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Image Analysis Software

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Huygens Deconvolution (SVI)

   Huygens performs image restoration and background reduction, interactive analysis and volume visualization in 2D, 3D, multi-channel and time. The package includes many image processing options, for bright field and all types of fluorescence microscopy images. Additional Server and GPU-based Options ensure maximization of hardware performance.
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  • Software manual: Huygens User Manuals

  • License: 1 x Huygens Pro (Everywhere for 2 concurrent)

  • Maintenance contract (SVI): until June 2027

Lab: JMS 2C33/34, 2C31

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Scan R Analysis (Olympus)

  Scan R Analysis is designed to analyse 3D/4D images taken by scan R Acquisition. The analysis covers from counting the labelled cells to radiometric feature-based analysis of multi-labelled objects and sub-objects. Image analysis is carried out as a logical multi-step workflow consisting of image processing, object detection, feature extraction and data analysis by gating and classification. 

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Lab: JMS 2C41

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IMARIS (Bitplane)

   Imaris delivers comprehensively the necessary functionality for image management, visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets from a few megabytes to multiple gigabytes in size.
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Lab: GDSC G3.19, CRPC 3.16

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Harmony (PerkinElmer)

   Harmony is an integrated HCS software for imaging and image analysis. Associated with the Operetta acquisition, it can analyse complex cellular/subcellular models and different phenotypes of 3D and 4D microscopy datasets from a few megabytes to multiple gigabytes in size.
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Lab: JMS 2C41

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SlideBook 6 (3i)

   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.
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Lab: JMS 2C33/34

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Spotfire (TIBCO)

   Spotfire is a data visualization and analytics software for chart presentation and analysis. It can import data from Matlab.
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Lab: JMS 2C41

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Fiji (Open Source)

   ImageJ is a public domain, Java-based image processing program that was designed with an open architecture providing 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. 

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Cell Profiler (Open Source)

   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.​​

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Image Processing Workstations

Operetta Offline Workstation

  • Host of Harmony & Spotfire

  • Dell Precision Tower 5810

  • CPU: Xeon E5-1650, RAM: 64GB, HDD: 1.72TB (RAID 0), GPU: Quadro M5000​

Lab: JMS 2C41

Scan R Offline Workstation

Lab: JMS 2C41

  • Host of ScanR Analysis, CellSens (AI module) & Spotfire

  • Dell Precision Tower 5810

  • CPU: Xeon E5-1630, RAM: 16 GB, HDD: 1.8TB (RAID 0), GPU: GeForce RTX 3600 Ti​

Workstation London

Lab: JMS 2C31

  • Host of Zen (Black) & Huygens

  • hp Z840: CPU: Xeon E5-2623, RAM: 192 GB, HDD: 3.38TB, GPU: Quadro K2200​

Workstation Berlin

  • Host of IMARIS, MATLAB & Spotfire

  • Dell Precision Tower 5810: CPU: Xeon E5-1660, RAM: 64 GB, HDD: 1 TB, GPU: Quadro K4200​

Lab: GDSC G3.19

Workstation Paris

Lab: GDSC G3.19

  • Host of Huygens, MATLAB, Cell Profiler & Spotfire

  • Dell Precision Tower 5810: CPU: Xeon E5-1660, RAM: 64 GB, HDD: 1 TB, GPU: Quadro K4200​

  • Data Management Rules

Data Safety

  • Users have full data ownership and the responsibility to the data safety.

  • The Centre has responsibility to store raw data for at least 5 years.

  • Local data drive is in general set in RAID 0.

  • Remote storage is set in RAID 6.

  • Raw data should be initially saved in local drive during imaging, but can be backed up immediately after an experiment.

  • Remote Storage is acting as a safe buffer where data in local drive can be relocated to make space for new experiment.

  • Valuable results should be saved by its user in Safe Storage that has backup facility. ​

 

Useful Guidance:

Data Recovery

  • Data in Local Storage will be recoverable unless both HDD fails at the same time.

  • Data being deleted from Local Storage and Remote Storage by mistake can NOT be recovered.

  • Data in Remote Storage will be recoverable unless more than 2 HDDs break simultaneously.

  • Maintenance of Safe Storage is not the responsibility of the Centre. Ask IT for more details.

  • Recommended Data Flow

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Raw Data Storage

  • Local Storage

  • Separate internal hard drive (name: Data) in the workstation of all microscopes

  • Individual user directories but no privilege

  • Users have full responsibility to their data

  • Most data drive is set as RAID 0

  • Data in the local storage are routinely checked and relocated to the Remote Storage if its space is full. 

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  • Remote Storage

QNAP TS-x73A (Operetta)

  • Data capacity: 76TB

  • Safety mode: RAID 6

  • Access: via facility staff

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QNAP TS-x73A (other microscopes)

  • Data capacity: 76TB

  • Safety mode: RAID 6

  • Access: via facility staff​​​

  • Safe Storage

Omero

  • Managed by IT department

  • Safety mode: RAID 6

  • Accessible in the Centre

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Cloud Storage

  • Managed by IT department

  • Box & One Drive account for all in Sussex

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Research Volume

  • Account for Sussex research staff

  • Managed by IT department

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