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NF1 Ephys Data

For these experiments, we recorded from the three Alphas ganglion cell types in loose-seal cell attached configuration while presenting light stimuli from darkness of different diamaters (30 to 1200 um). We measured:

  • Baseline firing rate before the light stimuli
  • Peak firing rates (Hz)
  • Peak Spot Size: the size of the light stimuli which elicited the most spikes.
  • Peak spike count: maximum number of spikes elicited by the light stimuli.

SMS spike curves

Example figure:

  • These are created directly from the NF1.h5 file located in Data_final.

  • It has the following hierarchy: animal_type (NF1_control, NF1_het, NF1_homo)-> celltype -> cellname.

  • For each cell, on the Y axis we plotted spikes_stim_mean for the ON response (cyan) and spikes_tail_mean for the OFF response (gray) and then computed the mean (darker lines). The SEM (shaded areas) are also part of the HDF5 file spikes_stim_sem and spikes_tail_sem for the ON and OFF response, respectiviel.

Mean and t-tests

Example figure:

In the result_tables, I have separated the two cohort analysis. In the result_tables/First_cohort directory there are .csv files for every celltype which include the relevant genotype,sex, eye side,quadrant and cell_type information and it's responses. Attached is also the Jupyer Notebook NF1_Analysis used to create plot the individual points, mean and run t-tests correcting for multiple comparisons.

Linear Mixed effects models

Example figure:

We ran linear mixed effects models using the fitlme function in Matlab and exported it results as CSVs result_tables/First_cohort for each celltype (separate directories). Also attached isthe Jupyter Notebook LME_results I used to create the plots.