Workspaces
A workspace saves your analysis, not your data: the gate tree, each file’s
compensation, file names and groups, plus references to the FCS files it applies
to. It is a single .cgws file.
- Ctrl+S (Cmd+S on macOS), or Save in the toolbar — save
- Ctrl+Shift+O, or Load in the toolbar — open a workspace
The first save of a new analysis asks where to put the file. After that, Save
writes to the same file. There is no Save As yet: to keep a copy, copy the
.cgws file.
Saving is never blocked by your license. Saving is how work already done survives, so it works with no license, during a trial and after a license expires. See Licensing.
What is in it
Section titled “What is in it”| Saved | Not saved |
|---|---|
| Gates, the hierarchy, gate colours and which gates are hidden | A copy of your FCS files |
| Each file’s compensation — its matrix, and on or off | Axis scales — on reopening, each axis gets the suggested scale again |
| The open files, and which one was active | Zoom, and the multi-plot grid |
| File display names (renamed files) and file groups | Plot annotations |
| Parameter names you edited, and parameter-name templates | Proposed gates you have not accepted |
| The population you were drilled into, and the X and Y parameters of the main plot | Graph Builder, batch and dose-response settings |
| Populations imported from a labels file, stored inside the workspace | Preferences and theme |
| Where AI-proposed or data-driven gates came from |
Because it references rather than copies, a workspace is small and your data stays where your lab put it. The trade-off is the section on moved files, below.
Compensation
Section titled “Compensation”Each file’s compensation is saved separately — matrix and on/off — and a workspace reopens exactly as saved, file by file. A file the workspace has no saved compensation for opens with its own acquisition matrix applied.
Workspaces saved by version 0.1.x stored one matrix for the whole workspace. They reopen with that matrix applied to every file if compensation was on when saved, and with every file uncompensated if it was off. The next save writes the per-file form. See Compensation.
Older workspaces
Section titled “Older workspaces”Workspaces from earlier versions open in this one. Quadrant gates saved by 0.1.x stay linked, so moving the crosshair still moves all four. A workspace written by a newer version than yours is refused with “Unsupported workspace version… Please update the application.” — update, then open it again.
Auto-save and recovery
Section titled “Auto-save and recovery”Auto-save never overwrites your workspace file. It writes a separate recovery copy:
next to the workspace (<name>.cgws.autosave) once you have saved it, or in the
app’s own data folder for an analysis you have not saved yet.
- Opening a workspace that has newer auto-saved changes asks “Recover unsaved changes?” — open the recovered version, or the last one you saved.
- Starting the app after it closed with unsaved work that was never saved as a workspace asks “Restore unsaved analysis?”. Choosing No discards it.
Set how often it runs, or turn it off, under Preferences → General → Auto-save interval (Off, 15 seconds to 2 minutes; 30 seconds by default).
Choosing Don’t Save when you close the app discards the recovery copy — except when your license has expired, where it is kept so a lapsed license can never cost you the only copy of your work.
When files have moved
Section titled “When files have moved”The workspace stores the full path of each FCS file. If a file has moved or been renamed since you saved, the rest of the workspace still opens, and a Missing Files list appears at the top of the file list.
- Click Locate beside a file and pick it in its new place. Its compensation, display name and group come with it, and the gates are evaluated on it.
- Repeat for each file — files are located one at a time.
Dismiss hides the list; the files are still missing. Saving while any file is missing warns you first (Missing files) and offers Save anyway, which saves the workspace without those files. (Before 0.2.2, saving after Dismiss dropped them without asking.)
This is worth knowing before it happens, because it is the predictable consequence of referencing files by path: a workspace that points at data on your local disk will not reopen with its data on a colleague’s machine. They can locate each file themselves, or you can agree on a path both of you can reach.
Closing every file
Section titled “Closing every file”If you close every file in a workspace, the app detaches from that workspace file. The next Save then asks where to save — suggesting the old file — so an empty analysis cannot silently overwrite a saved one.
Recent files and workspaces
Section titled “Recent files and workspaces”The small arrows beside Load and Open File in the toolbar list recent workspaces and recent files. The welcome screen lists both as well.
Renaming files
Section titled “Renaming files”Double-click a file in the file list to rename it. Enter keeps the new name, Escape cancels. This changes the label in the analysis — and the name saved in the workspace — not the file on disk, which is useful when acquisition filenames are long, cryptic, or identical apart from a digit.
Practical habits
Section titled “Practical habits”Save before you batch. Batch analysis across many files is the point at which you least want to rebuild a strategy.
Save a workspace alongside every exported figure. A figure without the workspace that produced it cannot be revisited. See what makes a result reproducible.