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Index ND2 files

This command line tool indexes ND2 files in a specified directory and extracts basic metadata:

limnd2-index <arguments>

The script also supports filtering, sorting, and output formatting (table, csv, json).

As an example, the following command indexes ND2 files in the current directory, keeps selected columns, and filters images with width greater than 1000 pixels:

limnd2-index . -c Name,Size,Experiment,Resolution -F "int(Resolution.split('x')[0]) > 1000"

Output:

+-----------------------------+----------+----------------+--------------+
| Name                        | Size     | Experiment     | Resolution   |
+-----------------------------+----------+----------------+--------------+
| 1 dfm tub pc.nd2            | 164.1 MB | Z (54)         | 1024 x 512   |
| convallaria_FLIM.nd2        | 6.3 GB   | XY (25), Z (5) | 1024 x 1024  |
| golgi01.nd2                 | 60.4 MB  | Z (24)         | 1280 x 1024  |
| underwater_bmx.nd2          | 2.5 MB   |                | 1076 x 773   |
+-----------------------------+----------+----------------+--------------+

Arguments

Important

Arguments highlighted in bold (paths) are required.

  • paths

    One or more paths to ND2 files or directories containing ND2 files. Required.

  • --recurse, -r

    Recursively search directories for ND2 files. Optional.

  • --glob-pattern <pattern>, -g <pattern>

    Glob pattern to search for ND2 files. Default: *.nd2. Optional.

  • --sort-by <column>, -s <column>

    Column to sort by. Choices are valid column names, or append a hyphen (-) for reverse order. If not specified, order is not guaranteed. Optional.

  • --format <format>, -f <format>

    Output format. Choices: table, csv, json. Default: table (if rich is available), otherwise json. Optional.

  • --include <list>, -i <list>

    Comma-separated list of columns to add to the default output. Optional.

  • --columns <list>, -c <list>

    Exact comma-separated list of columns to output (replaces default column selection). Optional.

  • --exclude <list>, -e <list>

    Comma-separated list of columns to remove from the selected output columns. Optional.

  • --all-columns

    Show all columns by default (instead of hiding selected columns). Optional.

  • --no-header

    Do not write the CSV header. Optional.

  • --filter <expression>, -F <expression>

    Filter the output using a Python expression (string) that evaluates to True or False for each row. Can be used multiple times. Example: "Frames > 50 and 'T' in Experiment". Optional.

Valid column names

The following columns are available for output, filtering, and sorting.

Column Data Type Description
Path str Full file path
Name str File name
Version str ND2 file version
Size str File size
Modified str Last modified timestamp
Experiment str Experiment names and frame count
Frames int Total number of frames
Dtype str Data type
Bits int Bit depth
Compression str Compression mode and parameter
Resolution str Image resolution
Channels int Number of channels
Binary str Binary metadata
Downsampled str Downsampled pyramid information
Software str Acquisition software
Grabber str Acquisition hardware/grabber

Default output hides: Compression, Downsampled, Software, Grabber.

Examples

Here are some example usages of the limnd2-index command:

Index all ND2 files in a directory 
limnd2-index ./data
Index ND2 files recursively in subdirectories 
limnd2-index ./data --recurse
Index ND2 files matching a glob pattern 
limnd2-index ./data --glob-pattern '*.nd2'
Sort output by frame count 
limnd2-index ./data --sort-by Frames
Output results as CSV and include only specific columns 
limnd2-index ./data --format csv --columns Name,Experiment
Filter files 
limnd2-index ./data --filter "Frames > 50 and 'T' in Experiment"