suite2p
dev
Basics:
Installation
Inputs
Settings (ops.npy)
Using the GUI
Outputs
Multiday recordings
Developer Documentation
Frequently Asked Questions
How it works:
Registration
Cell Detection
Signal extraction
Spike deconvolution
API:
suite2p.io package
suite2p.registration package
suite2p.detection package
suite2p.extraction package
suite2p.classification package
suite2p.gui package
suite2p
Index
Edit on GitHub
Index
A
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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X
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Y
A
add_square() (in module suite2p.detection.sparsedetect)
area (suite2p.detection.stats.EllipseData property)
aspect_ratio (suite2p.detection.stats.EllipseData property)
aspect_ratio() (in module suite2p.detection.stats)
C
cellpose_overlap() (in module suite2p.detection.chan2detect)
circleMask() (in module suite2p.detection.sourcery)
connected_region() (in module suite2p.detection.sourcery)
correct_bleedthrough() (in module suite2p.detection.chan2detect)
count_overlaps() (in module suite2p.detection.stats)
cov (suite2p.detection.stats.EllipseData attribute)
create_cell_mask() (in module suite2p.extraction.masks)
create_cell_pix() (in module suite2p.extraction.masks)
create_masks() (in module suite2p.extraction.masks)
create_neuropil_basis() (in module suite2p.detection.sourcery)
create_neuropil_masks() (in module suite2p.extraction.masks)
D
detect() (in module suite2p.detection.chan2detect)
distance_kernel() (in module suite2p.detection.stats)
do_crop (suite2p.detection.stats.ROI attribute)
downsample() (in module suite2p.detection.utils)
drawClusters() (in module suite2p.detection.sourcery)
dx (suite2p.detection.stats.EllipseData attribute)
dy (suite2p.detection.stats.EllipseData attribute)
E
ellipse (suite2p.detection.stats.EllipseData attribute)
EllipseData (class in suite2p.detection.stats)
estimate_spatial_scale() (in module suite2p.detection.sparsedetect)
Estimated (suite2p.detection.sparsedetect.EstimateMode attribute)
EstimateMode (class in suite2p.detection.sparsedetect)
extend_mask() (in module suite2p.detection.sparsedetect)
extendROI() (in module suite2p.detection.sourcery)
(in module suite2p.detection.sparsedetect)
F
filter_overlappers() (in module suite2p.detection.stats)
(suite2p.detection.stats.ROI class method)
find_best_scale() (in module suite2p.detection.sparsedetect)
fit_ellipse() (suite2p.detection.stats.ROI method)
fitMVGaus() (in module suite2p.detection.stats)
Forced (suite2p.detection.sparsedetect.EstimateMode attribute)
from_stat_dict() (suite2p.detection.stats.ROI class method)
G
get_connected() (in module suite2p.detection.sourcery)
get_mean_r_squared_normed_all() (suite2p.detection.stats.ROI class method)
get_n_pixels_normed_all() (suite2p.detection.stats.ROI class method)
get_overlap_count_image() (suite2p.detection.stats.ROI class method)
get_overlap_image() (suite2p.detection.stats.ROI method)
get_stat() (in module suite2p.detection.sourcery)
getStU() (in module suite2p.detection.sourcery)
getSVDdata() (in module suite2p.detection.sourcery)
getSVDproj() (in module suite2p.detection.sourcery)
getVmap() (in module suite2p.detection.sourcery)
H
hp_gaussian_filter() (in module suite2p.detection.utils)
hp_rolling_mean_filter() (in module suite2p.detection.utils)
I
intensity_ratio() (in module suite2p.detection.chan2detect)
iter_extend() (in module suite2p.detection.sourcery)
(in module suite2p.detection.sparsedetect)
L
lam (suite2p.detection.stats.ROI attribute)
localMax() (in module suite2p.detection.sourcery)
localRegion() (in module suite2p.detection.sourcery)
M
mask_ious() (in module suite2p.detection.utils)
mask_stats() (in module suite2p.detection.utils)
match_masks() (in module suite2p.detection.utils)
mean_r_squared (suite2p.detection.stats.ROI property)
mean_r_squared() (in module suite2p.detection.stats)
mean_r_squared0 (suite2p.detection.stats.ROI property)
mean_r_squared_compact (suite2p.detection.stats.ROI property)
med (suite2p.detection.stats.ROI attribute)
median_pix() (in module suite2p.detection.stats)
minDistance() (in module suite2p.detection.sourcery)
module
suite2p.detection.chan2detect
suite2p.detection.sourcery
suite2p.detection.sparsedetect
suite2p.detection.stats
suite2p.detection.utils
suite2p.extraction.dcnv
suite2p.extraction.masks
suite2p.version
morphOpen() (in module suite2p.detection.sourcery)
mu (suite2p.detection.stats.EllipseData attribute)
multiscale_mask() (in module suite2p.detection.sparsedetect)
N
n_pixels (suite2p.detection.stats.ROI property)
neuropil_subtraction() (in module suite2p.detection.sparsedetect)
norm_by_average() (in module suite2p.detection.stats)
npix_soma (suite2p.detection.stats.ROI property)
O
oasis() (in module suite2p.extraction.dcnv)
oasis_matrix() (in module suite2p.extraction.dcnv)
oasis_trace() (in module suite2p.extraction.dcnv)
P
pairwiseDistance() (in module suite2p.detection.sourcery)
postprocess() (in module suite2p.detection.sourcery)
preprocess() (in module suite2p.extraction.dcnv)
Q
quadrant_mask() (in module suite2p.detection.chan2detect)
R
r_squared() (in module suite2p.detection.sourcery)
radii (suite2p.detection.stats.EllipseData attribute)
radius (suite2p.detection.stats.EllipseData property)
ravel_indices() (suite2p.detection.stats.ROI method)
ROI (class in suite2p.detection.stats)
roi_stats() (in module suite2p.detection.stats)
rsort (suite2p.detection.stats.ROI attribute)
S
solidity (suite2p.detection.stats.ROI property)
soma_crop (suite2p.detection.stats.ROI property)
sourcery() (in module suite2p.detection.sourcery)
sparsery() (in module suite2p.detection.sparsedetect)
square_convolution_2d() (in module suite2p.detection.sparsedetect)
square_mask() (in module suite2p.detection.utils)
standard_deviation_over_time() (in module suite2p.detection.utils)
stats_dicts_to_3d_array() (suite2p.detection.stats.ROI class method)
sub2ind() (in module suite2p.detection.sourcery)
suite2p.detection.chan2detect
module
suite2p.detection.sourcery
module
suite2p.detection.sparsedetect
module
suite2p.detection.stats
module
suite2p.detection.utils
module
suite2p.extraction.dcnv
module
suite2p.extraction.masks
module
suite2p.version
module
T
temporal_high_pass_filter() (in module suite2p.detection.utils)
threshold_reduce() (in module suite2p.detection.utils)
to_array() (suite2p.detection.stats.ROI method)
two_comps() (in module suite2p.detection.sparsedetect)
X
xpix (suite2p.detection.stats.ROI attribute)
Y
ypix (suite2p.detection.stats.ROI attribute)
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