Data Nodes

OptiNiSt accepts a variety of data types. Data are added in “nodes”, depending on their type. Here we summarise the accepted data of each node.

Image (TIFF)

  • Format: 3D or 4D array shape (time, y, x) or (time, z, y, x).

  • File Extension: “.tif”, “.tiff”, “.TIF”, “.TIFF”

CSV

  • Format: 2D data structure

    • Can have an optional header.

    • Can be transposed.

  • File Extension: “.csv”

Fluo / Behavior

  • Format: 2D data structure (similar to CSV)

    • Rows typically represent time points

    • Columns typically represent individual cells or ROIs

    • Can have an optional header

    • Can be transposed if specified in parameters

  • File Extension: “.csv”

HDF5 / NWB

  • Format: Contains Groups, Datasets, Attributes (metadata).

    • A Group is similar to a folder and may contain an arbitrary number of other groups and datasets,

    • A Dataset describes an n-dimensional array and provides the primary means for storing data,

    • An Attribute* is a small dataset that is attached to a specific group or dataset and is typically used to store metadata specific to the object they are associated with.

  • “.hdf5”, “.nwb”, “.HDF5”, “.NWB”

Matlab

  • Format:

  • File Extension: “.mat”

Microscope

  • File Extensions: “.nd2”, “.oir”, “.isxd”, “.thor.zip”

Inscopix(.isxd)

  • We currently use py_isx <https://github.com/inscopix/py_isx>_ package with version 1.0.* for Inscopix data. This library only supports CellSet and Movie file types.

NIKON(.nd2)

Olympus(.oir)

  • We currently implement reading NIKON and Olympus files using a C library. This is only available on Linux and Windows (not on MacOS yet, sorry).

  • If you use Linux, use OptiNiSt by :ref:developer mode <native_platforms_developer>.

    • open studio/app/optinist/wrappers/optinist/conda/microscope.yaml and uncomment the - gcc=12 line.