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I noticed that there are different area_range used across analyses so just want to double-check on this.
Expectations:
nwbfile.acquisition['boundaries']['x_range'] and nwbfile.acquisition['boundaries']['z_range'] represent the x_boundary and z_boundary of the arena, which is fixed and identical in all nwb files.
Issues:
Player positions during the navigation period fall outside of the x_boundary and z_boundary range. See example in THF-wv004-0, where x_boundary, y_boundary = array([349.8549, 419.8549]), array([308. , 409.3358]). But from x_range, z_range = get_pos_ranges(positions_nav), x_range, z_range=[367.1234, 401.8272], [285.0, 433.0].
z_range is defined as nwbfile.acquisition['boundaries']['z_range'] + np. array([-10, 10]) in script, nwbfile.acquisition['boundaries']['z_range'] + np. array([-15, 15]) in 02-PlaceCells.ipynb. For place cell analysis, because the idea is to include data from the navigation period only, the buffer for tower transportation is not needed.
@TomDonoghue - could you please double-check these? Thanks!
The text was updated successfully, but these errors were encountered:
claire98han
changed the title
Inconsistency of area_range and optimal choices of bin size
Inconsistency of area_range and optimal choice of bin size
Jun 17, 2022
For the optimal choice of bin size, I'm thinking about defining bins such that each bin is a square. Currently, we are using bins = [6, 10] and chest_bins = [5, 7] which gives each bin a rectangular shape. Based on the range of the arena and chest_arena, it seems reasonable to have a 10-by-10 bin size.
02-PlaceCells & 03-SpatialTargetCells: I don't think we need to add a buffer to area_range for the actual analysis, even though it would be helpful to add it for visualization purposes.
Related to unit_analysis.py, line 201:
area_range should be the chest area [[360, 410], [320, 400]] instead of the whole field range, right?
I noticed that there are different
area_range
used across analyses so just want to double-check on this.Expectations:
nwbfile.acquisition['boundaries']['x_range']
andnwbfile.acquisition['boundaries']['z_range']
represent thex_boundary
andz_boundary
of the arena, which is fixed and identical in all nwb files.Issues:
Player positions during the navigation period fall outside of the
x_boundary
andz_boundary
range. See example in THF-wv004-0, wherex_boundary, y_boundary = array([349.8549, 419.8549]), array([308. , 409.3358])
. But fromx_range, z_range = get_pos_ranges(positions_nav), x_range, z_range=[367.1234, 401.8272], [285.0, 433.0]
.z_range is defined as
nwbfile.acquisition['boundaries']['z_range'] + np. array([-10, 10])
inscript
,nwbfile.acquisition['boundaries']['z_range'] + np. array([-15, 15])
in02-PlaceCells.ipynb
. For place cell analysis, because the idea is to include data from the navigation period only, the buffer for tower transportation is not needed.@TomDonoghue - could you please double-check these? Thanks!
The text was updated successfully, but these errors were encountered: