Institute of Molecular Genetics of the Czech Academy of Sciences
A high-performance workstation designed primarily for applications with demanding requirements for computing resources and RAM, such as image stitching, processing large datasets from light-sheet or spinning disk microscopes, and deep learning applications.
| Software | Imaris – Core and Measurement Pro + floating licenses: Vantage, Coloc, XT (4 of each) Track, Lineage, Cells Viewer, Filament, Batch (2 of each) Imaris Stitcher NIS-Elements with Machine Learning Module Anaconda (Python) FiJi ImageJ |
| Hardware | CPU 32-core RAM 1024 GB GPU Nvidia A40 24GB |
| Booking | Calpendo (“01 – Imaris, Stitcher, NIS-E (Gold)”) |
| Access | Virtual Desktop Infrastructure (“01 – Imaris, Stitcher, NIS-E (Gold)”) |
A high-performance workstation designed primarily for applications requiring significant computing resources and RAM, such as image stitching, processing large datasets from light-sheet or spinning disk microscopes, and deep learning. The Huygens deconvolution software on this virtual machine leverages a graphics processor (NVIDIA A40, 44GB) for computations and includes an option for light-sheet data deconvolution.
| Software | Huygens Professional – Widefield & Brightfield, Confocal, STED 3D, Light Sheet, Bleaching Corrector, Chromatic Aberration Corrector, Crosstalk corrector, Tile Stitching, Light Sheet Fuser, Object Stabilizer, PSF Distiler, Workflow Processor, Batch Feeder NIS-Elements 7.0 beta with Machine Learning Module Anaconda (Python) FiJi ImageJ |
| Hardware | CPU 32-core RAM 1024 GB GPU Nvidia A40 44GB |
| Booking | Calpendo (“02 – Huygens-GPU, NIS-E (Gold)”) |
| Access | Virtual Desktop Infrastructure (“02 – Huygens-GPU, NIS-E (Gold)”) |
A powerful workstation specifically designed for applications utilizing software packages on Linux. This machine is ideal for tackling complex tasks such as the analysis and registration of volumetric data, cell tracking in entire developing embryos, and training or inferencing deep learning networks for image or volume segmentation and classification tasks. Its capabilities are especially enhanced by the power of GPU computation. Specialized training is required to operate this virtual machine.
| Software | Anaconda (Python) Other software packages can be installed on demand |
| Hardware | CPU 8-core RAM 256 GB GPU Nvidia A40 16GB |
| Booking | Calpendo (“03 – Linux (Silver)”) |
| Access | Virtual Desktop Infrastructure (“03 – Linux (Silver)”) |
Powerful workstation for image analysis. In addition to the standard ImageJ and Python packages, it also offers Imaris software and NIS-Elements software.
| Software | Imaris – Core and Measurement Pro + floating licenses: – Vantage, Coloc, XT (4 of each) – Track, Lineage, Cells Viewer, Filament, Batch (2 of each) NIS-Elements with Machine Learning Module Anaconda (Python) FiJi ImageJ |
| Hardware | CPU 32-core RAM 256 GB GPU Nvidia A40 24GB |
| Booking | Calpendo (“05 – Imaris, NIS-E (Silver)”) |
| Access | Virtual Desktop Infrastructure (“05 – Imaris, NIS-E (Silver)”) |
Standard workstation for image analysis. In addition to the standard ImageJ and Python packages, it also offers Imaris software, NIS-Elements software. ZEN Black 3.0 software enables processing of SIM and SMLM super-resolution data from Elyra 7 microscope.
| Software | Imaris – Core and Measurement Pro + floating licenses: – Vantage, Coloc, XT (4 of each) – Track, Lineage, Cells Viewer, Filament, Batch (2 of each) ZEN Black 3.0 – Deconvolution, Lattice SIM & SIM2 Processing, Localization microscopy processing NIS-Elements with Machine Learning Module Anaconda (Python) FiJi ImageJ |
| Hardware | CPU 12-core RAM 128 GB GPU Nvidia A40 16GB |
| Booking | Calpendo (“06 – Imaris, ZEN-SR, NIS-E”) |
| Access | Virtual Desktop Infrastructure (“06 – Imaris, ZEN-SR, NIS-E”) |
Standard workstation for image analysis. In addition to the standard ImageJ and Python packages, it also offers Imaris software and NIS-Elements software. Matlab programming and numeric computing platform provides another tool for data analysis, signal and image processing. Imaris software can be bridged with Matlab via Imaris XT module.
| Software | Imaris – Core and Measurement Pro + floating licenses: – Vantage, Coloc, XT (4 of each) – Track, Lineage, Cells Viewer, Filament, Batch (2 of each) Matlab – Image processing toolbox, Signal processing toolbox, Statistical toolbox, Optimization toolbox, Curve fitting toolbox NIS-Elements with Machine Learning Module Anaconda (Python) FiJi ImageJ |
| Hardware | CPU 12-core RAM 128 GB GPU Nvidia A40 16GB |
| Booking | Calpendo (“07 – Imaris, Matlab, NIS-E”) |
| Access | Virtual Desktop Infrastructure (“07 – Imaris, Matlab, NIS-E”) |
Standard workstation for image analysis. In addition to the standard ImageJ and Python packages, it also offers Imaris software and NIS-Elements software. Matlab programming and numeric computing platform provides another tool for data analysis and image processing. Imaris software can be bridged with Matlab via Imaris XT module.
