Can I use the FlowAI script in FCS Express?
Yes, with FCS Express 7, you can run FlowAI directly within FCS Express using Pipelines. FlowAI is used to check the quality of the data based on the flow rate, signal acquisition, and dynamic range.
In FCS Express 6 you can run the FlowAI script via R Integration. Due to the script’s reliance upon $TIMESTEP and $PnR keywords, it will need to be modified as necessary for each file to processed.
What is Flow AI?
FlowAI is an algorithm available to be used for quality control of flow cytometry data written in FCS3.0 file format or later. Developed by Gianni Monaco et al, FlowAI can be used to detect and remove spurious events or regions automatically by evaluating flow rate, signal acquisition, and dynamic range. FlowAI checks data for:
- Flow rate steadiness using the $TIMESTEP keyword
- Signal acquisition stability by plotting each channel's median vs. time using equal-sized bins (typically displayed as Levy-Jennings-type plot)
- Dynamic range - identification and removal of outliers from lower limit of $PnR and margin events from upper limit of $PnR
Executing FlowAI in FCS Express
With the January 2021 release of FCS Express 7, FlowAI has been added as a standalone Pipeline step. FlowAI can now be run directly within FCS Express as a pre-defined algorithm without any external software requirements (i.e. R Integration is no longer required).
FlowAI evaluates data using specific keywords and requires non-compensated parameters. Because of these requirements, modifications to the FCS Express Layout Options are needed to run FlowAI with Pipelines.
- When running FlowAI with Pipelines, the uncompensated data, or raw fluorescence data, must be processed. To enable the use of uncompensated parameters on your layout:
- Navigate to the FCS Express Layout Options.
- In the Compensation Options, set the "New Compensated Parameters Should:" to "Append to data after uncompensated parameters".
- Uncompensated parameters will now be accessible on the layout. Uncompensated parameters will be indicated by the absence of the suffix "- Comp" in the parameter list.
- For further details on working with uncompensated data, see the Compensation Options section of our manual.
If you plan to use FlowAI with R Integration, modifications will need to be made to the FCS Express User Options and R script for each data file to be processed.
- When running FlowAI with R Integration, the uncompensated data, or raw flourescence data, are processed. Since plots are displaying compensated data by default in FCS Express, the compensated data are processed when executing FlowAI via the R Application Bridge in FCS Express.
FlowAI makes use of additional R packages that must be installed via R prior to using in FCS Express.
- To install FlowAI, start R and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("flowAI", version = "3.8")
To edit the time units options, click File tab > Options > Data Loading Options > FCS File Options > set dropdown for FCSv3.0 time units to Preserve FCS File Values (outlined in red below) > click OK.
- Monaco G, Chen H, Poidinger M, Chen J, de Magalhaes J, Larbi A (2016). “flowAI: automatic and interactive anomaly discerning tools for flow cytometry data.” Bioinformatics, 32(16).10.1093/bioinformatics/btw191.
- Can I get more information regarding the Add-Ons that can be purchased with a license?
- Can I lock my template based on an electronic signature?
- Does FCS Express have any features to help meet 21 CFR Part 11 compliance?
- Does FCS Express have Quality Control features?
- Does FCS Express offer Single Sign On capability?
- How do I configure SQL Server to host a database for FCS Express?
- What database options are available when I purchase the Security option?
- What is the difference between the different types of Users that are available with a Security and Logging license?
- What is the difference between the Logging option and System Level Audit Trails?
- What SQL Server permissions are needed?
- Can I track usage of the internet dongle?
- Can I try out the Internet Dongle before I make a purchase?
- Can the administrator log users out?
- Do you have to be connected to the internet at all times with the Internet dongle?
- How can users be added to an internet dongle license?
- How do I activate my dongle?
- How do I change my internet dongle/site license password?
- How many people can be logged in at the same time?
- How many user accounts can I create?
- If a user left the computer running can the user log themselves out from another computer?
- What are the differences between the internet dongle and network licensing options?
- What happens if I lose my internet connection?
- What happens if the user leaves the computer without logging out?
- What happens to the users login in case of an unexpected interruption? For instance, a software crash, power failure, etc.
- Why am I receiving a message that FCS Express cannot connect to De Novo Software servers?
- Can I mix Flow, Image, and Plus site licenses? Can I mix site licenses with and without add-ons?
- How are site licenses billed?
