diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/index.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/index.html
index 87bac69e..18d73067 100644
--- a/unravel/docs/_build/html/_modules/unravel/cluster_stats/index.html
+++ b/unravel/docs/_build/html/_modules/unravel/cluster_stats/index.html
@@ -383,7 +383,7 @@
-
[docs]
+
[docs]
def parse_args ():
parser = argparse . ArgumentParser ( formatter_class = SuppressMetavar )
parser . add_argument ( '-ci' , '--cluster_idx' , help = 'Path to the reverse cluster index NIfTI file.' , default = None , action = SM )
@@ -399,10 +399,11 @@
Source code for unravel.cluster_stats.index
# TODO: Look into consolidating csvs
+# TODO: A few regions are omitted (e.g., 2017-IDs: 728 1007 1025 1056 1064). Look into this (see Packaging_UNRAVEL.docx for notes) and add a warning when voxels are not accounted for in a sunburst.
-
[docs]
+
[docs]
def generate_sunburst ( cluster , img , atlas , xyz_res_in_um , data_type , output_dir ):
"""Generate a sunburst plot for a given cluster.
@@ -423,7 +424,7 @@
Source code for unravel.cluster_stats.index
-
[docs]
+
[docs]
@log_command
def main ():
install ()
diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/mean_IF.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/mean_IF.html
new file mode 100644
index 00000000..01bb2860
--- /dev/null
+++ b/unravel/docs/_build/html/_modules/unravel/cluster_stats/mean_IF.html
@@ -0,0 +1,566 @@
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+
unravel.cluster_stats.mean_IF — UNRAVEL docs
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+ Source code for unravel.cluster_stats.mean_IF
+#!/usr/bin/env python3
+
+"""
+Use ``cluster_mean_IF`` from UNRAVEL to measure mean intensity of immunofluorescence staining in clusters.
+
+Usage:
+------
+ cluster_mean_IF -ci path/rev_cluster_index.nii.gz
+
+Inputs:
+ - This can be run from the vstats directory (will process .nii.gz images in the current directory)
+
+Outputs:
+ - ./cluster_mean_IF_{cluster_index}/image_name.csv for each image
+
+Next:
+ - cd cluster_mean_IF...
+ - utils_prepend -sk <path/sample_key.csv> -f # If needed
+ - cluster_mean_IF_summary --order Control Treatment --labels Control Treatment -t ttest
+ - cluster_mean_IF_summary --order group3 group2 group1 --labels Group_3 Group_2 Group_1 # Tukey tests
+"""
+
+import argparse
+import csv
+import nibabel as nib
+import numpy as np
+from pathlib import Path
+from rich.traceback import install
+
+from unravel.core.argparse_utils import SuppressMetavar , SM
+from unravel.core.config import Configuration
+from unravel.core.utils import log_command , verbose_start_msg , verbose_end_msg
+from unravel.image_tools.unique_intensities import uniq_intensities
+
+
+
+
[docs]
+
def parse_args ():
+
parser = argparse . ArgumentParser ( formatter_class = SuppressMetavar )
+
parser . add_argument ( '-ip' , '--input_pattern' , help = "Pattern for NIfTI images to process relative to cwd. Default: '*.nii.gz'" , default = '*.nii.gz' , action = SM )
+
parser . add_argument ( '-ci' , '--cluster_index' , help = 'Path/rev_cluster_index.nii.gz from ``cluster_fdr``' , required = True , action = SM )
+
parser . add_argument ( '-c' , '--clusters' , help = 'Space-separated list of cluster IDs to process. Default: all clusters' , nargs = '*' , type = int , action = SM )
+
parser . add_argument ( '-v' , '--verbose' , help = 'Increase verbosity' , action = 'store_true' , default = False )
+
parser . epilog = __doc__
+
return parser . parse_args ()
+
[docs]
+
def calculate_mean_intensity_in_clusters ( cluster_index , img , clusters = None ):
+
"""Calculates mean intensity in the img ndarray for each cluster in the cluster index ndarray and saves it to a CSV file."""
+
+
print ( " \n Calculating mean immunofluorescence intensity for each cluster... \n " )
+
+
# Filter out background
+
valid_mask = cluster_index > 0
+
cluster_index = cluster_index [ valid_mask ] . astype ( int ) # Ensure int for bincount
+
img_masked = img [ valid_mask ]
+
+
# Use bincount to sum intensities for each cluster and count voxels
+
sums = np . bincount ( cluster_index , weights = img_masked )
+
counts = np . bincount ( cluster_index )
+
+
# Suppress the runtime warning and handle potential division by zero
+
with np . errstate ( divide = 'ignore' , invalid = 'ignore' ):
+
mean_intensities = sums / counts
+
+
mean_intensities = np . nan_to_num ( mean_intensities )
+
+
# Convert to dictionary (ignore background)
+
mean_intensities_dict = { i : mean_intensities [ i ] for i in range ( 1 , len ( mean_intensities ))}
+
+
# Filter the dictionary if a list of clusters is provided
+
if clusters :
+
mean_intensities_dict = { cluster : mean_intensities_dict [ cluster ] for cluster in clusters if cluster in mean_intensities_dict }
+
+
# Optional: Print results for the filtered clsutedrs
+
for cluster , mean_intensity in mean_intensities_dict . items ():
+
print ( f " Cluster ID: { cluster } \t Mean intensity: { mean_intensity } " )
+
+
return mean_intensities_dict
+
[docs]
+
def write_to_csv ( data , output_file ):
+
"""Writes the data to a CSV file."""
+
with open ( output_file , 'w' , newline = '' ) as csvfile :
+
writer = csv . writer ( csvfile )
+
writer . writerow ([ "Cluster_ID" , "Mean_IF_Intensity" ])
+
for key , value in data . items ():
+
writer . writerow ([ key , value ])
+
[docs]
+
@log_command
+
def main ():
+
install ()
+
args = parse_args ()
+
Configuration . verbose = args . verbose
+
verbose_start_msg ()
+
+
# Either use the provided list of region IDs or create it using unique intensities
+
if args . clusters :
+
clusters = args . clusters
+
else :
+
print ( f ' \n Processing these clusters IDs from { Path ( args . cluster_index ) . name } :' )
+
clusters = uniq_intensities ( args . cluster_index )
+
print ()
+
+
output_folder = Path ( f 'cluster_mean_IF_ { str ( Path ( args . cluster_index ) . name ) . replace ( ".nii.gz" , "" ) } ' )
+
output_folder . mkdir ( parents = True , exist_ok = True )
+
+
files = Path () . cwd () . glob ( args . input_pattern )
+
for file in files :
+
if str ( file ) . endswith ( '.nii.gz' ):
+
+
nii = nib . load ( file )
+
img = np . asanyarray ( nii . dataobj , dtype = nii . header . get_data_dtype ()) . squeeze ()
+
+
cluster_index = nib . load ( args . cluster_index )
+
cluster_index = np . asanyarray ( cluster_index . dataobj , dtype = cluster_index . header . get_data_dtype ()) . squeeze ()
+
+
# Calculate mean intensity
+
mean_intensities = calculate_mean_intensity_in_clusters ( cluster_index , img , clusters )
+
+
output_filename = str ( file . name ) . replace ( '.nii.gz' , '.csv' )
+
output = output_folder / output_filename
+
+
write_to_csv ( mean_intensities , output )
+
+
print ( f 'CSVs with mean IF intensities output to ./ { output_folder } /' )
+
+
verbose_end_msg () if __name__ == '__main__' :
+ main ()
+
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\ No newline at end of file
diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/mean_IF_summary.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/mean_IF_summary.html
new file mode 100644
index 00000000..4e1b9bf7
--- /dev/null
+++ b/unravel/docs/_build/html/_modules/unravel/cluster_stats/mean_IF_summary.html
@@ -0,0 +1,709 @@
+
+
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+
unravel.cluster_stats.mean_IF_summary — UNRAVEL docs
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+ Source code for unravel.cluster_stats.mean_IF_summary
+#!/usr/bin/env python3
+
+"""
+Use ``cluster_mean_IF_summary`` from UNRAVEL to output plots of mean IF intensities for each cluster in atlas space.
+
+Usage for t-tests:
+------------------
+ cluster_mean_IF_summary --order Control Treatment --labels Control Treatment -t ttest
+
+Usage for Tukey's tests w/ reordering and renaming of conditions:
+-----------------------------------------------------------------
+ cluster_mean_IF_summary --order group3 group2 group1 --labels Group_3 Group_2 Group_1
+
+Note:
+ - The first word of the csv inputs is used for the the group names (underscore separated).
+
+Inputs:
+ - <asterisk>.csv in the working dir with these columns: 'Cluster_ID', 'Mean_IF_Intensity'
+
+Prereqs:
+ - Generate CSV inputs withs ``cluster_IF_mean``
+ - Add conditions to input CSV file names: ``utils_prepend -sk $SAMPLE_KEY -f
+
+Outputs:
+ - cluster_mean_IF_summary/cluster_<cluster_id>.pdf for each cluster
+ - If significant differences are found, a prefix '_' is added to the filename to sort the files
+"""
+
+import argparse
+import matplotlib as mpl
+import matplotlib.pyplot as plt
+import numpy as np
+import os
+import pandas as pd
+import seaborn as sns
+import textwrap
+from rich import print
+from rich.traceback import install
+from pathlib import Path
+from scipy.stats import ttest_ind , dunnett
+from statsmodels.stats.multicomp import pairwise_tukeyhsd
+
+from unravel.core.argparse_utils import SuppressMetavar , SM
+from unravel.core.config import Configuration
+from unravel.core.utils import log_command , verbose_start_msg , verbose_end_msg
+
+
+
+
[docs]
+
def parse_args ():
+
parser = argparse . ArgumentParser ( formatter_class = SuppressMetavar )
+
parser . add_argument ( '--cluster_ids' , help = 'List of cluster IDs to process (Default: process all clusters)' , nargs = '*' , type = int , action = SM )
+
parser . add_argument ( '--order' , nargs = '*' , help = 'Group Order for plotting (must match 1st word of CSVs)' , action = SM )
+
parser . add_argument ( '--labels' , nargs = '*' , help = 'Group Labels in same order' , action = SM )
+
parser . add_argument ( '-t' , '--test' , help = 'Choose between "tukey", "dunnett", and "ttest" post-hoc tests. (Default: tukey)' , default = 'tukey' , choices = [ 'tukey' , 'dunnett' , 'ttest' ], action = SM )
+
parser . add_argument ( '-alt' , "--alternate" , help = "Number of tails and direction for Dunnett's test {'two-sided', 'less' (means < ctrl), 'greater'}. Default: two-sided" , default = 'two-sided' , action = SM )
+
parser . add_argument ( '-v' , '--verbose' , help = 'Increase verbosity. Default: False' , action = 'store_true' , default = False )
+
parser . epilog = __doc__
+
return parser . parse_args () # TODO: Also output csv to summarise t-test/Tukey/Dunnett results like in ``cluster_stats``. Make symbols transparent. Add option to pass in symbol colors for each group. Add ABA coloring to plots.
+# TODO: CSVs are loaded for each cluster. It would be more efficient to load them once for processing all clusters.
+# TODO: Perhaps functions in this script could be made more generic and used in rstats_mean_IF_summary.py as well.
+# TODO: Save a CSV with the results for each cluster.
