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Update README.md #29

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Sep 10, 2024
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Update README.md #29

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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -91,7 +91,7 @@ python src/chlamytracker/scripts/{script}.py --help
will display a help message that gives a description of what the script does as well as the arguments it accepts and their default values. The three scripts for processing biological image data also accept a `--glob` argument that can be used to filter the set of files to process. For example, to track cells from only one row of wells from a plate, one could run the command.

```bash
python src/chlamytracker/scripts/track_cells_in_wells.py \
python src/chlamytracker/scripts/track_cells.py \
/path/to/directory/of/nd2/files/ \
--glob "WellB*.nd2"
```
Expand All @@ -117,7 +117,7 @@ python src/chlamytracker/scripts/track_cells.py \
/path/to/directory/of/nd2/files/ \
--output-directory /path/to/writeable/storage/location/ \
--pool-radius 50 \
--num-cores 6
--num-workers 6
```

Note that in the above examples, `--output-directory` is an optional argument. If not provided, output will be written to a directory named `processed` within the input directory (first argument). If `{input-directory}/processed/` already exists, files may be overwritten.
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