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B
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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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J
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K
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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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U
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V
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W
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X
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Z
A
add() (imc.types.DataFrame method)
(imc.types.Series method)
add_axobserver() (imc.types.Figure method)
add_centroids() (in module imc.graphics)
add_legend() (in module imc.graphics)
add_minmax() (in module imc.graphics)
add_scale() (in module imc.graphics)
agg() (imc.types.DataFrame method)
(imc.types.Series method)
aggregate() (imc.types.DataFrame method)
(imc.types.Series method)
align() (imc.types.DataFrame method)
(imc.types.Series method)
all() (imc.types.DataFrame method)
(imc.types.Series method)
AnnData (class in imc.types)
any() (imc.types.DataFrame method)
(imc.types.Series method)
append() (imc.types.DataFrame method)
(imc.types.Series method)
apply() (imc.types.DataFrame method)
(imc.types.Series method)
applymap() (imc.types.DataFrame method)
area (imc.data_models.roi.ROI property)
argsort() (imc.types.Series method)
array (imc.types.Series property)
Array (in module imc.types)
asfreq() (imc.types.DataFrame method)
(imc.types.Series method)
assign() (imc.types.DataFrame method)
autocorr() (imc.types.Series method)
axes (imc.types.DataFrame property)
(imc.types.Figure property)
(imc.types.Series property)
Axis (class in imc.types)
axis_date() (imc.types.Axis method)
B
between() (imc.types.Series method)
bfill() (imc.types.DataFrame method)
(imc.types.Series method)
boxplot() (imc.types.DataFrame method)
C
cat (imc.types.Series attribute)
cell_labels_to_mask() (in module imc.graphics)
cell_mask (imc.data_models.roi.ROI property)
cell_mask_o (imc.data_models.roi.ROI property)
cells_per_area_unit() (imc.data_models.roi.ROI method)
channel_correlation() (imc.data_models.project.Project method)
channel_labels (imc.data_models.roi.ROI property)
channel_number (imc.data_models.roi.ROI property)
channel_summary() (imc.data_models.project.Project method)
chunk_X() (imc.types.AnnData method)
chunked_X() (imc.types.AnnData method)
cla() (imc.types.Axis method)
cleanup_channel_names() (in module imc.utils)
clear() (imc.types.Axis method)
(imc.types.Figure method)
clf() (imc.types.Figure method)
clip() (imc.types.DataFrame method)
(imc.types.Series method)
close_plots() (in module imc.graphics)
cluster_cells() (imc.data_models.project.Project method)
(imc.data_models.sample.IMCSample method)
ColorMap (in module imc.types)
columns (imc.types.DataFrame attribute)
combine() (imc.types.DataFrame method)
(imc.types.Series method)
combine_first() (imc.types.DataFrame method)
(imc.types.Series method)
compare() (imc.types.DataFrame method)
(imc.types.Series method)
concatenate() (imc.types.AnnData method)
contains() (imc.types.Patch method)
contains_point() (imc.types.Patch method)
contains_points() (imc.types.Patch method)
copy() (imc.types.AnnData method)
corr() (imc.types.DataFrame method)
(imc.types.Series method)
corrwith() (imc.types.DataFrame method)
count() (imc.types.DataFrame method)
(imc.types.Series method)
cov() (imc.types.DataFrame method)
(imc.types.Series method)
cummax() (imc.types.DataFrame method)
(imc.types.Series method)
cummin() (imc.types.DataFrame method)
(imc.types.Series method)
cumprod() (imc.types.DataFrame method)
(imc.types.Series method)
cumsum() (imc.types.DataFrame method)
(imc.types.Series method)
cytoplasm_mask (imc.data_models.roi.ROI property)
D
DataFrame (class in imc.types)
diff() (imc.types.DataFrame method)
(imc.types.Series method)
div() (imc.types.DataFrame method)
(imc.types.Series method)
divide() (imc.types.DataFrame method)
(imc.types.Series method)
divmod() (imc.types.Series method)
dot() (imc.types.DataFrame method)
(imc.types.Series method)
downcast_int() (in module imc.utils)
download_file() (in module imc.utils)
dpi (imc.types.Figure property)
draw() (imc.types.Axis method)
(imc.types.Figure method)
(imc.types.Patch method)
draw_artist() (imc.types.Figure method)
draw_without_rendering() (imc.types.Figure method)
drop() (imc.types.DataFrame method)
(imc.types.Series method)
drop_duplicates() (imc.types.DataFrame method)
(imc.types.Series method)
dropna() (imc.types.DataFrame method)
(imc.types.Series method)
dt (imc.types.Series attribute)
dtype (imc.types.Series property)
dtypes (imc.types.Series property)
duplicated() (imc.types.DataFrame method)
(imc.types.Series method)
E
eq() (imc.types.DataFrame method)
(imc.types.Series method)
estimate_noise() (in module imc.utils)
eval() (imc.types.DataFrame method)
execute_constrained_layout() (imc.types.Figure method)
explode() (imc.types.DataFrame method)
(imc.types.Series method)
export_images_for_topological_labeling() (in module imc.ops.domain)
extracellular_mask (imc.data_models.roi.ROI property)
F
ffill() (imc.types.DataFrame method)
(imc.types.Series method)
figimage() (imc.types.Figure method)
Figure (class in imc.types)
filename (imc.types.AnnData property)
fill (imc.types.Patch property)
fillna() (imc.types.DataFrame method)
(imc.types.Series method)
filter_kwargs_by_callable() (in module imc.utils)
find_communities() (imc.data_models.project.Project method)
floordiv() (imc.types.DataFrame method)
(imc.types.Series method)
fractal_dimension() (in module imc.utils)
from_dict() (imc.types.DataFrame class method)
from_records() (imc.types.DataFrame class method)
G
ge() (imc.types.DataFrame method)
(imc.types.Series method)
get_aa() (imc.types.Patch method)
get_adjacency_graph() (in module imc.ops.adjacency)
get_antialiased() (imc.types.Patch method)
get_axes() (imc.types.Figure method)
get_canny_edge_image() (in module imc.utils)
get_capstyle() (imc.types.Patch method)
get_children() (imc.types.Axis method)
get_constrained_layout() (imc.types.Figure method)
get_constrained_layout_pads() (imc.types.Figure method)
get_data_interval() (imc.types.Axis method)
get_data_transform() (imc.types.Patch method)
get_distinct_marker_sets() (imc.data_models.roi.ROI method)
get_domain_areas() (in module imc.ops.domain)
get_domains_per_cell() (in module imc.ops.domain)
get_dpi() (imc.types.Figure method)
get_ec() (imc.types.Patch method)
get_edgecolor() (imc.types.Patch method)
get_extents() (imc.types.Patch method)
get_facecolor() (imc.types.Patch method)
get_fc() (imc.types.Patch method)
get_figheight() (imc.types.Figure method)
get_figwidth() (imc.types.Figure method)
get_fill() (imc.types.Patch method)
get_grid_dims() (in module imc.graphics)
get_gridlines() (imc.types.Axis method)
get_hatch() (imc.types.Patch method)
get_input_filename() (imc.data_models.project.Project method)
(imc.data_models.roi.ROI method)
(imc.data_models.sample.IMCSample method)
get_inverted() (imc.types.Axis method)
get_joinstyle() (imc.types.Patch method)
get_label() (imc.types.Axis method)
get_label_position() (imc.types.Axis method)
get_label_text() (imc.types.Axis method)
get_linestyle() (imc.types.Patch method)
get_linewidth() (imc.types.Patch method)
get_ls() (imc.types.Patch method)
get_lw() (imc.types.Patch method)
get_major_formatter() (imc.types.Axis method)
get_major_locator() (imc.types.Axis method)
get_major_ticks() (imc.types.Axis method)
get_majorticklabels() (imc.types.Axis method)
get_majorticklines() (imc.types.Axis method)
get_majorticklocs() (imc.types.Axis method)
