The Experiment Annotator
FlowJo's Experiment Annotator is a graphical user interface for describing an experiment's staining setup using attribute/value pairs. It makes setting up an experiment easier and faster for clinical sites and high throughput research labs. It also allows the user to edit sample descriptions after data collection.
The evolution of flow cytometry is moving toward plate based assays. Working with collections of 96 or 384 wells at a time adds new dimensionality to the biological questions that can be asked. The high throughput approach meshes very well with FlowJo's structured approach to groups of samples. You can easily create groups by row, column or plate, so that you can analyze the resulting data systematically, and identify the wells of interest efficiently.
The structure of your analysis comes from keyword metadata embedded in the FCS files. Although it is possible to assign keyword annotations to samples after they have been collected, it is strongly recommended that keywords be assigned prior to collection. Analysis keywords can be saved into BD DiVa experiments, or copied to the FlowJo workspace acquired with the Cypod acquisition module.
Although it shown here as a 8 x 12 plate, the dimensions of the grid may be anything you want. There is nothing that prevents tube-based collection from also using the plate editor to annotate samples. You can even switch dimensions on the fly to mark, e.g., every fourth sample with one keyword, and every fifth sample with another.
Mouse over the red dots for more details.
The File menu:
- Save your annotation and reopen it at a later date.
- Open... Open a Plate Annotation that you have previously saved.
- Close Close the Plate Editor
- Save Save the Plate Annotation
- Save as... Save the Plate Annotation with a new name
The Edit menu:
- Cut, Empties the selected well or wells of their current content.
- Copy Copy selected items to the clipboard
- Paste Paste contents of the clipboard at cursor
- Select All Select all cells
- Clear Clear contents of currently selected item
The Plate menu:
- Write DiVa Acquisition File, Writes an XML file that, when opened on the Cytek machine, will annotate the sample data during acquisition.
- Move Wells to Workspace, Transfers all wells with assigned attributes to the workspace.
- Add Keywords from File, Imported Attribute/Value pairs separated by a carriage return in a .txt file to populate the List Window with a customised list of parameters.
- Clear Keywords, Empties the List Window Attribute/Value list.
- Add Staging Well, Adds more empty Staging Wells if needed.
- Set Plate Dimensions, Enter the number of rows and columns you want in your plate.
- Toggle Notation, Changes the markings within the cells from Row/Column notation (A1, A2, A3 for example) to numbers only, 1-96, left to right, top to bottom.
The Help menu:
- Using the Plate Editor Opens this manual page
- Protocol Specification Opens the Plate Editor Specification manual page
- Hide Instructions Hides the instructions at the top of the Plate Editor
