For Flow Cytometry & Fluorescence Assisted Cell Sorting (FACS) services, we offer instrument training, assisted sessions and project based work-flow optimization. In addition, we offer support on all Flow cytometry analysis software applications that are available on our Cyto analysis workstation.
Communication:
Training and Assistance can be requested via the request forms in PPMS.
Please send any remaining inquiries to cytometry@ist.ac.at → the cytometry team will reply to your ticket query!
More info about…
Usage rights on our cytometers require a trainnig by IOF staff. This consists out of two individual trainings. The first with beads, and the second with your sample. A third training might be necessary to assert proficiency.
After the training, users get novice rights, meaning they can use the cytometers within our working hours (including start-up and shutdown). After a few sessions users can request autonomous rights which allows usage outside of IOF office hours.
There are no autonomous user rights on Aria, as start-up and shut down are done by IOF staff.
Our assisted sessions are designed to provide expert guidance and hands-on support for researchers at various stages of their experiments. This service is particularly beneficial if you are:
- Initiating a new experiment and require assistance with optimizing software settings.
- Less confident with system operation and prefer the comfort and assurance of expert support during your experimental runs.
- Conducting a one-time experiment and do not require full instrument training, allowing you to access our capabilities without extensive commitment.
- Working with sensitive samples or complex protocols where expert oversight can significantly enhance experimental success and data quality.
- Returning to the system after a prolonged period of inactivity, or anticipate infrequent future use, and wish to refresh your skills with professional assistance.
Our experienced staff will work alongside you to ensure optimal results and efficient use of the systems.
For more intricate and long-term requirements, we offer multi-day application optimization projects. These projects are tailored to address complex experimental challenges and require initial project discussion and approval from the Principal Investigator (PI).
This service is ideal for situations demanding iterative assistance from our Cyto team and in-depth optimization, such as:
- Defining target populations when, for example, starting from scratch with a new cell type.
- Optimizing sample handling: Investigating the impact of sorting conditions, such as optimal temperature maintenance or the effects of agitation on cell integrity and viability.
- Determining optimal sorting parameters: Testing various nozzles sizes and identifying the most suitable sorting format to meet specific downstream application requirements.
* Assistance and project support on Cytometers is also available to users without a training.
This is especially meant for users which will not sort repeatedly, or have special requirements such as sorting for downstream applications like sequencing or -omics approaches.
While we cannot guarantee a positive outcome of your experiments, we highly recommend to make use of our expertise in experimental set-up!
- BC Cytoflex LX Cell Analyser (room i04.EG.017): book in PPMS
This advanced analyzer is ideal for high-parameter cell analysis, offering exceptional sensitivity and multi-color detection capabilities. The plate-reader mode also allows full automation of up to 96 samples at once.
CytoFlex is a pure analyzer and has no sorting capabilities!
- BD FACSAria III Cell Sorter(room i04.EG.017): book in PPMS
This high-speed cell sorter provides precise and efficient cell isolation for a wide range of research applications. It is the most versatile and powerful of sorters we have in our machine park and can accommodate almost any experiment.
This system requires startup and shutdown procedures to be performed by the Cyto team staff. A one-hour charge will apply for each of these procedures. Should an additional aseptic startup or shutdown be necessary, users must book an extra hour during their session, and an additional 30 minutes will be charged beyond the conventional startup or shutdown fees.
In exchange, the System will be ready for you when your booking starts, and you do not need to worry about shutdown, letting you take care of your cells immediately.
- BD FACS Melody Cell Sorter(room i24.O2.014): book in PPMS
This smaller sister of our BD FACSAria provides user-friendly reliable cell sorting, making advanced cytometry accessible to more researchers (especially the ones situated in i24). This System has no red laser, so opt for our other systems if you require this laser line.
- SONY SH800 Cell Sorter(room i04.EG.017): book in PPMS
This benchtop cell sorter is renowned for its simplicity of use and highly accurate sorting capabilities, particularly with its single-use chip technology. It is not suited for high parameter analysis due to it’s single interrogation spot (all lasers excite at once), so opt for our other machines if you have overlapping fluorophores.
Available remotely, this workstation provides Cytometry Analysis software for comprehensive data analysis.
| SONY SH800 Cell Sorter |
BD Aria III Cell sorter |
BD FACS Melody Cell Sorter |
BC Cytoflex LX Cell Analyzer |
|
| Can analyze |
✔️ |
✔️ |
✔️ |
✔️ |
| Excitation lasers |
405, 488, 561, 638nm |
375 OR 405, 488 561, 633nm |
405, 488, 561nm |
355, 405, 488, 561, 638, 808nm |
| multiple interrogation spots (better for multicolor) |
❌ |
✔️ |
✔️ |
✔️ |
| can sort (recover) cells |
✔️ |
✔️ |
✔️ |
❌ |
| 4-way sorting | ❌ | ✔️ | ✔️ | ❌ |
| Sample input format | 5ml cyto tube or 15ml falcon | 5ml cyto tube | 5ml cyto tube | 5ml cyto tube or 96 well plate (flat- or U-bottom) |
| Sample output format | 5ml cyto tube, 15ml falcon or plates (up to 384 well) | Eppendorf tubes, 5ml cyto tube, 15ml falcon or plates (up to 384 well) † | Eppendorf tubes, 5ml cyto tube or plates (up to 384 well) | – |
| Can cool to 4°C | ✔️ | ✔️ | ✔️ | ❌ |
| Can set other temperatures than 4°C | ❌ | ✔️ | ✔️ | ❌ |
| Available on weekends (Set up & Shutdown by user) | ✔️ | ❌ | ✔️ | ✔️ |
| Available only in IOF office hours (Set up & Shutdown by IOF) †† | ❌ | ✔️ | ❌ | ❌ |
| Aseptic Start-up available | ❌ | ✔️ | ❌ | – |
| UV sheath-sterilization available | (✔️) | ✔️ | ❌ | ❌ |
| Bio-safety level | BSL1 | BSL1 | BSL1 | BSL1 |
† smaller formats like PCR tubes are available using a custom adaptor.
