User guide¶
The walkthrough is a sequence of small screens, each asking one question.
If you have not run the wizard at all yet, do your first walkthrough first.
What the landing screen carries¶
A Cell templates list — seeded with your host's files, and yours to edit. It is the library every import starts from, unlike files loaded at the cell-templates step itself, which a re-import discards. Everything else the wizard needs, it asks for at the step that needs it.
How steps are chosen¶
Before each screen BIWT walks an ordered list of predicates and shows the first step whose condition is true. A step whose condition is false is skipped entirely.
| # | Step | Shown when |
|---|---|---|
| 1 | Spot deconvolution | Data has probability columns and spatial coordinates, and you have not been asked yet |
| 2 | Cluster column | No column selected yet, and you are not doing spot deconvolution |
| 3 | Spatial query | Data has spatial coordinates and you have not answered yet |
| 4 | Edit cell types | The keep/merge/delete choices have not been made |
| 5 | Rename cell types | Final names have not been assigned |
| 6 | Cell counts | You are not using spatial data, and counts are unconfirmed |
| 7 | Positions | Positions have not been set |
| 8 | Cell templates | Templates have not been assigned |
When every condition is false, BIWT assembles the result and hands it to the host.
The step numbers in the title bar are relative
BIWT numbers steps by which ones are actually being shown, so the same screen gets different numbers on different paths. Using spatial data, Positions is "Step 5"; without it, cell counts takes that number and Positions becomes "Step 6". The pages in this guide are deliberately unnumbered — follow the names, not the count.
Two consequences:
- Your answers change which screens exist. Saying "yes" at the spatial query removes the cell-counts screen, because spatial data already determines how many cells there are.
- Going back can invalidate later choices. If you navigate back and change an earlier answer, BIWT clears the downstream state that depended on it. You will be asked those questions again.
The two screens that aren't steps¶
The domain editor is a dialog, not a step. It opens on its own the first time the positions screen appears if BIWT detects a mismatch between your data's extent and the host's domain, and it can be reopened at any time from the positions screen.
Finishing up describes what BIWT hands back.
A note on units¶
BIWT distinguishes data units (whatever is in your file — e.g. Visium pixels) from host units (what the simulation uses — microns, for PhysiCell). It never guesses a unit name from your data. Where a conversion is needed, you supply or confirm a scale factor in the domain editor. This matters most for imaging-derived coordinates, where the raw numbers can be in the thousands while the domain is typically much smaller.