Floreada.io supports the FCS2.0, FCS3.0 and FCS 3.1 file formats. To open a file, click "File" then "Open File(s)". This opens a menu where you can select one or more FCS files from your computer to analyze. When selected, files are parsed and displayed in your browser as dot plots. When files are loaded in the browser, they remain entirely on your computer. No data is sent to our servers.
If you try to open a file and you receive an error message, that particular file is not currently supported. Please contact us if you encounter any problems. Although there is an official standard way in which FCS files are supposed to be internally organized, cytometers are notorious for breaking the rules when exporting their FCS files. If you are able to send us a file from your specific cytometer, we can usually add support for it within a day or two.
The "FCS files" file tree lists all open files grouped by project and highlights the name of the file you are currently viewing. Each file is grouped into a project using the "$PROJ" keyword in its FCS file. There is no way to change this behavior at this time.
FCS files contain a "TEXT" section in the file format which contain key-value pairs. Many of these are used to interpret the data in the file correctly. Others contain information such as the number of events in the file, of the project name. You can view all the keywords in the currently displayed file by selecting "Keyword" button in the side panel.
Keywords can not be added or edited at this time.
File Name Pattern
By default, the name that is given to an FCS file is taken from the $FIL keyword stored in the file. You can change this naming pattern to anything you want though. To set the pattern, in the main menu go to "Settings"->"File Name Pattern".
Some common options which you can add to the pattern include:
- The $FIL keyword in the fcs file
- The $WELLID keyword in the fcs file
- The local name that your file is saved as on your computer
You can use one or more of these to construct a pattern that will be used when naming all files in the future. It does not change the names for files that have already been loaded. You can also include other characters, as well as other keywords in the file. We just have shortcuts for these since they are likely to be the most commonly used.