+
+
+# Set Arial as the font
+mpl . rcParams [ 'font.family' ] = 'Arial'
+
+
+
[docs]
+
def load_data ( cluster_id ):
+
data = []
+
+
# Load all CSVs in the directory
+
for filename in os . listdir ():
+
if filename . endswith ( '.csv' ):
+
group_name = filename . split ( "_" )[ 0 ]
+
df = pd . read_csv ( filename )
+
+
# Filter by the cluster ID
+
mean_intensity = df [ df [ "Cluster_ID" ] == cluster_id ][ "Mean_IF_Intensity" ] . values
+
+
if len ( mean_intensity ) > 0 :
+
data . append ({
+
'group' : group_name ,
+
'mean_intensity' : mean_intensity [ 0 ]
+
})
+
+
if data :
+
return pd . DataFrame ( data )
+
else :
+
raise ValueError ( f " [red1]No data found for cluster ID: { cluster_id } " )
+
[docs]
+
def plot_data ( cluster_id , order = None , labels = None , test_type = 'tukey' , alt = 'two-sided' ):
+
df = load_data ( cluster_id )
+
+
if 'group' not in df . columns :
+
raise KeyError ( f " [red1]'group' column not found in the DataFrame for { cluster_id } . Ensure the CSV files contain the correct data." )
+
+
# Define a list of potential colors
+
predefined_colors = [
+
'#2D67C8' , # blue
+
'#D32525' , # red
+
'#27AF2E' , # green
+
'#FFD700' , # gold
+
'#FF6347' , # tomato
+
'#8A2BE2' , # blueviolet
+
# ... add more colors if needed
+
]
+
+
# Check if order is provided and slice the color list accordingly
+
if order :
+
selected_colors = predefined_colors [: len ( order )]
+
group_colors = dict ( zip ( order , selected_colors ))
+
else :
+
groups_in_df = df [ 'group' ] . unique () . tolist ()
+
selected_colors = predefined_colors [: len ( groups_in_df )]
+
group_colors = dict ( zip ( groups_in_df , selected_colors ))
+
+
# If group order and labels are provided, update the DataFrame
+
if order and labels :
+
df [ 'group' ] = df [ 'group' ] . astype ( pd . CategoricalDtype ( categories = order , ordered = True ))
+
df = df . sort_values ( 'group' )
+
labels_mapping = dict ( zip ( order , labels ))
+
df [ 'group_label' ] = df [ 'group' ] . map ( labels_mapping )
+
else :
+
df [ 'group_label' ] = df [ 'group' ]
+
+
# Bar plot
+
plt . figure ( figsize = ( 4 , 4 ))
+
ax = sns . barplot ( x = 'group_label' , y = 'mean_intensity' , data = df , color = 'white' , errorbar = ( 'se' ), capsize = 0.1 , linewidth = 2 , edgecolor = 'black' )
+
+
# Formatting
+
ax . set_ylabel ( 'Mean IF Intensity' , weight = 'bold' )
+
ax . set_xticks ( np . arange ( len ( df [ 'group_label' ] . unique ())))
+
ax . set_xticklabels ( ax . get_xticklabels (), weight = 'bold' )
+
ax . tick_params ( axis = 'both' , which = 'major' , width = 2 )
+
ax . spines [ 'top' ] . set_visible ( False )
+
ax . spines [ 'right' ] . set_visible ( False )
+
ax . spines [ 'bottom' ] . set_linewidth ( 2 )
+
ax . spines [ 'left' ] . set_linewidth ( 2 )
+
+
# Swarm plot
+
sns . swarmplot ( x = 'group_label' , y = 'mean_intensity' , hue = 'group' , data = df , palette = group_colors , size = 8 , linewidth = 1 , edgecolor = 'black' )
+
+
# Remove the legend created by hue
+
if ax . legend_ :
+
ax . legend_ . remove ()
+
+
# Perform the chosen post-hoc test
+
if test_type == 'tukey' :
+
test_results = pairwise_tukeyhsd ( df [ 'mean_intensity' ], df [ 'group' ]) . summary ()
+
test_df = pd . DataFrame ( test_results . data [ 1 :], columns = test_results . data [ 0 ])
+
elif test_type == 'dunnett' :
