Image Analysis

The – ISTA -Imaging and Optics Facility provides several high-end Image Analysis Workstations equipped with state-of-the-art Image Analysis Software. To best coordinate the utilization of these resources, inclduing data storage & data transer, please make yourself familiar with our Booking policy & Data storage policy.

The available  infrastructure is capable to optimize your Image Analysis Workkflow: AcquisitionImage Processing (stitching, decovolution) → Image Analysis (segemtation, tracking) → Data Presentation (visualization and plotting).

We provide project-based solutions for custom-tailored image analysis tasks: we assist in automation of your image analysis workflow, or establishment of new image analysis routines using the image analysis programs available. We aim to make the developed analysis routines, such as workflow or  scripts, available as resources to for all users via our GitLAB repository.



Workstation Overview

Image Analysis Workstations are catagorized in ‘CUDA capable’ and ‘Standart’ workstations. More information about workstation can be found on the Image Analysis Workstations page.

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 (7x float)9.3.19.3.19.3.1.9.3.19.3.19.3.1
Imaris Stitcheryesyesyesyesyesyes
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
-----
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 (7x float)9.3.19.3.1.9.3.19.3.1
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---

Analysis Software Overview

The Imaging and Optics Facility provides various types of software for analysis of data acquired on our systems. The software can be used on our workstations based on their specifications. We aim to keep all the software up to date and in line with current trends in image analysis. More information about workstation can be found on the Image Analysis Software page.

Analysis Software

Image Analysis Resources

Image analysis services rely on a good data-infrastucture ensure safe and reliable data-transfer and data-storage (Data storage policy). Besides mediating in this data infrastructure towars our IT department, the Imaging and Optics Facility also provide assitance to establish analysis workflow and/or develop scripts. We aim to place workflows potocols and scripts in a repository (GitLAB), as well as that some of these scripts are available on our website. More information about our Image Analysis Resources can be found on the Image Analysis Resources page.


Image Analysis Community Resources

Image anlysis is driven by a strong community, aiming to contribute and share findings and resources. please see below:

COMMUNITY RESOURCES

Reading tips:

Courses and network: