Image Analysis Workstations

HELMI 3D VM is a virtual machine which is used from your own workstation by a VMware Horizon Client. Instructions for connection are in LMU wiki. At the moment major software for the virtual machine are full Imaris installation and Fiji but we will add other software later. Workstation has CUDA capability so FIji plugins that are made for CUDA computing works there. Capabilities of computing is generally between 3D and LMU LS workstation except local hardisk is quite small which limits how much data can be stored in Imaris Arena.

Helmi 3D also includes Microvolution Deconvolution software

More details on workstation at LMU wiki

Reservations: Open Iris

LS workstation is a powerful workstation for 3D image analysis by Imaris or Fiji 64x and deconvolution (Autoquant X). This workstation has a limited Imaris software package. ImarisXT module allows you to use Matlab and Python scripts and Fiji modules within Imaris.

LS workstation can be accesses remotedly, please contact LMU staff for details.

Some information is on our wiki pages: https://wiki.helsinki.fi/display/LMU/Remote+connection+to+LS+workstation

Soft­ware

Bitplane Imaris
Autoquant X
Fiji 64x
Matlab 64x

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3D workstation is a powerful workstation for 3D image analysis and processing for large data sets. This workstation has an Imaris software package. ImarisXT module allows you to use Matlab and Python scripts and Fiji modules within Imaris.  Huygens Professional for deconvolution and image fusions.

Soft­ware

Bitplane Imaris suite with Batch coordinator
Huygens Professional
Fiji 64x
Matlab 64x

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2D Workstation is meant for analysis of images from Cell-IQ by Cell-IQ Analyser. 2D Workstation is behind LMu firewall so it has only very limited connection to internet.

Soft­ware

Cell-IQ Analyser
Leica Application Suite X Core Offline
ZEN Lite
Fiji 64x
IrfanView

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HCA Workstation is an older workstation with different 2D microscope image analysis software. It is suitabler for usage where you don't need 3D visualisation or GPU computing. Its major usage is analysing high content data from MD Nano and Fluorescence lifetime imaging data. It can be used also to use LAS X Core, Zen Lite or other microscope offline software When you need more memory than is available at normal office workstation.

RAM: 64 GB

Soft­ware:

CellProfiler
CellProfiler Analyst
Ilastik
PicoQuant SymPhoTime
Fiji x64
MetaXpress
Python
Slidebook (full offline version)
ZEN 2012 Lite
Leica Application Suite X Core Offline
AIDA
Anvil

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