+
# Assuming control is the first group in the order (change as needed)
+
control_data = df [ df [ 'group' ] == order [ 0 ]][ 'mean_intensity' ] . values
+
experimental_data = [ df [ df [ 'group' ] == group ][ 'mean_intensity' ] . values for group in order [ 1 :]]
+
test_stats = dunnett ( * experimental_data , control = control_data , alternative = alt )
+
# Convert the result to a DataFrame similar to the Tukey output for easier handling
+
test_df = pd . DataFrame ({
+
'group1' : [ order [ 0 ]] * len ( test_stats . pvalue ),
+
'group2' : order [ 1 :],
+
'p-adj' : test_stats . pvalue
+
})
+
test_df [ 'reject' ] = test_df [ 'p-adj' ] < 0.05
+
elif test_type == 'ttest' :
+
test_df = perform_t_tests ( df , order )
+
test_df [ 'reject' ] = test_df [ 'p-adj' ] < 0.05
+
+
significant_comparisons = test_df [ test_df [ 'reject' ] == True ]
+
y_max = df [ 'mean_intensity' ] . max ()
+
y_min = df [ 'mean_intensity' ] . min ()
+
height_diff = ( y_max - y_min ) * 0.1
+
y_pos = y_max + 0.5 * height_diff
+
+
groups = df [ 'group' ] . unique ()
+
+
for _ , row in significant_comparisons . iterrows ():
+
group1 , group2 = row [ 'group1' ], row [ 'group2' ]
+
x1 = np . where ( groups == group1 )[ 0 ][ 0 ]
+
x2 = np . where ( groups == group2 )[ 0 ][ 0 ]
+
+
plt . plot ([ x1 , x1 , x2 , x2 ], [ y_pos , y_pos + height_diff , y_pos + height_diff , y_pos ], lw = 1.5 , c = 'black' )
+
+
if row [ 'p-adj' ] < 0.0001 :
+
sig = '****'
+
elif row [ 'p-adj' ] < 0.001 :
+
sig = '***'
+
elif row [ 'p-adj' ] < 0.01 :
+
sig = '**'
+
else :
+
sig = '*'
+
+
plt . text (( x1 + x2 ) * .5 , y_pos + 0.8 * height_diff , sig , horizontalalignment = 'center' , size = 'xx-large' , color = 'black' , weight = 'bold' )
+
y_pos += 3 * height_diff
+
+
# Calculate y-axis limits
+
y_max = df [ 'mean_intensity' ] . max ()
+
y_min = df [ 'mean_intensity' ] . min ()
+
height_diff = ( y_max - y_min ) * 0.1
+
y_pos = y_max + 0.5 * height_diff
+
+
# Ensure the y-axis starts from the minimum value, allowing for negative values
+
plt . ylim ( y_min - 2 * height_diff , y_pos + 2 * height_diff )
+
+
# plt.ylim(0, y_pos + 2*height_diff)
+
ax . set_xlabel ( None )
+
+
# Save the plot
+
output_folder = Path ( 'cluster_mean_IF_summary' )
+
output_folder . mkdir ( parents = True , exist_ok = True )
+
+
title = f "Cluster: { cluster_id } "
+
wrapped_title = textwrap . fill ( title , 42 ) # wraps at x characters. Adjust as needed.
+
plt . title ( wrapped_title )
+
plt . tight_layout ()
+
+
is_significant = not significant_comparisons . empty
+
file_prefix = '_' if is_significant else ''
+
file_name = f " { file_prefix } cluster_ { cluster_id } .pdf"
+
plt . savefig ( output_folder / file_name )
+
+
plt . close ()
+
[docs]
+
@log_command
+
def main ():
+
install ()
+
args = parse_args ()
+
Configuration . verbose = args . verbose
+
verbose_start_msg ()
+
+
if ( args . order and not args . labels ) or ( not args . order and args . labels ):
+
raise ValueError ( "Both --order and --labels must be provided together." )
+
+
if args . order and args . labels and len ( args . order ) != len ( args . labels ):
+
raise ValueError ( "The number of entries in --order and --labels must match." )
+
+
# Print CSVs in the working dir
+
print ( f ' \n [bold]CSVs in the working dir to process (the first word defines the groups): \n ' )
