Configuration#

MATLAB#

Certain features of the application require MATLAB to be installed on your system. If you have MATLAB installed in a non-standard location, you will need to manually adjust the location of your MATLAB installation to the default location:

  • Windows: C:\Program Files\MATLAB\R2024a

  • MacOS: /Applications/MATLAB_R2024a.app

Note

Luckily, the application will automatically detect the MATLAB installation on your system if it is installed in the default location.

Tip

If you cannot install MATLAB on your system, when using the application, make sure the Use C++ option is checked before running an analysis.

Configuring Input Files#

Downsampled and exported .brw files are ready to be loaded into YSA.

Note

  • The ysa-GUI functions best when input files are under 1 GB, depending on the RAM capabilities of your machine:

    • For devices with a RAM of 64 GB, optimal size is < ~1 GB

    • For devices with a RAM of 16 GB, optimal size is < ~500 MB

    • For devices with a RAM of 8 GB, optimal size is < ~300 MB

  • Since raw MEA files can be quite large >100 GB, we recommend using files of an hour or less that are downsampled signals around 100-300 Hz for optimal performance.

  • Spatially downsampling MEA files by selecting specific regions and channels in the MEA recording can also decrease file size

  • The maximum grid size compatible with the ysa-GUI is 64 x 64 (Any grid dimension that can fit within this maximum 64 x 64 grid size are compatible)

    • Most MEA systems have grid sizes of 64 x 64 or less, however if a larger grid size is used, a spatial downsampling that trims channels within the 64 x 64 size will render the data compatible with yse-GUI

Code to downsample and export .brw MEA files can be found here: ParrishLab/MEA_file_Extract_Downsample.git

Data File (.h5 or other HDF5 extension, e.g. .brw)#

To make an .h5 file compatible with YSA, follow these formatting specifications in configuring the data structure.

/3BData#

Raw (Raw dataset values in 1D vector)

  • Size: 1xn

  • Type: H5T_INTEGER

ChunkSize (Data are stored in chunks of this size)

  • Size: 1xn

  • Type: H5T_INTEGER

/3BRecInfo#

/3BRecInfo/3BMeaChip

Layout

  • Size: [‘NRows’ ‘NCols’]

  • Type: H5T_INTEGER

NCols

  • Size: 1 Type: H5T_INTEGER

NRows

  • Size: 1 Type: H5T_INTEGER

/3BRecInfo/3BMeaStreams

Chs

  • Size: n (where n is the number of channels available in the exported data)

  • Type: H5T_COMPOUND [‘Row’ ‘Col’] (List of the [Row Col] locations of the stored channels)

/3BRecInfo/3BRecVars

BitDepth

  • Size: 1

  • Type: H5T_INTEGER

ExperimentType

  • Size: 1

  • Type: H5T_INTEGER

MaxVolt (mV)

  • Size: 1

  • Type: H5T_FLOAT

MinVolt (mV)

  • Size: 1

  • Type: H5T_FLOAT

NRecFrames (Total number of samples for each channel recorded)

  • Size: 1

  • Type: H5T_INTEGER

SamplingRate (Hz)

  • Size: 1

  • Type: H5T_FLOAT

SignalInversion (-1 or 1)

  • Size: 1

  • Type: H5T_FLOAT