/NF1

NF1 data, LME results and plotting notebooks to share between labs.

Primary LanguageJupyter Notebook

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.