+
for filename in os . listdir ():
+
if filename . endswith ( '.csv' ):
+
print ( f ' { filename } ' )
+
print ()
+
+
# If cluster IDs are provided, use them; otherwise, get all cluster IDs from the first CSV
+
clusters_to_process = args . cluster_ids if args . cluster_ids else pd . read_csv ( next ( Path () . glob ( '*.csv' ))) . Cluster_ID . unique ()
+
+
# Process each cluster ID
+
for cluster_id in clusters_to_process :
+
plot_data ( cluster_id , args . order , args . labels , test_type = args . test , alt = args . alternate )
+
+
verbose_end_msg () if __name__ == '__main__' :
+ main ()
+
+
+
+
+
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\ No newline at end of file
diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/table.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/table.html
index a8645790..93380aaa 100644
--- a/unravel/docs/_build/html/_modules/unravel/cluster_stats/table.html
+++ b/unravel/docs/_build/html/_modules/unravel/cluster_stats/table.html
@@ -407,12 +407,14 @@
Source code for unravel.cluster_stats.table
parser . add_argument ( '-t' , '--top_regions' , help = 'Number of top regions to output. Default: 4' , default = 4 , type = int , action = SM )
parser . add_argument ( '-pv' , '--percent_vol' , help = 'Percentage of the total volume the top regions must comprise [after collapsing]. Default: 0.8' , default = 0.8 , type = float , action = SM )
parser . add_argument ( '-csv' , '--info_csv_path' , help = 'CSV name or path/name.csv. Default: CCFv3-2020_info.csv' , default = 'CCFv3-2020_info.csv' , action = SM )
+ parser . add_argument ( '-rgb' , '--sunburst_rgbs' , help = 'CSV name or path/name.csv. Default: sunburst_RGBs.csv' , default = 'sunburst_RGBs.csv' , action = SM )
parser . add_argument ( '-v' , '--verbose' , help = 'Increase verbosity. Default: False' , action = 'store_true' , default = False )
parser . epilog = __doc__
return parser . parse_args () # TODO: Correct font color for the volumes column. 'fiber tracts' is filled with white rather than the color of the fiber tracts
+
# TODO: 'CUL4, 5' is not filled with the color of the region.
@@ -766,7 +768,10 @@
Source code for unravel.cluster_stats.table
print ( f ' \n { top_regions_and_percent_vols_df . to_string ( index = False ) } \n ' )
# Load csv with RGB values
- sunburst_RGBs_df = pd . read_csv ( Path ( __file__ ) . parent . parent / 'core' / 'csvs' / 'sunburst_RGBs.csv' , header = None )
+ if args . sunburst_rgbs == 'sunburst_RGBs.csv' :
+ sunburst_RGBs_df = pd . read_csv ( Path ( __file__ ) . parent . parent / 'core' / 'csvs' / 'sunburst_RGBs.csv' , header = None )
+ else :
+ sunburst_RGBs_df = pd . read_csv ( args . sunburst_rgbs , header = None )
# Parse the dataframe to get a dictionary of region names and their corresponding RGB values
rgb_values = {}
diff --git a/unravel/docs/_build/html/_modules/unravel/core/utils.html b/unravel/docs/_build/html/_modules/unravel/core/utils.html
index d778d07f..66fe1d0c 100644
--- a/unravel/docs/_build/html/_modules/unravel/core/utils.html
+++ b/unravel/docs/_build/html/_modules/unravel/core/utils.html
@@ -585,6 +585,7 @@ Source code for unravel.core.utils
[docs]
def log_command ( func ):
"""A decorator for main() to log the command and execution times to a hidden file (.command_log.txt)."""
