional
    • Logon to the Huygens server with x11 forwarding enabled. On a Mac or Linux machine use a terminal window. On a PC you should use Exceed X-term
    • In the terminal window type: ssh -Y userid@huygens.hpc.susx.ac.uk where "userid" is your university (email) id (example: ssh -Y yg90@huygens.hpc.susx.ac.uk)
    • When you get a logon prompt then logon using your university (email) credentials
    • Once you’ve logged onto the server simply type: huygenspro, The huygenspro software will then open in a window
  • Local copy of Huygens Professional
    • Version:
    • Location: Workstation_Paris
Logo of Imaris Imaris
Application

  Imaris delivers comprehensively the necessary functionalities for image management, visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets from a few megabytes to multiple gigabytes.

General Information
  • Manufacturer: Bitplane
  • Accessibility: all users
  • Host workstation
    • Workstation_Berlin (GDSC 3.19)
    • Dragonfly (CRPC 3.16)
  • User induction required
  • Booking
    • Workstation_Berlin: not required
    • Dragonfly: QReseve
  • Software manual: Imaris Reference Manual
  • Level of support: software induction and troubleshooting
  • Maintenance: N/A
Imaris modules
  • Copy on Dragonfly (Version 9.2.1)
    • File Reader
    • Base
    • Surpass
    • Time
    • Topography
  • Copy on Workstation_Berlin (Version 8.3.1)
    • File Reader
    • Batch
    • Coloc
    • MeasurementPro
    • Track
    • Vantage
    • ReferenceFrame
    • Surpass
    • Time
    • Topography
Logo of Harmony Harmony
Application

  Harmony is an integrated HCS software for imaging and image analysis. The software analyse complex cellular/subcellular models and different phenotypes of 3D and 4D microscopy datasets from a few megabytes to multiple gigabytes.

General Information
  • Manufacturer: PerkinElmer
  • Accessibility: all users
  • Host workstation
  • Registed user only, induction required
  • Booking: QReseve
  • Software manual: Harmony Video Tutorials
  • Level of support: software induction, protocol development and troubleshooting
  • Maintenance: PerkinElmer, part of Operetta maintenance contract
Logo of ScanR ScanR Analysis
Application

  ScanR Analysis is designed to analyse 3D/4D images taken by scanR Acquisition. The analysis covers from counting the labeled cells to ratiometric feature-based analysis of multilabeled objects and sub-objects in different cell types. Image analysis is carried out as a logical multi-step procedure consisting of image processing, object detection, feature extraction and data analysis by gating and classification. A workflow-oriented user interface guides users through all steps.

General Information
  • Manufacturer: Olympus
  • Accessibility: Scan R users
  • Host workstation
    • Scan R (JMS 2C41)
    • Workstation_Madrid (JMS 2C41)
  • Registed user only, induction required
  • Booking
    • Workstation_Madrid: not required
    • Scan R: QReseve
  • User manual: Scan R Analysis Manual
  • Level of support: software induction, protocol development and troubleshooting
  • Maintenance: Olympus
Logo of slidebook SlideBook 6
Application

  SlideBook is an integrated imaging and image processing software. The image processing includes mathematical operations, statistics functions, analysis scripting and import/export to/from MATLAB. Additional modules are available for special applications ranging from deconvolution to photomanipulation.

General Information
  • Manufacturer: 3i
  • Accessibility: 3i Spinning disc users
  • Host workstation: 3i Spinning disc (GDSC G2.10)
  • Registed user only, induction required
  • Booking: QReseve
  • Software manual: Getting Started
  • Level of support: software induction and troubleshooting
  • Maintenance: 3i, part of 3i spinning disc service contract
Logo of Zenblack Zen (black)
Application

  Zen (black) is an image acquisition software with image processing functions. Its image processing includes Airyscan processing, image stitching, 3D axial projection. Zen can also be used to do quantification study such extracting pixel value of ROI and FRET analysis.

General Information
  • Manufacturer: Zeiss
  • Accessibility: all users
  • Host workstation
    • LSM880 (JMS 2C31)
    • Workstation_London (JMS 2C31)
  • Registed user only, induction required
  • Booking
    • Workstation_London: not required
    • LSM880: QReseve
  • Software manual: Zen (black)
  • Level of support: software induction and troubleshooting
  • Maintenance: Zeiss, part of LSM880 service contract
Logo of Image Zenblue Zen (blue)
Application

  Zen (blue) is an image acquisition software with image processing functions. Its image processing includes image stitching, 3D rendering and axial projection. Zen can also be used to do quantification study such extracting pixel value of ROI.

General Information
  • Manufacturer: Zeiss
  • Accessibility: GDSC users
  • Host workstation
    • Apotome (GDSC 3.10)
    • Workstation_London (JMS 2C31)
  • Registed user only, induction required
  • Booking
    • Workstation_London: not required
    • Apotome: QReseve
  • Software manual: Zen (blue)
  • Level of support: software induction and troubleshooting
  • Maintenance: Zeiss, part of Apotome service contract
Logo of Isis Isis
Application

  Isis combines imaging and image processing in the same package. Besides image acquisition, it also provides a variety of tools to enhance, edit, annotate, archive, measure, and print of the images. The optimized user interface guarantees rapid results in research and clinic routine. Multiple customizable color display modes (RGB, individual colors, modified colors, merged colors, gray scale, inverted gray scale, combinatorial false colors) allow detailed analysis of images.

General Information
  • Manufacturer: Metasystems
  • Accessibility: Apotome users only
  • Host workstation
    • Apotome (GDSC 3.10)
    • Workstation_Berlin
  • Registed user only, induction required
  • Booking
    • Apotome: QReseve
    • Workstation_Berlin: not required
  • Software manual: Product Borchure
  • Level of support: software induction and troubleshooting
  • Maintenance: Zeiss, part of Apotome service contract
Logo of Spotfire Spotfire
Application

  Spotfire is a data visualization and analytics software for chart presentation and analysis. It can import data from Matlab and spreadsheets.

General Information
  • Manufacturer: TIBC Spotfire
  • Accessibility: all users
  • Host workstation
    • Workstation_Madrid (JMS 2C41)
    • Workstation_Rome (JMS 2C41)
  • Booking: QReseve
  • Software manual: User's Manual
  • Level of support: login details
  • Maintenance: N/A
Logo of Matlab MATLAB
Application

  MATLAB combines a desktop environment tuned for iterative analysis and design processes with a programming language that expresses matrix and array mathematics directly.

General Information
  • Manufacturer: MathWorks
  • Accessibility: all users
  • Host workstation
    • Workstation_Berlin (GDSC G3.19)
    • can also be installed on any office computer by ITs
  • Booking: not required
  • Software manual: MatLab Manual
  • Level of support: N/A
  • Maintenance: ITs
Open Source Image Processing Software
Logo of Image Quant TL Image J
Application

  ImageJ is a public domain, Java-based image processing program. It was designed with an open architecture that provides extensibility via Java plugins and recordable macros. Custom acquisition, analysis and processing plugins can be developed using ImageJ's built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging to radiological image processing, multi-system data comparisons to automated hematology systems.

General Information
  • Manufacturer: NIH
  • Accessibility: all users
  • Download path: Image J
  • Host workstation
    • On all offline workstations
    • Can be installed on any office computer
  • Booking: not required
  • Software manual: Image J User Guide
  • Level of support: software induction, plugin development and troubleshooting
  • Maintenance: N/A
  • Advance application development: Image analysis using Image J
Logo of Image Quant TL Cell Profiler
Application

  CellProfiler is public domain software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. Advanced algorithms for image analysis are available as individual modules that can be placed in sequential order together to form a pipeline; the pipeline is then used to identify and measure biological objects and features in microscope images.

General Information
Offline Workstations
   Workstation Berlin
Computer details
  • Location: GDSC G3.19
  • Booking: not required
  • CPU: Intel Xeon E5-1660
  • RAM: 64GB
  • GPU: NVIDIA Quadro K4200(1344 core & 4GB RAM)
  • Windows 10 64-bit
  • Local data drive (D:) 1TB
  • Network name:gc04014216.ad.susx.ac.uk
On-board image processing software
  • Imaris
  • Isis
  • Matlab
  • Image Quant TL
  • Image J
   Workstation London
Computer details
  • Location: JMS 2C31
  • Booking: not required
  • CPU: Intel Xeon E5-2623
  • RAM: 192GB
  • GPU: N/A
  • Windows 10 64-bit
  • Local data drive (D:) 3.6 TB
  • Network name: lsm880-analysis.ad.susx.ac.uk
On-board image processing software
  • Zen (black)
  • Zen (blue)
  • Image J
   Workstation Madrid
Computer details
  • Location: JMS 2C41
  • Booking: not required
  • Model: Dell Precision Tower5810
  • CPU: Intel Xeon E5-1630 V3 @3.7 GHz
  • RAM: 16GB
  • GPU: N/A
  • Windows 10 64-bit
  • Local data drive (D:) 2 TB
  • Network name: gc04016705.ad.susx.ac.uk
  • Direct access to data drive of Scan R
On-board image processing software
  • Scan R Analysis
  • Spotfire
  • Image J
   Workstation Paris
Computer details
  • Location: GDSC G3.19
  • Booking: not required
  • CPU: Intel Xeon E5-1660
  • RAM: 64GB
  • GPU: GPU: 2x NVIDIA Quadro K4200(1344 core & 4GB RAM each)
  • Windows 10 64-bit
  • Local data drive (D:) 1 TB
  • Network name: gc04014987.ad.susx.ac.uk
On-board image processing software
  • Huygens Pro (old version)
  • Matlab
  • Image J
   Workstation Rome
Computer details
  • Location: JMS 2C41
  • Booking: QReseve
  • Model: Dell Precision T5500
  • CPU: Intel X5650 @2.67GHz (2 processors)
  • RAM: 18GB
  • GPU: N/A
  • Windows 10 64-bit
  • Local data drive (D:) 2 TB
  • Network name: gc01007293.ad.susx.ac.uk
  • Direct access to Harmony database on Operetta
On-board image processing software
  • Harmony
  • Spotfire
  • Image J
   HPC Facility
Setup details
  • Location: ITs HPC facility
  • Booking: not required
  • Register user only
On-board image processing software