Rename cell types

Shown when: always.

The question

Each cell type that survived the edit step gets a text field, pre-filled with its first original name. Change any of them, or accept them all.

Original name on the left, the name that will reach your simulation on the right.

The names you set here appear in the type column of the output, in cell_type_map, and as the keys of cell_templates. Whether they become cell definitions in a simulation config is the host's decision — BIWT generates none.

Why bother

Two reasons.

Cluster IDs are not names. If you selected a seurat_clusters column, your types are currently 0, 1, 2. A config full of <cell_definition name="7"> is unreadable and unmaintainable.

Matching the host's existing definitions. If your simulation config already defines a tumor cell type, naming yours tumor lets them line up instead of creating a near-duplicate.

Suggestions from the host

If the host application passed BIWT its current cell-type names — Studio does this from its cell-definitions tab — BIWT looks for a match and offers it as placeholder text in each field.

A case-insensitive exact match wins outright. Failing that, BIWT compares the names for similarity and takes the first host name it accepts, in alphabetical order — so Fibroblasts matches a host Fibroblast, but nothing is ranked and you get the first acceptable name, not the best one.

Digits are treated as significant rather than as spelling noise, so M1 Macrophage is never suggested for M2 Macrophage, nor a CD4 type for a CD8 one, even though those names are otherwise near-identical. Pairs distinguished by a non-numeric qualifier — PD-1hi versus PD-1lo — are not caught; a host with names of that shape can supply its own comparison via create_biwt_widget(name_matches=…), which replaces BIWT's rule entirely.

Placeholder text only shows in an empty field, and every field arrives pre-filled with your original name. Clear a field and it appears, grayed out, as Suggestion: <host name>.

Nothing is filled in for you, so if you want the suggested name you have to type it. An empty field is accepted as an empty name — only duplicates are blocked — so do not leave one cleared just to keep the hint in view.

Naming rules

Exact duplicates are blocked. Two types cannot share a name; BIWT warns and keeps you on the screen.

Case matters. CD8 and cd8 are treated as different names and both are allowed, because PhysiCell treats them as distinct. If you meant them to be the same type, merge them at the previous step instead.

Pick names your config can live with

Avoid spaces and punctuation if your downstream tooling is picky about XML attribute values. CD8_T_cell travels better than CD8+ T cell (exhausted).

Next

Cell counts → if you are not using spatial data; otherwise positions →.