+ # TODO: avoid logging when -h or --help is used
@functools . wraps ( func )
def wrapper ( * args , ** kwargs ):
log_file = ".command_log.txt" # Name of the hidden log file
diff --git a/unravel/docs/_build/html/_modules/unravel/image_tools/unique_intensities.html b/unravel/docs/_build/html/_modules/unravel/image_tools/unique_intensities.html
index 2f3c3026..1c5ed96a 100644
--- a/unravel/docs/_build/html/_modules/unravel/image_tools/unique_intensities.html
+++ b/unravel/docs/_build/html/_modules/unravel/image_tools/unique_intensities.html
@@ -408,7 +408,7 @@ Source code for unravel.image_tools.unique_intensities """
if str ( input ) . endswith ( ".nii.gz" ):
nii = nib . load ( input )
-
img = np . asanyarray ( nii . dataobj , dtype = np . uint16 ) . squeeze ()
+
img = np . asanyarray ( nii . dataobj , dtype = nii . header . get_data_dtype ()) . squeeze ()
else :
img = load_3D_img ( input )
diff --git a/unravel/docs/_build/html/_modules/unravel/region_stats/rstats_mean_IF.html b/unravel/docs/_build/html/_modules/unravel/region_stats/rstats_mean_IF.html
index db665e91..8d8bad92 100644
--- a/unravel/docs/_build/html/_modules/unravel/region_stats/rstats_mean_IF.html
+++ b/unravel/docs/_build/html/_modules/unravel/region_stats/rstats_mean_IF.html
@@ -385,7 +385,7 @@
Source code for unravel.region_stats.rstats_mean_IF parser = argparse . ArgumentParser ( formatter_class = SuppressMetavar )
parser . add_argument ( '-i' , '--input' , help = "Pattern for NIfTI images to process (e.g., '*.nii.gz')" , required = True , action = SM )
parser . add_argument ( '-a' , '--atlas' , help = 'Path/atlas.nii.gz' , required = True , action = SM )
- parser . add_argument ( '-r' , '--regions' , nargs = '*' , type = int , help = 'Space-separated list of region intensities to process' )
+ parser . add_argument ( '-r' , '--regions' , help = 'Space-separated list of region intensities to process' , nargs = '*' , type = int , action = SM )
parser . add_argument ( '-v' , '--verbose' , help = 'Increase verbosity. Default: False' , action = 'store_true' , default = False )
parser . epilog = __doc__
return parser . parse_args ()
@@ -401,10 +401,10 @@
Source code for unravel.region_stats.rstats_mean_IF # Filter out background
valid_mask = atlas > 0
-
valid_atlas = atlas [ valid_mask ] . astype ( int )
+
valid_atlas = atlas [ valid_mask ] . astype ( int ) # Convert to int for bincount
valid_image = image [ valid_mask ]
-
# Use bincount to get sums for each region
+
# Use bincount to sum intensities for each cluster and count voxels
sums = np . bincount ( valid_atlas , weights = valid_image )
counts = np . bincount ( valid_atlas )
diff --git a/unravel/docs/_build/html/_modules/unravel/region_stats/rstats_mean_IF_summary.html b/unravel/docs/_build/html/_modules/unravel/region_stats/rstats_mean_IF_summary.html
index 5da6c69d..41fa5d36 100644
--- a/unravel/docs/_build/html/_modules/unravel/region_stats/rstats_mean_IF_summary.html
+++ b/unravel/docs/_build/html/_modules/unravel/region_stats/rstats_mean_IF_summary.html
@@ -375,7 +375,11 @@
Source code for unravel.region_stats.rstats_mean_IF_summary Prereqs:
- Generate CSV inputs withs ``rstats_IF_mean`` or ``rstats_IF_mean_in_seg``
- After ``rstats_IF_mean_in_seg``, aggregate CSV inputs with ``utils_agg_files``
-
- If needed, add conditions to input CSV file names: utils_prepend -sk $SAMPLE_KEY -f
+
- If needed, add conditions to input CSV file names: ``utils_prepend`` -sk $SAMPLE_KEY -f
+
+
Outputs:
+
- rstats_mean_IF_summary/region_<region_id>_<region_abbr>.pdf for each region
+
- If significant differences are found, a prefix '_' is added to the filename to sort the files
The look up table (LUT) csv has these columns:
'Region_ID', 'Side', 'Name', 'Abbr'
@@ -418,6 +422,8 @@
Source code for unravel.region_stats.rstats_mean_IF_summary # TODO: Also output csv to summarise t-test/Tukey/Dunnett results like in ``cluster_stats``. Make symbols transparent. Add option to pass in symbol colors for each group. Add ABA coloring to plots.
