Igor

Igor is a licensed software used for recording and preprocessing of 2P data.

In Igor you install software packages by putting them in the user folder, which is typically found here:

C:\Users\username\Documents\WaveMetrics\Igor Pro X User Files\, where x is the Igor version and username is your local username. These packages will be recompiled every time you open Igor.

Install Igor Pro

1. Ask Thomas for free license and the Igor version
2. Download the Igor for this license
   1. https://www.wavemetrics.com/downloads/current
3. Install plug-ins like SAFIRA and ScanM by following the readme here: https://github.com/eulerlab/ret_preproc
   1. In Igor 8, you can get the HDF5 loader under Data/Load Waves/Packages/Install HDF5 Package
   2. Igor 9 should have this by default
4. You may need to install this https://www.wavemetrics.com/project/progresswindow
   1. Unzip the file and copy it to the other *.ipf files in ...\Igor Pro X User Files\User Procedures
   2. Create a link to this files and place it in ...\Igor Pro X User Files\Igor Procedures

Image preprocessing

First install Igor Pro, ScanM and SAFIRA as described above. https://github.com/eulerlab/ret_preproc does also described how ScanM is to be used.

• To process data recorded as .smp and .smh data pairs you
  • Load data with ScanM/Load ScanM data file …
  • Select file in Data Browser and Set Current Data Folder (red arrow)
    • You can open the Data Browser under Data/Data Browser

• Process data with ScanM/Open OS GUI
  • Make New Parameter Table
    • Most of the following should be detected automatically, but not TriggerMode which is stimulus dependent and is used to create snippets from the traces
      • #26 TriggerMode = How many triggers per repetition. Here are some examples:
        • Chirp: 2
        • Moving Bar: 8
        • Spotsize: 10
        • DN: 1500
      • #7 LightArtifact_cut = Columns for light artifact
        • Setup 1: 1 and Setup 3: 3
      • #8 Stimulator delay
        • Setup 1: 64 and Setup 3: 75
      • #23 Ignorse1stXsecond = Seconds to ignore
    • Close Table
    • ROI drawing with Automated Cell Lab
      • Margin left can be ignored or set to LightArtifact_cut
      • Click add cell first, then draw
      • When you are done click Make SAFIRA Mask
    • Close Menu window
      • Traces and Triggers
      • Export to create HD5 file that can be loaded in Python and DataJoint

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