Image Analysis Workstations

The Imaging & Optics Facility hosts a number of Image Analysis Workstations. The physical machines are located in the server room, but can be used via i) Connection terminals in rooms i01.o3.52a/b or remotely via ii) Remote Desktop Applications (RDP) and iii) Specific connection for Machine Learning (ML) applications. The connection terminals are equipped with 2 monitors and provide an optimized workspace to focus on your image analysis tasks. The Analysis workstations can be used after following the introduction to IOF, without further raining. whereas training, software introduction; image analysis support can be requested on demand. To coordinate the use of these resources, please comply with the following policies:

ANALYSIS WORKSTATIONS POLICIES

  • Always leave a clean and tidy work space, and SIGN OUT!
  • Consumption of food is also not allowed at the workstation terminal desks in rooms i01.o3.52a/b
  • Analysis workstation can only be used for image and data analysis
  • Always book in PPMS (required for access)
  • If you cancel a booking less than 24 hours prior to the starting time, make sure you send out a SIFFY e-mail.
  • In case you are over 30 minutes late for your booking, you need to send out an SIFFY e-mail: not doing so will be considered a ‘no-show’. A ‘no-show’ is eligible to be penalized, since you are blocking resources for other users
  • Image analysis computers usage need to follow our booking policy and cancellation policy
  • Please take note of our data storage policy
  • Speed-test of any analysis workstation (or microscope) can be done using the speed-docker
  • Usage of Imaris (floating) licenses can be done with Imaris license checker

IMAGE ANALYSIS WORKSTATION SPECIFICATIONS OVERVIEW

CUDA capable workstations
 PC 01PC 02PC 10PC 11PC ML 01VDI 01VDI 02VDI 03VDI 04VDI 05
Hostnamewdbiif024wdbiif023wdbiif025wdbiif026wdbiif020IOF-VDI-AWS01IOF-VDI-AWS02IOF-VDI-AWS03IOF-VDI-AWS04IOF-VDI-AWS05
LocationI01.O3.052bI01.O3.052bI01.O3.052aI01.O3.052aremoteI01.O3.052bI01.O3.052bI01.O3.052bremoteremote
Connection optionsvia terminalvia terminalvia terminalvia terminalremotevia terminalvia terminalvia terminalremoteremote
ProcessorIntel® Xeon® W “Skylake” W-2145, 3.60 GHzIntel® Xeon® W “Skylake” W-2145, 3.60 GHz Intel® Xeon® W “Skylake” W-2145, 3.60 GHzIntel® Xeon® W “Skylake” W-2145, 3.60 GHz Intel® Xeon® W “Skylake” W-2145, 3.60 GHzAMD EPYC™ 7302, 3GHz
RAM128 GB128 GB128 GB128 GB128 GB128 GB
Graphics cardNVIDIA Quadro P4000 - CUDANVIDIA Quadro P4000 - CUDANVIDIA Quadro P4000 - CUDANVIDIA Quadro P4000 - CUDANVIDIA GeForce RTX 2080TiNVIDIA Quadro RTX 8004
SSD (OS)1 Tb1 Tb1 Tb1 TbHDD 500GB
arivis Vision 4D (1 x floating license)yes yes yes yes yes
C.A.R.E. / N2Voptionaloptionaloptionaloptionalyes-
Huygens Professional (2x float)v 21.10 GPU acceleratedv 21.10 GPU acceleratedv 21.10 GPU acceleratedv 21.10 GPU acceleratedv 21.10 GPU acceleratedv 21.10 GPU accelerated
ilastik1.3.31.3.31.3.31.3.31.3.3 & 1.4.0b1.3.3
Imaris (8x float)9.9.19.9.19.9.19.9.19.9.19.9.1
Imaris Stitcher and Clearviewyesyesyesyesyesyes
Imspector Pro (dongle needed)yesyesyesyes--
RG trackeryesyesyesyesyesyes
ISTabilizer-yesyesyesyes-
MATLAB-2018b, 2020b2019b, 2020a2019a, 2020b-
Matlab Compiler runtime7.1; 8.4; 9.17.1; 8.4; 9.17.1; 8.4; 9.1-
NIS-Elements Viewerv4.2v4.2v4.2v4.2v4.2v4.2
Zen litev 2.5v 2.5v 2.5-v 3.4
CellPoseyes--yesyes-
Sleapyesyesyes-yes-
ZEN full version-v 2.3
must be enabled by script
-----
QuPath0.3.2
Standard workstations
 PC 03PC 07PC 08PC 09
Hostnamewdbiif019wdbiif006wdbiif005wdbiif007
LocationI01.O3.052bI01.O3.052aI01.O3.052aI01.O3.052a
Connection optionsvia terminalvia terminalvia terminalvia terminal
Processor Intel® Xeon® W “Skylake” W-2145, 3.60 GHzIntel Xeon E5-1680 v4, 3.40 GHzIntel Xeon E5-1680 v4, 3.40 GHzIntel Xeon E5-1680 v4, 3.40 GHz
RAM128 GB128 GB128 GB128 GB
Graphics cardNVIDIA Quadro P4000 - CUDAAMD Radeon Vega 64
SSD (OS)137 GB137 GB137 GB
arivis Vision 4D (1 x floating license)yes yes yes yes
Huygens Professional (2x float)v 21.10v 21.10v 21.10v 21.10
ilastik1.3.31.3.3 & 1.4.0b1.3.31.3.3
Imaris (8x float)9.3.1 and 9.9.19.3.1. and 9.9.19.3.1 and 9.9.19.3.1 and 9.9.1
Imaris Stitcheryesyesyesyes
RG trackeryesyesyesyes
ISTabilizeryesyesyes
MATLAB2019a, 2020b2017b, 2020b2017b, 2018b, 2020b2015b, 2017a, 2017b
Matlab Compiler runtime7.1; 8.4; 9.17.1; 8.4; 9.17.1; 8.4; 9.17.1; 8.4; 9.1
NIS-Elements Viewerv4.2v4.2v4.2v4.2
Zen litev 2.1v 2.5v 2.3v 2.3
Autolot-v3.3.14.2--
Doric studio---yes
ZenBlue full versionv 2.3---