get_mean_all_channels() (imc.data_models.roi.ROI method)
get_minor_formatter() (imc.types.Axis method)
get_minor_locator() (imc.types.Axis method)
get_minor_ticks() (imc.types.Axis method)
get_minorticklabels() (imc.types.Axis method)
get_minorticklines() (imc.types.Axis method)
get_minorticklocs() (imc.types.Axis method)
get_n_colors() (in module imc.graphics)
get_offset_text() (imc.types.Axis method)
get_patch_transform() (imc.types.Patch method)
get_path() (imc.types.Patch method)
get_pickradius() (imc.types.Axis method)
get_scale() (imc.types.Axis method)
get_size_inches() (imc.types.Figure method)
get_slice() (imc.graphics.InteractiveViewer method)
get_tick_space() (imc.types.Axis method)
get_ticklabel_extents() (imc.types.Axis method)
get_ticklabels() (imc.types.Axis method)
get_ticklines() (imc.types.Axis method)
get_ticklocs() (imc.types.Axis method)
get_ticks_direction() (imc.types.Axis method)
get_tight_layout() (imc.types.Figure method)
get_tightbbox() (imc.types.Axis method)
get_transform() (imc.types.Axis method)
(imc.types.Patch method)
get_units() (imc.types.Axis method)
get_verts() (imc.types.Patch method)
get_view_interval() (imc.types.Axis method)
get_volume() (in module imc.graphics)
get_window_extent() (imc.types.Patch method)
ginput() (imc.types.Figure method)
glob() (imc.types.Path method)
grid() (imc.types.Axis method)
groupby() (imc.types.DataFrame method)
(imc.types.Series method)
gt() (imc.types.DataFrame method)
(imc.types.Series method)
H
hasnans (imc.types.Series property)
have_units() (imc.types.Axis method)
hist() (imc.types.DataFrame method)
(imc.types.Series method)
I
idxmax() (imc.types.DataFrame method)
(imc.types.Series method)
idxmin() (imc.types.DataFrame method)
(imc.types.Series method)
illustrate_domains() (in module imc.ops.domain)
imc.data_models.project
module
imc.data_models.roi
module
imc.data_models.sample
module
imc.graphics
module
imc.ops.adjacency
module
imc.ops.clustering
module
imc.ops.community
module
imc.ops.compensation
module
imc.ops.domain
module
imc.ops.mixture
module
imc.ops.quant
module
imc.ops.signal
module
imc.types
module
imc.utils
module
IMCSample (class in imc.data_models.sample)
index (imc.types.DataFrame attribute)
(imc.types.Series attribute)
info() (imc.types.DataFrame method)
(imc.types.Series method)
insert() (imc.types.DataFrame method)
InteractiveViewer (class in imc.graphics)
interpolate() (imc.types.DataFrame method)
(imc.types.Series method)
is_view (imc.types.AnnData property)
isbacked (imc.types.AnnData property)
isin() (imc.types.DataFrame method)
(imc.types.Series method)
isna() (imc.types.DataFrame method)
(imc.types.Series method)
isnull() (imc.types.DataFrame method)
(imc.types.Series method)
items() (imc.types.DataFrame method)
(imc.types.Series method)
iterdir() (imc.types.Path method)
iteritems() (imc.types.DataFrame method)
(imc.types.Series method)
iterrows() (imc.types.DataFrame method)
itertuples() (imc.types.DataFrame method)
J
join() (imc.types.DataFrame method)
K
keys() (imc.types.Series method)
kurt() (imc.types.DataFrame method)
(imc.types.Series method)
kurtosis() (imc.types.DataFrame method)
(imc.types.Series method)
L
label_clusters() (imc.data_models.project.Project method)
label_domains() (in module imc.ops.domain)
lacunarity() (in module imc.utils)
layers (imc.types.AnnData property)
le() (imc.types.DataFrame method)
(imc.types.Series method)
log_slice() (imc.graphics.InteractiveViewer method)
lookup() (imc.types.DataFrame method)
lt() (imc.types.DataFrame method)
(imc.types.Series method)
M
mad() (imc.types.DataFrame method)
(imc.types.Series method)
map() (imc.types.Series method)
mask (imc.data_models.roi.ROI property)
mask() (imc.types.DataFrame method)
(imc.types.Series method)
max() (imc.types.DataFrame method)
(imc.types.Series method)
mean() (imc.types.DataFrame method)
(imc.types.Series method)
measure_adjacency() (imc.data_models.project.Project method)
measure_cell_type_adjacency() (in module imc.ops.adjacency)
median() (imc.types.DataFrame method)
(imc.types.Series method)
melt() (imc.types.DataFrame method)
membrane_mask (imc.data_models.roi.ROI property)
memory_usage() (imc.types.DataFrame method)
(imc.types.Series method)
merge() (imc.types.DataFrame method)
merge_channels() (in module imc.graphics)
min() (imc.types.DataFrame method)
(imc.types.Series method)
minmax_scale() (in module imc.utils)
mod() (imc.types.DataFrame method)
(imc.types.Series method)
mode() (imc.types.DataFrame method)
(imc.types.Series method)
module
imc.data_models.project
imc.data_models.roi
imc.data_models.sample
imc.graphics
imc.ops.adjacency
imc.ops.clustering
imc.ops.community
imc.ops.compensation
imc.ops.domain
imc.ops.mixture
imc.ops.quant
imc.ops.signal
imc.types
imc.utils
mul() (imc.types.DataFrame method)
(imc.types.Series method)
multi_slice_viewer() (imc.graphics.InteractiveViewer method)
MultiIndexSeries (in module imc.types)
multiply() (imc.types.DataFrame method)
(imc.types.Series method)
N
n_obs (imc.types.AnnData property)
n_vars (imc.types.AnnData property)
name (imc.types.Series property)
ne() (imc.types.DataFrame method)
(imc.types.Series method)
next_slice() (imc.graphics.InteractiveViewer method)
nlargest() (imc.types.DataFrame method)
(imc.types.Series method)
notna() (imc.types.DataFrame method)
(imc.types.Series method)
notnull() (imc.types.DataFrame method)
(imc.types.Series method)
nsmallest() (imc.types.DataFrame method)
(imc.types.Series method)
nuclei_mask (imc.data_models.roi.ROI property)
nuclei_mask_o (imc.data_models.roi.ROI property)
nunique() (imc.types.DataFrame method)
O
obs (imc.types.AnnData property)
obs_keys() (imc.types.AnnData method)
obs_names (imc.types.AnnData property)
obs_names_make_unique() (imc.types.AnnData method)
obs_vector() (imc.types.AnnData method)
obsm (imc.types.AnnData property)
obsm_keys() (imc.types.AnnData method)
obsp (imc.types.AnnData property)
P
Patch (class in imc.types)
Path (class in imc.types)
pivot() (imc.types.DataFrame method)
pivot_table() (imc.types.DataFrame method)
plot (imc.types.DataFrame attribute)
(imc.types.Series attribute)
plot_cell_types() (imc.data_models.roi.ROI method)
plot_channel() (imc.data_models.roi.ROI method)
plot_channels() (imc.data_models.project.Project method)
(imc.data_models.roi.ROI method)
(imc.data_models.sample.IMCSample method)
plot_overlayied_channels_subplots() (imc.data_models.roi.ROI method)
plot_panoramas_rois() (in module imc.utils)
plot_probabilities_and_segmentation() (imc.data_models.roi.ROI method)
plot_rois() (imc.data_models.sample.IMCSample method)
plot_single_channel() (in module imc.graphics)
polygon_to_mask() (in module imc.utils)
pop() (imc.types.DataFrame method)
(imc.types.Series method)
pow() (imc.types.DataFrame method)
(imc.types.Series method)
previous_slice() (imc.graphics.InteractiveViewer method)
process_key() (imc.graphics.InteractiveViewer method)
prod() (imc.types.DataFrame method)
(imc.types.Series method)
product() (imc.types.DataFrame method)
(imc.types.Series method)
Project (class in imc.data_models.project)
Q
quantify_cell_intensity() (imc.data_models.project.Project method)
(imc.data_models.roi.ROI method)
(imc.data_models.sample.IMCSample method)
(in module imc.ops.quant)
quantify_cell_intensity_rois() (in module imc.ops.quant)
quantify_cell_morphology() (imc.data_models.project.Project method)
(imc.data_models.roi.ROI method)
(imc.data_models.sample.IMCSample method)
quantify_cell_morphology_rois() (in module imc.ops.quant)
quantify_cells() (imc.data_models.project.Project method)
(imc.data_models.sample.IMCSample method)
quantify_cells_rois() (in module imc.ops.quant)
quantile() (imc.types.DataFrame method)
(imc.types.Series method)