| Software | Imaris – Core and Measurement Pro + floating licenses: – Vantage, Coloc, XT (4 of each) – Track, Lineage, Cells Viewer, Filament, Batch (2 of each) Matlab – Image processing toolbox, Statistical toolbox NIS-Elements with Machine Learning Module Anaconda (Python) FiJi ImageJ |
| Hardware | CPU 12-core RAM 128 GB GPU Nvidia A40 16GB |
| Booking | Calpendo (“08 – Imaris, Matlab, NIS-E”) |
| Access | Virtual Desktop Infrastructure (“08 – Imaris, Matlab, NIS-E”) |
Standard workstation for image analysis. In addition to the standard ImageJ and Python packages, it also offers Imaris software and Arivis software.
| Software | Imaris – Core and Measurement Pro + floating licenses: – Vantage, Coloc, XT (4 of each) – Track, Lineage, Cells Viewer, Filament, Batch (2 of each) Arivis 3.1.3 Anaconda (Python) FiJi ImageJ |
| Hardware | CPU 12-core RAM 128 GB GPU Nvidia A40 16GB |
| Booking | Calpendo (“09 – Imaris, Arivis”) |
| Access | Virtual Desktop Infrastructure (“09 – Imaris, Arivis”) |
A high-performance workstation designed primarily for applications with demanding requirements for computing resources and RAM, such as image stitching, processing large datasets from light-sheet or spinning disk microscopes, and deep learning applications. The Huygens deconvolution software on this virtual machine utilizes a CPU (AMD EPYC 7713, 64-core, 2.0GHz) for computations and includes an option for spinning disk data deconvolution.
| Software | Huygens Professional – Widefield & Brightfiled , Confocal, Spinning Disk & SoRa, STED 3D, Bleaching Corrector, Chromatic Aberration Corrector, Object Stabilizer, PSF Distiler, Movie Maker, Object Analyzer, Object Tracker, Colocalization Analyzer with RBNCC option, Workflow Processor, Batch Feeder ZEN Blue 3.4 – Deconvolution, Light sheet Processing, MultiView & Dual Side Fusion NIS-Elements with Machine Learning Module Anaconda (Python) FiJi ImageJ |
| Hardware | CPU 64-core RAM 512 GB GPU Nvidia A40 24GB |
| Booking | Calpendo (“10 – Huygens-CPU, ZEN-LS, NIS-E (Gold)”) |
| Access | Virtual Desktop Infrastructure (“10 – Huygens-CPU, ZEN-LS, NIS-E (Gold)”) |
Standard workstation for image analysis. CellSense Dimensions software and ScanR Analysis software from Evident (Olympus) are available. Workstation also offers AI deep learning module that works together with both software packages and enables deep learning of new AI models for segmentation.
| Software | ScanR Analysis software with AI Deep Learning Module cellSense Dimension – Deconvolution, AI Deep Learning Module Anaconda (Python) FiJi ImageJ |
| Hardware | CPU 12-core RAM 128 GB GPU Nvidia A40 16GB |
| Booking | Calpendo (“11 – ScanR, cellSense”) |
| Access | Virtual Desktop Infrastructure (“11 – ScanR, cellSense”) |
Standard workstation for image analysis. It offers ZEN software for working with Zeiss specific file formats. In collaboration with the Flow Cytometry Core Facility, it also enables analysis of image cytometry data from the Image Stream flow cytometer using IDEAS software with a machine learning module.
| Software | IDEAS software with Machine Learning Module ZEN – Time Series, Multi-Channel, Measurement Anaconda (Python) FiJI ImageJ |
| Hardware | CPU 12-core RAM 64 GB GPU Nvidia A40 8GB |
| Booking | Calpendo (“12 – Ideas ML, ZEN”) |
| Access | Virtual Desktop Infrastructure (“12 – Ideas ML, ZEN”) |
Standard workstation for image analysis. It offers the analysis of FLIM and FCS data from the Stellaris 8 microscope. In collaboration with the Flow Cytometry Core Facility, it also enables the analysis of image cytometry data from the Image Stream flow cytometer using the IDEAS and Amnis AI software packages.
| Software | IDEAS software Amins AI Software Leica LAS X – FLIM, Phasor FLIM, FCS Anaconda (Python) FiJI ImageJ |
| Hardware | CPU 12-core RAM 64 GB GPU Nvidia A40 8GB |
| Booking | Calpendo (“13 – Ideas AI, LAS X”) |
| Access | Virtual Desktop Infrastructure (“13 – Ideas AI, LAS X”) |
Workstation operated in collaboration with the Flow Cytometry Core Facility, that provides access to FlowJo software for flow cytometry data analysis. It can be used for more sophisticated analysis of FCS files exported from ScanR Analysis software. In addition, R programming language is also available.
| Software | FlowJo software R software |
| Hardware | CPU 8-core RAM 32 GB GPU not dedicated |
| Booking | Calpendo (“14 – FlowJo”) |
| Access | Virtual Desktop Infrastructure (“14 – FlowJo”) |
Huygens Core compute engine is available on the powerful server with two GPUs, that allows simultaneous batch deconvolution of files up to 100 GB. The Huygens Remote Manager (HRM) interface allows user to configure and run deconvolution batch jobs.
| Software | Huygens Core – Widefield & Brightfiled, Confocal, Spinning Disk & SoRa, Multi Photon, STED 3D, Light Sheet, Object Stabilizer, Chromatic Aberration Corrector |
| Hardware | CPU 24-core RAM 1760 GB GPU 2 x Nvidia RTX A5000 24GB |
| Booking | Not needed |
| Access | Huygens Remote Manager |