†† IOF office hours: Mon to Thu: 09:00 to 17:30, Fri 09:00 to 15:30.
Cytometry Workstation:
The Cyto Workstation is a physical Workstation similar to our physical image analysis workstations. You can find information on how to use them here. Rights are given after the Intro to Newcomers and no additional training is required, but we are always happy to support you!
Available Cytometry Analysis software:
For the analysis of Flow Cytometry data, we provide various cytometry analysis software applications on our analysis workstation:
CytExpert: A powerful software package from Beckman Coulter, designed for instrument control, data acquisition, and comprehensive analysis of CytoFLEX data. This software can ONLY handle data From CytoFLEX.
CytExpert is free to download on the BC Homepage → here
Cytoflow: An open-source, point-and-click program and Python library for quantitative flow cytometry, emphasizing metadata integration and workflow-based analysis. It is the most complex of the programs and allows advanced analysis routines including complex statistics and model-fitting.
Cytoflow is free to download → here
Kaluza: Beckman Coulter’s advanced software for efficient analysis of multicolor flow cytometry data, capable of processing large datasets with an intuitive interface.
Kaluza is proprietary Software (Beckman Coulter) and only available on our Cyto-Workstation.
FlowJo: Widely used software platform for flow cytometry analysis, providing a comprehensive environment for data viewing, analysis, and interpretation with advanced features for various research needs.
FlowJo is proprietary Software (FlowJo LLC) and only available on our Cyto-Workstation.
We have a collection of FlowJo plugins installed. You can find a descriptive list below. If you require any additional plugins, get into contact with us.
| Category | Plugin Name | Description |
| Dimensionality Reduction | UMAP | Projects high-dimensional data into 2D space, facilitating the visualization of complex flow cytometry datasets with numerous parameters. |
| TriMap | Similar to UMAP and t-SNE, TriMap excels at preserving the global structure of data while reducing it to two or three dimensions, enhancing the interpretability of large datasets. | |
| PaCMAP | Preserves both local and global data structures effectively, making it useful for visualizing intricate patterns in high-dimensional flow cytometry data. | |
| Phate | Maintains the integrity of local neighborhoods and the overall global structure in lower-dimensional spaces, aiding in the accurate representation of complex datasets. | |
| Clustering & Population Analysis | FlowSOM | Utilizes self-organizing maps (SOM) to cluster and visualize flow cytometry data, enabling the identification of intricate and diverse cell populations. |
| Phenograph | Partitions high-dimensional single-cell data into distinct phenotypic populations, facilitating the discovery of unique cell subsets within complex datasets. | |
| Xshift | Specializes in identifying rare cell populations by clustering data based on density and proximity, making it effective for detecting small, uncommon groups within large datasets. | |
| Flowmeans | Automatically identifies cell populations through non-parametric clustering combined with segmented-regression-based change point detection, streamlining the discovery of distinct cell groups. | |
| T-REX | Integrates dimensionality reduction with differential analysis to identify and highlight clusters that differ between two specified conditions, enhancing comparative studies. | |
| Data Visualization | ClusterExplorer | Generates summary plots from clustering results and maps these clusters onto dimension-reduced spaces, making it easier to interpret and visualize complex data relationships. |
| ViolinBox | Creates various visualization plots, including violin plots, box-and-whisker plots, and Raincloud plots (a hybrid of violin plots and raw data scatter), effectively illustrating data distributions and variability. | |
| Data Preprocessing & Quality Control | DownsampleV3 | Reduces the number of events in a dataset to normalize population sizes or accelerate computations, particularly useful for managing large datasets or balancing sample sizes before analysis. |
| PeacoQC | Performs quality control by detecting and removing outliers caused by issues like clogs or flow rate changes, ensuring cleaner and more reliable flow cytometry data for subsequent analysis. | |
| Euclid | Assesses the quality of clustering results in high-dimensional datasets using statistical methods like ClustRCheck and the Taylor index, ensuring robust and reliable clustering outcomes. | |
| AutoGateCategorical | Automates the creation of gates based on categorical parameters, simplifying the initial stages of data analysis by streamlining the gating process. | |
| cyCombine | Integrates data across different sorting days to reduce variability among batches, ensuring consistent results when analyzing similar sample types collected at different times. | |
| Supervised auto-gating | ezDAFi | Implements a supervised auto-gating strategy that applies gates based on models trained from manual gating, enhancing the efficiency and consistency of cell population identification. |
| Elastigate | Mimics manual gating practices through a supervised auto-gating approach, enabling accurate and automated identification of cell populations with a high degree of precision. | |
| SVM | Utilizes support vector machines (SVM) to apply gates based on previously defined manual gates, facilitating rapid and consistent population identification through machine learning techniques. | |
| Calibration & Labeling | FJCalibration | Calibrates derived parameters by performing linear regression between automatically detected peaks and known molecular values from MESF beads, ensuring accurate and reliable data calibration. |
| Astrolabeimport | Automatically labels numerous subsets within large datasets, significantly speeding up the process of identifying and annotating specific cell populations in complex datasets. |