query() (imc.types.DataFrame method)
R
radd() (imc.types.DataFrame method)
(imc.types.Series method)
rainbow_text() (in module imc.graphics)
rasterize_scanpy() (in module imc.graphics)
ravel() (imc.types.Series method)
raw (imc.types.AnnData property)
rdiv() (imc.types.DataFrame method)
(imc.types.Series method)
rdivmod() (imc.types.Series method)
read_all_inputs() (imc.data_models.roi.ROI method)
(imc.data_models.sample.IMCSample method)
read_image_from_file() (in module imc.utils)
read_input() (imc.data_models.roi.ROI method)
reindex() (imc.types.DataFrame method)
(imc.types.Series method)
remove_keymap_conflicts() (imc.graphics.InteractiveViewer method)
remove_overlapping_locs (imc.types.Axis property)
rename() (imc.types.DataFrame method)
(imc.types.Series method)
rename_categories() (imc.types.AnnData method)
reorder_levels() (imc.types.DataFrame method)
(imc.types.Series method)
repeat() (imc.types.Series method)
replace() (imc.types.DataFrame method)
(imc.types.Series method)
resample() (imc.types.DataFrame method)
(imc.types.Series method)
reset_index() (imc.types.DataFrame method)
(imc.types.Series method)
reset_ticks() (imc.types.Axis method)
rfloordiv() (imc.types.DataFrame method)
(imc.types.Series method)
rmod() (imc.types.DataFrame method)
(imc.types.Series method)
rmul() (imc.types.DataFrame method)
(imc.types.Series method)
ROI (class in imc.data_models.roi)
rois (imc.data_models.project.Project property)
round() (imc.types.DataFrame method)
(imc.types.Series method)
rpow() (imc.types.DataFrame method)
(imc.types.Series method)
rsub() (imc.types.DataFrame method)
(imc.types.Series method)
rtruediv() (imc.types.DataFrame method)
(imc.types.Series method)
run_shell_command() (in module imc.utils)
S
sample_comparisons() (imc.data_models.project.Project method)
saturize() (in module imc.graphics)
savefig() (imc.types.Figure method)
searchsorted() (imc.types.Series method)
select_dtypes() (imc.types.DataFrame method)
sem() (imc.types.DataFrame method)
(imc.types.Series method)
Series (class in imc.types)
set() (imc.types.Axis method)
(imc.types.Figure method)
(imc.types.Patch method)
set_aa() (imc.types.Patch method)
set_alpha() (imc.types.Patch method)
set_antialiased() (imc.types.Patch method)
set_axis() (imc.types.DataFrame method)
(imc.types.Series method)
set_canvas() (imc.types.Figure method)
set_capstyle() (imc.types.Patch method)
set_channel_exclude() (imc.data_models.roi.ROI method)
set_clip_path() (imc.types.Axis method)
set_clusters() (imc.data_models.project.Project method)
set_color() (imc.types.Patch method)
set_constrained_layout() (imc.types.Figure method)
set_constrained_layout_pads() (imc.types.Figure method)
set_data_interval() (imc.types.Axis method)
set_default_intervals() (imc.types.Axis method)
set_dpi() (imc.types.Figure method)
set_ec() (imc.types.Patch method)
set_edgecolor() (imc.types.Patch method)
set_facecolor() (imc.types.Patch method)
set_fc() (imc.types.Patch method)
set_figheight() (imc.types.Figure method)
set_figwidth() (imc.types.Figure method)
set_fill() (imc.types.Patch method)
set_hatch() (imc.types.Patch method)
set_image() (imc.graphics.InteractiveViewer method)
set_index() (imc.types.DataFrame method)
set_inverted() (imc.types.Axis method)
set_joinstyle() (imc.types.Patch method)
set_label_coords() (imc.types.Axis method)
set_label_position() (imc.types.Axis method)
set_label_text() (imc.types.Axis method)
set_linestyle() (imc.types.Patch method)
set_linewidth() (imc.types.Patch method)
set_ls() (imc.types.Patch method)
set_lw() (imc.types.Patch method)
set_major_formatter() (imc.types.Axis method)
set_major_locator() (imc.types.Axis method)
set_minor_formatter() (imc.types.Axis method)
set_minor_locator() (imc.types.Axis method)
set_pickradius() (imc.types.Axis method)
set_size_inches() (imc.types.Figure method)
set_tick_params() (imc.types.Axis method)
