Using folder names

import { FileTree } from ‘@astrojs/starlight/components’;

When folders encode your experiment (for example /data/DrugA/24h/img01.tif), you can use a folder pattern to tell PhenoMe what each folder represents.

Simplest case: folders by treatment

- data/ - Control/ - img_01.tif - img_02.tif - Drug1/ - img_01.tif - img_02.tif

from phenome import get_metadata_from_path

metadata_fn = get_metadata_from_path(".../(condition)/(filename).*")
pheno.find_files("data", metadata_fn=metadata_fn)

Pattern rules

A pattern matches a file path from right to left. You choose the names of the tokens in parentheses—they become the column names in your results.

Token	Meaning
`...`	Matches any parent folders you do not care about.
`(name)`	Captures a path segment into the `name` metadata field.
`.*`	Matches any file extension.

For example, (drug) or (condition) are common choices. Avoid spaces inside the parentheses and keep names consistent across your experiments, as downstream filters are case-sensitive.

Multiple levels

For a folder like /data/Plate1/Drug1/24h/img_001.tif:

metadata_fn = get_metadata_from_path(
    ".../(plate)/(drug)/(time)/(filename).*"
)

Common mistakes

Mistake	Why it fails	Correct version
`(drug)/(filename)`	Missing `.../` to match parents.	`.../(drug)/(filename).*`
`.../(drug)/img.tif`	Hardcoded filename; matches one file.	`.../(drug)/(filename).*`
`(drug)/(drug)/(filename)`	Duplicate key `drug`.	`(plate)/(drug)/(filename).*`

When folder patterns are not enough

Switch to a custom function (see Advanced patterns) when:

Paths mix encodings (some fields in folders, others in filenames).
You need to cast values (int, float, stripping units).
You need derived fields (for example is_control).