- How do you calculate the number of site license users?
- How many people can be logged into the site license at the same time?
- How many user accounts can I create on the site license?
- Can I convert my Cytek license from the countercode licensing option to another licensing option?
- How can I claim my license purchased through BD Accuri Cytometers?
- How can I claim my license purchased through BD Biosciences?
- How can I claim my license purchased through Nexcelom Biosciences?
- How can I claim my license purchased through Sysmex-Partec GmbH?
- How can I claim the FCS Express license that came with my Cytek instrument purchase?
- Can FCS Express integrate Python scripts?
- Can I use the FlowAI script in FCS Express?
- Can I use the FlowClean R Script with FCS Express?
- How can I recreate ratiometric data acquired in FACSDiva?
- How do I use R Integration with FCS Express?
- How does FCS Express implement software compensation?
- If my data does not have a Time parameter, can I create one?
- What is compensation?
- What is the compensation workflow in FCS Express?
- Can I customize the display of my data from different instruments?
- Can I disable the live updating feature?
- How can I display all of my detectors for my Cytek data?
- How can I set FCS Express so my FCS 3.0 biexponential data looks the same as it did in the BD FACSDiva software?
- How do I display Summit data in FCS Express as it appears in the Summit Software?
- How do I fix the biexponential axes on a plot?
- How do I rescale CytoFLEX data so it displays as it did at acquisition?
- How do I update my density and contour plots created in Version 4 to use the newest color palette?
- What are resolution options?
- What is Biexponential and Hyperlog Scaling?
- What is the best way to set FCS Express to display FCS 3.0 data from FACSDiva on a 4 decade log scale?
- Where can I get more information regarding DNA analysis using the Multicycle AV?
- Why can’t I change my plot axis labels from the Name keyword to the Stain keyword?
- Why do my dot plots appear sparse and blocky?
- Why is the text on the right most label cut off my plot?
- How are statistics in FCS Express calculated compared to how they are calculated in BD FACSDiva?
- How can I display my statistical data in Scientific Notation?
- What is “Stain Index” and how do I calculate it with FCS Express?
- What is MFI (Mean or Median Fluorescence Intensity) and how do I calculate it in FCS Express?
- Why is the Geometric Mean being reported as NaN or ##ERROR##?
- Are Beckman Coulter LMD files unique?
- Can I find a support resource page for the analysis of Cytek data in FCS Express?
- How can I easily create the "filename" column in the "ExtraKeywordsTable.csv" file?
- How can I load data from the BD Accuri C6 Flow Cytometer?
- How do I change the display in my plots from one data file to another data file?
- How do I export .ICE files from Thermo Cellomics HCS Studio?
- How do I tell FCS Express what plate size to use if that information is not included in the data file?
- How do I upload files to the De Novo Software FTP site?
- How do I use BD Accuri CFlow files with Multicycle DNA analysis in FCS Express?
- What is the Elapsed Time setting in the Gallios software and how do I convert it to real time?
- Why are there sometimes access violations when I save and load files?
- Why do I get the message that a data file exported from a FACSDiva™ Experiment is invalid?
- How do I adjust the axes to display small particle data from Amnis CellStream?
- How do I choose which images and parameters to view in a Data Grid?
- How do I export/save data from IDEAS software and load it in FCS Express?
- How do I make my images in the data grid larger?
- How do I pseudo-color images in a data grid?
- How do I work with Amnis derived image cytometry data in FCS Express?
- Can I display heat maps with my Image Cytometry data?
- Can I work with data from PerkinElmer Instruments?
- Do you offer 21 CFR Part 11 compliance options for the Image Cytometry Version?
- Do you offer image segmentation or image analysis?
- How do I use CellProfiler Data with FCS Express?
- How do I use ImageJ with FCS Express?
- What file formats are compatible with FCS Express Image Cytometry?
- Where can I find Nexcelom Resources and Applications?
FCS Express on Mac
Upgrading FCS Express
- Can different versions of FCS Express exist on the same computer?
- How can I view and convert my V3 layouts to FCS Express 7?
- How do I import my version 3 security databases into newer versions of FCS Express?
- How do I update Density Plots created in Version 4?
- Is there an upgrade discount from earlier versions of FCS Express?
- Why are my density plots from V3 not displayed correctly in later versions?
- Why are there fewer outlier dots on my FCS Express 5 and later density plots than in V4?