HOW TO CONNECT TO DIFFERENT IMAGE ANALYSIS WORKSTATIONS

i) CONNECTION TERMINALS – rooms i01.o3.52a/b
How to use a connection terminal
  1. Make sure to use the correct terminal since the terminals are linked to 1 workstation (see signs on the tables).
  2. Log-in with .\bif-user, and the password “Useme!11”. Not with your own account!
  3. Open the remote connection shortcut on the desktop and log in with your credentials
    1. Never allow the system to remember your credentials! It blocks the usage of the terminal for future users!
  4. At the end of your session: to sign out from the workstation using the windows ‘Sign out’ button, as instructed here
  5. Switch off the terminal and monitors.

ii) How to Remote Connect to Workstations (correctly)
How to book, log-on and sign-out of an IOF workstations

Due to high demand, there is a 6h limit per workstation during peak hours (Monday to Friday, 08:00 to 20:00)

We have installed a script that synchronized with your reservation in PPMS booking system: this script allows you to access and prevents that others can ‘break-in’ into your analysis session while you are working (data-loss). To make sure this works smoothly the following points need to be considered:

  1. Book in PPMS – also software licenses: You can not sign in if you do not have a booking → you can also only sign in the PPMS-tracker pop-up screen when you have a booking. 
  • After placing your booking, please allow 5-10 min before log-on time for the script to synchronize!
  1. Remote: VPN required
    • Use VPN to connect to IST network
    • Use your remote desktop client to connect to the workstation:
    • Hostname.ist.local (eg wdbiif020.ist.local)
  2. Log-on (remote or local): Log-on with your IST credential as user-account in the following format: IST\username
  3. Log out after your session: start -> sign out (not only disconnect!!)
  4. It is important to sign out to free-up resources for the next users; disconnecting is not the same. Failing to comply with this will lead to penalization:

! please be aware that when a session reaches the end of a booking, the system will end the session and you will be automatically disconnected at the end of a session (after warnings): there is a risk of potential data loss in case you did not book long enough! To prevent data-loss: make sure to book sufficient time for your analysis to complete and cancel the remaining time of your booking in case your jobs finish early.

! Do not switch – off the workstations → they do not switch on by themselves!!!

iii) REMOTE DESKTOP CONNECTION FOR MACHINE LEARNING (ML)
Machine Learning PC 'ML 01' (CARE / N2V/ CellPose / SLEAP) - training required

Machine learning routines such as CARE, Noise-2-Void, CellPose & SPEAP are available on Machine Learning PC ML 01. Booking rights are granted upon a successfully completed training (request training here). The system can only be accessed after it is booked in PPMS booking (book here). To connect, please use your remote desktop client to connect to the computer wdbiif020, with your own user name (IST\username).

Booking guidelines:

      • You need to log in with your own credentials to PC ML 01
      • You can not log in if you do not have a booking rights
      • You can not unlock the tracker pop-up screen when you do not have a booking
      • When a booked session reaches its end, the system will end the session and you will be automatically disconnected (after warnings). This blocks your used resources for other users! Please be aware that there is a risk of potential data loss in case you did not book long enough! To prevent data loss, make sure to book sufficient time for your analysis to complete and cancel the remaining time of your booking in case your jobs finish early.

DATA TRANSFER SPEED

Speed-test to any analysis workstation (or microscope) can be done in the following ways:

https://fast.com/ ← how fast is your internet connection
https://speed.docker.ist.ac.at/ ← how fast is your connection to the IST Network


WHEN SOMETHING DOES NOT WORK