Data analysis tools

Hardware:

  • 5 Offline analysis computers (OA1-5) – on-site and remote access
  • 3 Workstations (WS1-3) with high computation power and with available leading-edge Image Analysis software (Amira, Imaris, NIS-Elements AI, Huygens) – remote access only
  • To get access to workstations and OA computers remotely, users outside the Faculty of Science at BIOCEV need to contact Dalibor Pánek, dalibor.panek@natur.cuni.cz. Please, provide your BIOCEV user name for access via VPN and/or IP address for direct access from computers at BIOCEV.

PCRemote Desktop Connection
IPUsernamePassword
Workstation110.11.17.55User Workstation 1imcf
Workstation210.11.16.23ws2userIMCF_2
Workstation310.11.17.135w3userimcf
OA110.11.16.63oa1userimcf
OA210.11.16.62User OA2imcf
OA310.11.16.64User OA3imcf
OA410.11.16.66oa4userimcf
OA510.11.16.60User OA5imcf

PCCPUGPURAMRoomAdditional
Workstation1Intel Xeon W-2145NVIDIA Quadro RTX 5000128GBremote access only
Workstation2AMD EPYC 7302 3.0 GHz, 16 coresNVIDIA GeForce RTX 3090128GBremote access only
Workstation3AMD EPYC2 Rome 7302P
3.0 GHz, 16 cores
NVIDIA GeForce RTX 3090128GBremote access only
OA1Intel Core i5-13500
2.5 GHz, 14 cores
NVIDIA GeForce GTX 1650 4GB32GBBIOCEV L1.005
OA2Intel Core i7-4790 3.0 GHz, 4 coresNVIDIA Quadro M400032GBBIOCEV L1.005Touch screen and pen
OA3Intel Core i7-4790 3.0 GHz, 4 coresAMD Radeon R7 20016GBBIOCEV L1.005
OA4Intel Core i5-13500
2.5 GHz, 14 cores
NVIDIA GeForce GTX 1650 4GB32GBBIOCEV L1.005
OA5Intel Core i7-4790 3.0 GHz, 4 coresAMD Radeon R7 20016GBBIOCEV L1.005

Software:

  • When using software with limited number of licences on dedicated IMCF computer, reservation of both software license and PC is required.

Commercial software

Amira
Imaris
Kaluza
  • 10 floating licenses available for your personal PCs
    available as well on OA5 PC (personal PCs preferred – users using FlowJo are therefore not blocked)
  • manual for remote access [PDF]
FlowJo
Huygens
  • 1 license available on Workstation 3 via remote connection
  • charged per hour - see Price list
  • for setting up connection to Workstation 3 refer to Huygens manual [PDF]
NIS-Elements (with AI)
  • 2 licenses can be used at the same time
  • pre-installed on Workstation1, Workstation2, OA1, OA2, and OA3 PCs (reservation required)
  • for remote access to our workstations refer to general manual [PDF]
Matlab
  • available on OA1-4 PCs and Workstation1
    currently installed toolboxes: Curve Fitting, Image Processing, Parallel Computing, Signal Processing
  • all toolboxes are available, just contact member of IMCF for upgrade
  • for remote access refer to general manual [PDF]
LabVIEW
  • home-made tools “TTTR Data Analysis” and “Data analysis_18” for FLIM and point and line-scan FCS data analysis
  • available on OA3 PC
  • for remote access refer to general manual [PDF]

Installed freeware tools

FIJI
  • available on OA1-4, Workstation1-3, and most microscopic computers
ICY
  • available on OA1-4

OA1OA2OA3OA4OA5Workstation 1Workstation 2Workstation 3
Amira
Imaris
NIS-Elements
Huygens
LabVIEW
Matlab
FIJI
ICY
Kaluza
FlowJo

Data management (OMERO):

OMERO (Open Microscopy Environment) is a powerful platform designed to facilitate the management, sharing, and analysis of microscopy data. Researchers can access OMERO at IMCF through a web interface at omero.natur.biocev.org, making it easy to view and analyze their datasets remotely.

OMERO aligns with the FAIR principles, which stand for Findable, Accessible, Interoperable, and Reusable. By adhering to these principles, OMERO ensures that microscopy data becomes more discoverable and accessible, fostering data sharing and reusability across research communities. The FAIR principles promote open science and contribute to the integrity and transparency of research.

For access to OMERO, users must have a valid BIOCEV account.

  1. Request an access to OMERO from IMCF staff and wait for confirmation.
  1. Log in at omero.natur.biocev.org with your BIOCEV credentials.
  1. If successfully logged in, an account has been created for you. You should see something like this (with your name instead)
  1. Let the IMCF staff know that you successfully logged in and your account will be linked with relevant data repositories.
  1. When linked, you can access shared data by clicking on the panel users ‘yourname’. List of groups you have been granted access to will be shown. To show data, choose All Members from the associated group.
  1. Images are to be found inside Project (grey) and Dataset (green) folders.