# Running a Full Pipeline

```python
import isx
from ci_pipe.pipeline import CIPipe

# Note:
# The import path for CIPipe depends on your installation method
# (see the "Installing the Library" section).

# Create the pipeline using input and output directories
pipeline = CIPipe.with_videos_from_directory(
    'input_dir',
    outputs_directory='output_dir',
    isx=isx
)
# Replace 'input_dir' and 'output_dir' with your actual directories.
```

#### Full Pipeline Execution with ISX Algorithms

The following example runs a complete sequence of ISX processing steps:

```python
(
    pipeline
    .set_defaults(
        isx_bp_subtract_global_minimum=False,
        isx_mc_max_translation=25,
        isx_acr_filters=[
            ('SNR', '>', 3),
            ('Event Rate', '>', 0),
            ('# Comps', '=', 1)
        ]
    )
    .isx.preprocess_videos()
    .isx.bandpass_filter_videos()
    .isx.motion_correction_videos(isx_mc_series_name="series1")
    .isx.normalize_dff_videos()
    .isx.extract_neurons_pca_ica()
    .isx.detect_events_in_cells()
    .isx.auto_accept_reject_cells()
)
```

After execution, you can visualize the results of your pipeline using:

```python
pipeline.info(1)
pipeline.trace()
```


---

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