How do I use ImageJ with FCS Express?
ImageJ is free open-source software designed to process and analyze images and image data sets. Through the use of macros and plugins users can automate tasks and create custom tools. De Novo Software has created macros and plugins for ImageJ that allow you to export your imaging data from ImageJ to FCS Express .
Once your data is properly exported from ImageJ, you can use FCS Express for 2D plot visualizations, Histograms, Gates (equivalent to thresholding), and advanced statistics and to move between images, plots, and cell galleries to get information on populations, sub-populations, and even the single cells.
The best way to see what FCS Express can do for your ImageJ data sets is to download a free 30 day trial of the software. You can also watch our short videos and recorded webinars to learn about specific topics, or explore data yourself with one of our many ImageJ application examples below. Of course if you have any other questions you can contact our knowledgeable support team at support@denovosoftware.com.
ImageJ Macros for FCS Express Image Cytometry Data Analysis
- DNSMacroExample.ijm: Export Data from ImageJ to FCS Express
- DNS-IJXwriter.xlsm: Automatically create a .ijx Analysis Configuration File from your data directory(recommended; macro written by Peter Haub)
- DNSAnalysisCreator.ijm: Manually create a .ijx Analysis Configuration File from your data directory
Application Examples
FCS Express can also be used in conjunction with ImageJ to get data from your images. By using ImageJ to segment your images and the macros above you can quickly export and analyze your data with FCS Express. See for yourself while learning FCS Express with our ImageJ Export tutorial. You may also explore the layout using the free FCS Express Reader: Image J Analysis with FCS Express.
Multiwell plate data processed in ImageJ can be exported using the ImageJ macros above and analyzed with FCS Express. You may also explore the layout using the free FCS Express Reader: Image J Analysis with FCS Express .
Histological sections with tiled images (i.e., contiguous fields of view) which have been segmented in ImageJ can be exported and stitched together in FCS Express, using the ImageJ macros above. You may explore the layout using the free FCS Express Reader: Image J Analysis of Tiled Images with FCS Express.
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Installation
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Licenses
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- 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?
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- Can I share my USB dongle or countercode license with another user?
- 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?
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- 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?
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Layouts & Loading Data
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- 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 a Sony MA900 Index Sort file into FCS Express?
- How can I load data from the BD Accuri C6 Flow Cytometer?
- How can I load MACSQuantify files that were exported from MACSQuantify software version 3.0.1?
- 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?
- How do I work with images from the Thermo Scientific Attune CytPix?
- What is the Elapsed Time setting in the Gallios software and how do I convert it to real time?
- Why are iterations in my Data List gray?
- 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?
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Data Analysis
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- Caveats when using Biexponential Scaling with automatic Below Zero parameter detection in the presence of outliers.
- How can I create a merged data with equally-sized downsampled samples?
- How can I do pre-processing for high-dimensional data analysis?
- How can I explore tSNE/UMAP plots?
- How do I use SPADE?
- What is FlowSOM?
- What is T-SNE?
- What is UMAP?
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- 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?
- When acquiring spectral data, should my single-stained controls be "as bright or brighter" than my fully-stained sample?
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- Can a set of quadrants be both percentile and floating?
- 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?
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- Can I create an output file that contains the same plot from each data file on a single page?
- How can I export my spectral data files from FCS Express with unmixing applied?
- How can I successfully export a GatingML file?
- How do the batch processing run modes differ, and why would I use them?
- Why do I get an “Old format or invalid type library” error when using Microsoft excel during batch analysis?
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- 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?
- How do I calculate EC/IC Anything?
- 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 have percentages reported by quadrants changed after updating to FCS Express version 7.20.20?
- Why is the Geometric Mean being reported as NaN or ##ERROR##?
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Image Cytometry
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- 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?
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- 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 can Attune™ CytPix data sets with images (.ACS files) be merged for high dimensional 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?
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FCS Express on Mac
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Upgrading FCS Express
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- Can different versions of FCS Express exist on the same computer?
- How are existing quadrants handled when an old layout is opened in version 7.20 and later?
- 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?
- Version 4 Internet Dongle Retirement
- 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?
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Clinical & Validation Ready
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- 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?
- 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?
