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Update out dated Arrow documentation #137

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Aug 22, 2023
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Update out dated Arrow documentation #137

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3 changes: 1 addition & 2 deletions README.md
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Expand Up @@ -287,7 +287,7 @@ Note that both of these methods have an optional argument for a path to be provi
arrow_array = nyx.get_arrow_memory_mapping()
```

This functionality is also available in the through the command line using the flag `--arrowOutputType`. If this flag is set to `--arrowOutputType=arrow` then the results will be written to an Arrow IPC file in the output directory and `--arrowOutputType=parquet` will write to a Parquet file.
This functionality is also available in the through the command line using the flag `--outputType`. If this flag is set to `--outputType=arrow` then the results will be written to an Arrow IPC file in the output directory and `--outputType=parquet` will write to a Parquet file.

## Available features
The feature extraction plugin extracts morphology and intensity based features from pairs of intensity/binary mask images and produces a csv file output. The input image should be in tiled [OME TIFF format](https://docs.openmicroscopy.org/ome-model/6.2.0/ome-tiff/specification.html). The plugin extracts the following features:
Expand Down Expand Up @@ -383,7 +383,6 @@ Assuming you [built the Nyxus binary](#building-from-source) as outlined below,
--hpar | (optional) Channel number that should be used as a provider of parent segments. Example: '--hpar=1' | integer
--hchi | (optional) Channel number that should be used as a provider of child segments. Example: '--hchi=0' | integer
--hag | (optional) Name of a method how to aggregate features of segments recognized as children of same parent segment. Valid options are 'SUM', 'MEAN', 'MIN', 'MAX', 'WMA' (weighted mean average), and 'NONE' (no aggregation, instead, same parent child segments will be laid out horizontally) | string
--arrowOutputType | (optional) Type of Arrow file to write the feature results to. Current options are `arrow` for Arrow IPC or `parquet` for Parquet | string

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