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: Acquisition → Image 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 01 | PC 02 | PC 10 | PC 11 | PC ML 01 | VDI 01 | VDI 02 | VDI 03 | VDI 04 | VDI 05 |
| Hostname | wdbiif024 | wdbiif023 | wdbiif025 | wdbiif026 | wdbiif020 | IOF-VDI-AWS01 | IOF-VDI-AWS02 | IOF-VDI-AWS03 | IOF-VDI-AWS04 | IOF-VDI-AWS05 |
| Location | I01.O3.052b | I01.O3.052b | I01.O3.052a | I01.O3.052a | remote | I01.O3.052b | I01.O3.052b | I01.O3.052b | remote | remote |
| Connection options | via terminal | via terminal | via terminal | via terminal | remote | via terminal | via terminal | via terminal | remote | remote |
| Processor | Intel® Xeon® W “Skylake” W-2145, 3.60 GHz | Intel® Xeon® W “Skylake” W-2145, 3.60 GHz | Intel® Xeon® W “Skylake” W-2145, 3.60 GHz | Intel® Xeon® W “Skylake” W-2145, 3.60 GHz | Intel® Xeon® W “Skylake” W-2145, 3.60 GHz | | AMD EPYC™ 7302, 3GHz |
| RAM | 128 GB | 128 GB | 128 GB | 128 GB | 128 GB | | 128 GB |
| Graphics card | NVIDIA Quadro P4000 - CUDA | NVIDIA Quadro P4000 - CUDA | NVIDIA Quadro P4000 - CUDA | NVIDIA Quadro P4000 - CUDA | NVIDIA GeForce RTX 2080Ti | | NVIDIA Quadro RTX 8004 |
| SSD (OS) | 1 Tb | 1 Tb | 1 Tb | 1 Tb | | | HDD 500GB |
| arivis Vision 4D (1 x floating license) | | yes | yes | yes | yes | | yes |
| C.A.R.E. / N2V | optional | optional | optional | optional | yes | | - |
| Huygens Professional (2x float) | v 21.10 GPU accelerated | v 21.10 GPU accelerated | v 21.10 GPU accelerated | v 21.10 GPU accelerated | v 21.10 GPU accelerated | | v 21.10 GPU accelerated |
| ilastik | 1.3.3 | 1.3.3 | 1.3.3 | 1.3.3 | 1.3.3 & 1.4.0b | | 1.3.3 |
| Imaris (7x float) | 9.3.1 | 9.3.1 | 9.3.1. | 9.3.1 | 9.3.1 | | 9.3.1 |
| Imaris Stitcher | yes | yes | yes | yes | yes | | yes |
| Imspector Pro (dongle needed) | yes | yes | yes | yes | - | | - |
| RG tracker | yes | yes | yes | yes | yes | | yes |
| ISTabilizer | - | yes | yes | yes | yes | | - |
| MATLAB | - | 2018b, 2020b | 2019b, 2020a | 2019a, 2020b | | | - |
| Matlab Compiler runtime | | 7.1; 8.4; 9.1 | 7.1; 8.4; 9.1 | 7.1; 8.4; 9.1 | | | - |
| NIS-Elements Viewer | v4.2 | v4.2 | v4.2 | v4.2 | v4.2 | | v4.2 |
| Zen lite | | v 2.5 | v 2.5 | v 2.5 | - | | v 3.4 |
| CellPose | yes | - | - | yes | yes | | - |
| Sleap | yes | yes | yes | - | yes | | - |
| ZEN full version | - | v 2.3
must be enabled by script | - | - | - | - | - |
Standard workstations
| | PC 03 | PC 07 | PC 08 | PC 09 |
| Hostname | wdbiif019 | wdbiif006 | wdbiif005 | wdbiif007 |
| Location | I01.O3.052b | I01.O3.052a | I01.O3.052a | I01.O3.052a |
| Connection options | via terminal | via terminal | via terminal | via terminal |
| Processor | Intel® Xeon® W “Skylake” W-2145, 3.60 GHz | Intel Xeon E5-1680 v4, 3.40 GHz | Intel Xeon E5-1680 v4, 3.40 GHz | Intel Xeon E5-1680 v4, 3.40 GHz |
| RAM | 128 GB | 128 GB | 128 GB | 128 GB |
| Graphics card | NVIDIA Quadro P4000 - CUDA | AMD Radeon Vega 64 | | |
| SSD (OS) | | 137 GB | 137 GB | 137 GB |
| arivis Vision 4D (1 x floating license) | yes | yes | yes | yes |
| Huygens Professional (2x float) | v 21.10 | v 21.10 | v 21.10 | v 21.10 |
| ilastik | 1.3.3 | 1.3.3 & 1.4.0b | 1.3.3 | 1.3.3 |
| Imaris (7x float) | 9.3.1 | 9.3.1. | 9.3.1 | 9.3.1 |
| Imaris Stitcher | yes | yes | yes | yes |
| RG tracker | yes | yes | yes | yes |
| ISTabilizer | | yes | yes | yes |
| MATLAB | 2019a, 2020b | 2017b, 2020b | 2017b, 2018b, 2020b | 2015b, 2017a, 2017b |
| Matlab Compiler runtime | 7.1; 8.4; 9.1 | 7.1; 8.4; 9.1 | 7.1; 8.4; 9.1 | 7.1; 8.4; 9.1 |
| NIS-Elements Viewer | v4.2 | v4.2 | v4.2 | v4.2 |
| Zen lite | v 2.1 | v 2.5 | v 2.3 | v 2.3 |
| Autolot | - | v3.3.14.2 | - | - |
| Doric studio | - | - | - | yes |
| ZenBlue full version | v 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.
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:
