CalSciPy
latest
CONTENTS
Getting Started
Loading/Saving Images
Image Pre-Processing
Trace Processing
Events and Spiking
Arranging and Aligning Data
Regions of Interest
Optogenetics
Style
Dependencies
Contributions
API Reference
CalSciPy
Index
Edit on GitHub
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
|
X
|
Y
|
Z
A
add_path() (CalSciPy.organization.files.FileTree method)
add_photostimulation_group() (CalSciPy.optogenetics.Photostimulation method)
align_data() (in module CalSciPy.conversion)
approx_method (CalSciPy.roi_tools.ROI property)
ApproximateROI (class in CalSciPy.roi_tools)
approximation (CalSciPy.roi_tools.ROI attribute)
author (in module CalSciPy.version)
B
baseline_calculation() (in module CalSciPy.traces.baseline)
BRUKER_XML_OBJECT_MODULES (CalSciPy.bruker.CONSTANTS attribute)
build() (CalSciPy.organization.files.FileTree method)
C
calc_firing_rates() (in module CalSciPy.events)
calc_mean_firing_rates() (in module CalSciPy.events)
calculate_centroid() (in module CalSciPy.roi_tools)
calculate_dfof() (in module CalSciPy.traces)
calculate_mask() (in module CalSciPy.roi_tools)
calculate_mask_pixels() (in module CalSciPy.roi_tools)
calculate_radius() (in module CalSciPy.roi_tools)
calculate_standardized_noise() (in module CalSciPy.traces)
CalSciPy.bruker
module
CalSciPy.color_scheme
module
CalSciPy.conversion
module
CalSciPy.events
module
CalSciPy.images
module
CalSciPy.io_tools
module
CalSciPy.optogenetics
module
CalSciPy.organization.files
module
CalSciPy.roi_tools
module
CalSciPy.traces
module
CalSciPy.traces.baseline
module
CalSciPy.version
module
centroid (CalSciPy.roi_tools.ApproximateROI attribute)
(CalSciPy.roi_tools.ROI attribute)
clear() (CalSciPy.organization.files.FileTree method)
CONSTANTS (class in CalSciPy.bruker)
convert_one_roi() (CalSciPy.roi_tools.ROIHandler static method)
(CalSciPy.roi_tools.Suite2PHandler static method)
D
DEFAULT_PRAIRIEVIEW_VERSION (CalSciPy.bruker.CONSTANTS attribute)
deinterlace() (in module CalSciPy.images)
delay (CalSciPy.optogenetics.StimulationGroup attribute)
(CalSciPy.optogenetics.StimulationSequence attribute)
detrend_polynomial() (in module CalSciPy.traces)
directory (CalSciPy.organization.files.FileSet attribute)
E
external_align() (in module CalSciPy.conversion)
F
FIELD_OF_VIEW_MICRONS (CalSciPy.bruker.CONSTANTS attribute)
FIELD_OF_VIEW_PIXELS (CalSciPy.bruker.CONSTANTS attribute)
FileMap (class in CalSciPy.organization.files)
files (CalSciPy.organization.files.FileSet property)
FileSet (class in CalSciPy.organization.files)
FileTree (class in CalSciPy.organization.files)
find_file_type() (CalSciPy.organization.files.FileSet method)
find_matching_files() (CalSciPy.organization.files.FileSet method)
folders (CalSciPy.organization.files.FileSet property)
from_file() (CalSciPy.roi_tools.ROIHandler static method)
(CalSciPy.roi_tools.Suite2PHandler static method)
G
gaussian_filter() (in module CalSciPy.images)
generate_raster() (in module CalSciPy.events)
generate_reference_image() (CalSciPy.roi_tools.ROIHandler static method)
(CalSciPy.roi_tools.Suite2PHandler static method)
get() (CalSciPy.organization.files.FileTree method)
I
identify_vertices() (in module CalSciPy.roi_tools)
import_rois() (CalSciPy.roi_tools.ROIHandler class method)
(CalSciPy.roi_tools.Suite2PHandler class method)
interval (CalSciPy.optogenetics.StimulationSequence attribute)
items() (CalSciPy.organization.files.FileTree method)
iter() (CalSciPy.organization.files.FileTree method)
K
keys() (CalSciPy.organization.files.FileTree method)
L
load() (CalSciPy.roi_tools.ROIHandler class method)
(CalSciPy.roi_tools.Suite2PHandler class method)
load_binary() (in module CalSciPy.io_tools)
load_bruker_tifs() (in module CalSciPy.bruker)
load_gif() (in module CalSciPy.io_tools)
load_images() (in module CalSciPy.io_tools)
load_rois() (CalSciPy.optogenetics.Photostimulation class method)
load_video() (in module CalSciPy.io_tools)
load_voltage_recording() (in module CalSciPy.bruker)
low_pass_baseline() (in module CalSciPy.traces.baseline)
M
MAGNIFICATION (CalSciPy.bruker.CONSTANTS attribute)
maintainer (in module CalSciPy.version)
mask (CalSciPy.roi_tools.ApproximateROI property)
(CalSciPy.roi_tools.ROI property)
matrix_to_tensor() (in module CalSciPy.conversion)
mean_baseline() (in module CalSciPy.traces.baseline)
mean_filter() (in module CalSciPy.images)
median_baseline() (in module CalSciPy.traces.baseline)
median_filter() (in module CalSciPy.images)
merge_factorized_matrices() (in module CalSciPy.conversion)
method (CalSciPy.roi_tools.ApproximateROI property)
module
CalSciPy.bruker
CalSciPy.color_scheme
CalSciPy.conversion
CalSciPy.events
CalSciPy.images
CalSciPy.io_tools
CalSciPy.optogenetics
CalSciPy.organization.files
CalSciPy.roi_tools
CalSciPy.traces
CalSciPy.traces.baseline
CalSciPy.version
moving_mean_baseline() (in module CalSciPy.traces.baseline)
N
name (CalSciPy.optogenetics.StimulationGroup attribute)
(in module CalSciPy.version)
normalize_firing_rates() (in module CalSciPy.events)
num_groups (CalSciPy.optogenetics.Photostimulation property)
num_neurons (CalSciPy.optogenetics.Photostimulation property)
num_targets (CalSciPy.optogenetics.Photostimulation property)
(CalSciPy.optogenetics.StimulationGroup property)
O
OBJECTIVE (CalSciPy.bruker.CONSTANTS attribute)
ordered_index (CalSciPy.optogenetics.StimulationGroup attribute)
P
percentile_baseline() (in module CalSciPy.traces.baseline)
perona_malik_diffusion() (in module CalSciPy.traces)
Photostimulation (class in CalSciPy.optogenetics)
PIXELS_PER_MICRON (CalSciPy.bruker.CONSTANTS attribute)
plane (CalSciPy.roi_tools.ApproximateROI attribute)
(CalSciPy.roi_tools.ROI attribute)
point_interval (CalSciPy.optogenetics.StimulationGroup attribute)
pop() (CalSciPy.organization.files.FileTree method)
popitem() (CalSciPy.organization.files.FileTree method)
POWER_SCALE (CalSciPy.bruker.CONSTANTS attribute)
properties (CalSciPy.roi_tools.ApproximateROI attribute)
(CalSciPy.roi_tools.ROI attribute)
R
radius (CalSciPy.roi_tools.ApproximateROI attribute)
(CalSciPy.roi_tools.ROI attribute)
randomize_targets() (in module CalSciPy.optogenetics)
rc (CalSciPy.roi_tools.ApproximateROI property)
(CalSciPy.roi_tools.ROI property)
rc_vert (CalSciPy.roi_tools.ApproximateROI property)
(CalSciPy.roi_tools.ROI property)
reference_image (CalSciPy.optogenetics.Photostimulation attribute)
reference_shape (CalSciPy.optogenetics.Photostimulation property)
(CalSciPy.optogenetics.StimulationGroup property)
(CalSciPy.roi_tools.ApproximateROI attribute)
(CalSciPy.roi_tools.ROI attribute)
reindex() (CalSciPy.organization.files.FileSet method)
(CalSciPy.organization.files.FileTree method)
remap() (CalSciPy.organization.files.FileSet method)
(CalSciPy.organization.files.FileTree method)
remapped_sequence (CalSciPy.optogenetics.Photostimulation property)
repetitions (CalSciPy.optogenetics.StimulationGroup attribute)
(CalSciPy.optogenetics.StimulationSequence attribute)
ROI (class in CalSciPy.roi_tools)
roi_to_target() (CalSciPy.optogenetics.Photostimulation method)
ROIHandler (class in CalSciPy.roi_tools)
rois (CalSciPy.optogenetics.Photostimulation attribute)
(CalSciPy.optogenetics.StimulationGroup attribute)
S
save_binary() (in module CalSciPy.io_tools)
save_gif() (in module CalSciPy.io_tools)
save_images() (in module CalSciPy.io_tools)
save_video() (in module CalSciPy.io_tools)
sliding_mean_baseline() (in module CalSciPy.traces.baseline)
sliding_median_baseline() (in module CalSciPy.traces.baseline)
sliding_percentile_baseline() (in module CalSciPy.traces.baseline)
SPIRAL_SCALE (CalSciPy.bruker.CONSTANTS attribute)
stim_sequence (CalSciPy.optogenetics.Photostimulation attribute)
stimulated_neurons (CalSciPy.optogenetics.Photostimulation property)
StimulationGroup (class in CalSciPy.optogenetics)
StimulationSequence (class in CalSciPy.optogenetics)
Suite2PHandler (class in CalSciPy.roi_tools)
T
target_to_roi() (CalSciPy.optogenetics.Photostimulation method)
tensor_to_matrix() (in module CalSciPy.conversion)
U
update() (CalSciPy.organization.files.FileMap method)
V
validate() (CalSciPy.organization.files.FileSet method)
(CalSciPy.organization.files.FileTree method)
values() (CalSciPy.organization.files.FileTree method)
version (in module CalSciPy.version)
vertices (CalSciPy.roi_tools.ApproximateROI attribute)
(CalSciPy.roi_tools.ROI attribute)
X
X_GALVO_VOLTAGE_RANGE (CalSciPy.bruker.CONSTANTS attribute)
x_pixels (CalSciPy.roi_tools.ApproximateROI property)
(CalSciPy.roi_tools.ROI property)
xy (CalSciPy.roi_tools.ApproximateROI property)
(CalSciPy.roi_tools.ROI property)
xy_vert (CalSciPy.roi_tools.ApproximateROI property)
(CalSciPy.roi_tools.ROI property)
Y
Y_GALVO_VOLTAGE_RANGE (CalSciPy.bruker.CONSTANTS attribute)
y_pixels (CalSciPy.roi_tools.ApproximateROI property)
(CalSciPy.roi_tools.ROI property)
Z
z_pixels (CalSciPy.roi_tools.ApproximateROI attribute)
(CalSciPy.roi_tools.ROI attribute)
Read the Docs
v: latest
Versions
latest
Downloads
html
On Read the Docs
Project Home
Builds