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01 Inputs and Outputs

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Jane Ling edited this page Oct 31, 2023 · 1 revision

File Organization

For simplicity of using the scripts, it is recommended to organize your files as shown in the figure below. Create one folder for the imaging files and one folder for storing the image processing outputs. In the outputs folder, a folder should be created for each dataset. Sub-folders will be created automatically while running the script.

image

Inputs

Scope

This project aims to extract multi-cellular spontaneous synaptic activities from a single-plane recording of iGluSNFR3 in human neurons.

File Type

Bioformat Toolbox is used for reading the input file. Hence, it is not necessary for the input file to be a .cxd. Other microscopy file types can also be used as input.

Outputs

Outputs of the script would be saved in processed_data.mat. Parameters include:

  • event_cluster : (structure array) (N_cluster, 1) Information of each event cluster. Each row represents an event cluster

  • ind : (N_px, 1) Linear indices of the location of pixels.

  • ops : (struct) Parameters used in the analysis.

  • px : (structure array) (N_px, 1) Information of each pixel. Each row represents a pixel

  • ROI : (structure array) (N_ROI, 1) Information of each ROI. Each row represents a ROI

  • signal_raw : (Nt, N_px) Raw fluorescence.

  • signal_baseline : (Nt, N_px) Baseline fluorescence.

  • signal_df : (Nt, N_px) Delta F.

  • signal_dfof : (Nt, N_px) Delta F over F.

  • signal_dfof_movemean : (Nt, N_px) Moving average of delta F over F.

  • signal_edge : (Nt, N_px) Rising slope of delta F.

  • signal_edge_nve : (Nt, N_px) Falling slope of delta F.

  • stats : (struct) Statistics of events.

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