Tutorial Create dataset project

Note

This page is currently being converted from this source: https://docs.google.com/document/d/1L-mNvQndJAmCoKHh_3m2bU1brHJnXJ_U9yFflwdR_RA/edit?tab=t.0

Caution

Work in progress

Setup New Project

1. Create a New Project
   • Run: nansen.createProject()
   • Enter a short project name (this will be the subfolder where your project will be saved).
   • Select a folder to be the root folder of your Project.
   • Click Create New Project.

Caution

*Error in nansen.app.setup.SetupWizard/createModuleManagerUI

(line 241): if isfield(p.Preferences, 'DataModule')*

Pop up window may be created behind other windows—can cause confusion.

2. Select Modules
   • Choose from:
     • Two Photon Imaging
     • NANSEN-NWB
     • Sharebrain
   • Click the right arrow to proceed.

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Adding Data

1. Add Data Locations

   • Specify the root of your dataset folder.
   • Clearly distinguish between Rawdata and Processed:
     • Processed folder will be created within the subfolder (default: [Rawdata]/Processed).

2. Specify Data Organization

   • Clarify how far the organization goes: is it the subfolder containing .mat files, or the .mat files themselves?

3. Detect Data Information

   • Subject ID / Session ID can be filled in automatically from subfolder information.
   • You can truncate and choose limited letters (e.g. m7123 for Subject ID and m7123-20220727-01 for Session ID).
   • Sessions will appear in a table.

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Find Variables of Interest

1. Switch to File Viewer
   • Right click on a .mat file.
   • Select Create New Variable From File.

Note

The above steps should be simplified—consider adding a Select Variables button.

2. Data Variable Selector

   • Popup window with dropdown for selecting data variables.
   • Pick the variable.

3. Create New Variable

   • Specify FileNameExpression. (e.g. _sessiondata)
   • Not clear what this is—may cause confusion. Suggestion: include all .mat files for now.

Note

Sometimes popup may appear off-screen or not visible. The Save icon may not be consistent with other UI elements.

- In the future, provide pre-made File Adapters in a dropdown menu.
- Consider a basic copy function for File Adapters.
- Example File Adapter should be available in `+fileadapter`.

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Convert to NWB

1. Configure NWB File
   • Go to Tools > Nwb > Configure NWB File
   • Set:
     • PrimaryGroupName = Acquisition
     • NwbModule = base
     • NeuroDataType = TimeSeries
   • Close the window to save (no save button).

Warning

This step should have default settings—users may not know what to select. A Save button should be added for clarity and confidence.

2. Write NWB File
   • Return to Overview session tables.
   • Select session.
   • Go to Data > Nwb > Write NWB File.

Caution

If Processed folder is not found, errors will occur. If Processed folder is removed, unexpected behavior may result.