set_ticklabels() (imc.types.Axis method)
set_ticks() (imc.types.Axis method)
set_tight_layout() (imc.types.Figure method)
set_units() (imc.types.Axis method)
set_view_interval() (imc.types.Axis method)
shape (imc.data_models.roi.ROI property)
(imc.types.AnnData property)
(imc.types.DataFrame property)
share_axes_by() (in module imc.graphics)
shift() (imc.types.DataFrame method)
(imc.types.Series method)
show() (imc.types.Figure method)
skew() (imc.types.DataFrame method)
(imc.types.Series method)
sort_index() (imc.types.DataFrame method)
(imc.types.Series method)
sort_values() (imc.types.DataFrame method)
(imc.types.Series method)
sorted_nicely() (in module imc.utils)
sparse (imc.types.DataFrame attribute)
(imc.types.Series attribute)
stack (imc.data_models.roi.ROI property)
stack() (imc.types.DataFrame method)
stack_eq (imc.data_models.roi.ROI property)
stack_to_probabilities() (in module imc.utils)
std() (imc.types.DataFrame method)
(imc.types.Series method)
str (imc.types.Series attribute)
strings_to_categoricals() (imc.types.AnnData method)
style (imc.types.DataFrame property)
sub() (imc.types.DataFrame method)
(imc.types.Series method)
subtract() (imc.types.DataFrame method)
(imc.types.Series method)
sum() (imc.types.DataFrame method)
(imc.types.Series method)
swaplevel() (imc.types.DataFrame method)
(imc.types.Series method)
T
T (imc.types.AnnData property)
take() (imc.types.Series method)
tight_layout() (imc.types.Figure method)
to_df() (imc.types.AnnData method)
to_dict() (imc.types.DataFrame method)
(imc.types.Series method)
to_feather() (imc.types.DataFrame method)
to_frame() (imc.types.Series method)
to_gbq() (imc.types.DataFrame method)
to_html() (imc.types.DataFrame method)
to_markdown() (imc.types.DataFrame method)
(imc.types.Series method)
to_memory() (imc.types.AnnData method)
to_numpy() (imc.types.DataFrame method)
to_parquet() (imc.types.DataFrame method)
to_period() (imc.types.DataFrame method)
(imc.types.Series method)
to_records() (imc.types.DataFrame method)
to_stata() (imc.types.DataFrame method)
to_string() (imc.types.DataFrame method)
(imc.types.Series method)
to_timestamp() (imc.types.DataFrame method)
(imc.types.Series method)
to_xml() (imc.types.DataFrame method)
transform() (imc.types.DataFrame method)
(imc.types.Series method)
transpose() (imc.types.AnnData method)
(imc.types.DataFrame method)
truediv() (imc.types.DataFrame method)
(imc.types.Series method)
txt_to_tiff() (in module imc.utils)
U
unique() (imc.types.Series method)
unlink() (imc.types.Path method)
uns (imc.types.AnnData property)
uns_keys() (imc.types.AnnData method)
unstack() (imc.types.DataFrame method)
(imc.types.Series method)
update() (imc.types.DataFrame method)
(imc.types.Series method)
update_from() (imc.types.Patch method)
update_units() (imc.types.Axis method)
V
value_counts() (imc.types.DataFrame method)
values (imc.types.DataFrame property)
(imc.types.Series property)
values_to_rgb_colors() (in module imc.graphics)
var (imc.types.AnnData property)
var() (imc.types.DataFrame method)
(imc.types.Series method)
var_keys() (imc.types.AnnData method)
var_names (imc.types.AnnData property)
var_names_make_unique() (imc.types.AnnData method)
var_vector() (imc.types.AnnData method)
varm (imc.types.AnnData property)
varm_keys() (imc.types.AnnData method)
varp (imc.types.AnnData property)
view() (imc.types.Series method)
W
waitforbuttonpress() (imc.types.Figure method)
where() (imc.types.DataFrame method)
(imc.types.Series method)
write() (imc.types.AnnData method)
write_csvs() (imc.types.AnnData method)
write_h5ad() (imc.types.AnnData method)
write_loom() (imc.types.AnnData method)
write_ometiff() (in module imc.utils)
write_zarr() (imc.types.AnnData method)
X
X (imc.types.AnnData property)
Z
z_score() (in module imc.utils)
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