# TODO: CSVs are loaded for each region. It would be more efficient to load them once for processing all regions.
+
# TODO: Update coloring of plots to match ABA colors (i.e., use code from rstats_summary.py)
+
# TODO: Save a CSV with the results of the statistical tests for each region.
# Set Arial as the font
diff --git a/unravel/docs/_build/html/_modules/unravel/unravel_commands.html b/unravel/docs/_build/html/_modules/unravel/unravel_commands.html
index c6c586a2..43189b43 100644
--- a/unravel/docs/_build/html/_modules/unravel/unravel_commands.html
+++ b/unravel/docs/_build/html/_modules/unravel/unravel_commands.html
@@ -603,6 +603,16 @@
Source code for unravel.unravel_commands
"description" : "Crop clusters to a bounding box." ,
"common" : False
},
+ "cluster_mean_IF" : {
+ "module" : "unravel.cluster_stats.mean_IF" ,
+ "description" : "Compute mean immunofluo intensities for each cluster. " ,
+ "common" : False
+ },
+ "cluster_mean_IF_summary" : {
+ "module" : "unravel.cluster_stats.mean_IF_summary" ,
+ "description" : "Plot mean immunofluo intensities for each cluster." ,
+ "common" : False
+ },
"effect_sizes" : {
"module" : "unravel.cluster_stats.effect_sizes.effect_sizes" ,
"description" : "Calculate effect sizes for clusters." ,
@@ -642,7 +652,7 @@ Source code for unravel.unravel_commands
},
"rstats_mean_IF_summary" : {
"module" : "unravel.region_stats.rstats_mean_IF_summary" ,
- "description" : "Summarize mean immunofluo intensities for regions." ,
+ "description" : "Plot mean immunofluo intensities for regions." ,
"common" : False
}
},
diff --git a/unravel/docs/_build/html/_sources/guide.md.txt b/unravel/docs/_build/html/_sources/guide.md.txt
index 552fb39f..fbc3d1bd 100644
--- a/unravel/docs/_build/html/_sources/guide.md.txt
+++ b/unravel/docs/_build/html/_sources/guide.md.txt
@@ -179,6 +179,8 @@ unravel_commands -m
- [**cluster_sunburst**](unravel.cluster_stats.sunburst): Create a sunburst plot of regional volumes.
- [**cluster_find_incongruent_clusters**](unravel.cluster_stats.find_incongruent_clusters): Find clusters where the effect direction does not match the prediction of cluster_fdr (for validation of non-directional p value maps).
- [**cluster_crop**](unravel.cluster_stats.crop): Crop clusters to a bounding box.
+- [**cluster_mean_IF**](unravel.cluster_stats.cluster_mean_IF): Compute mean immunofluo intensities for each cluster.
+- [**cluster_mean_IF_summary**](unravel.cluster_stats.cluster_mean_IF_summary): Plot mean immunofluo intensities for each cluster.
- [**effect_sizes**](unravel.cluster_stats.effect_sizes.effect_sizes): Calculate effect sizes for clusters.
- [**effect_sizes_sex_abs**](unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute): Calculate absolute effect sizes by sex.
- [**effect_sizes_sex_rel**](unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative): Calculate relative effect sizes by sex.
@@ -189,7 +191,7 @@ unravel_commands -m
- [**rstats_summary**](unravel.region_stats.rstats_summary): Summarize regional cell densities.
- [**rstats_mean_IF**](unravel.region_stats.rstats_mean_IF): Compute mean immunofluo intensities for regions.
- [**rstats_mean_IF_in_seg**](unravel.region_stats.rstats_mean_IF_in_segmented_voxels): Compute mean immunofluo intensities in segmented voxels.
-- [**rstats_mean_IF_summary**](unravel.region_stats.rstats_mean_IF_summary): Summarize mean immunofluo intensities for regions.
+- [**rstats_mean_IF_summary**](unravel.region_stats.rstats_mean_IF_summary): Plot mean immunofluo intensities for regions.
:::
:::{tab-item} Image I/O
diff --git a/unravel/docs/_build/html/_sources/unravel/cluster_stats/index.rst.txt b/unravel/docs/_build/html/_sources/unravel/cluster_stats/index.rst.txt
index b16c6033..f92151e2 100644
--- a/unravel/docs/_build/html/_sources/unravel/cluster_stats/index.rst.txt
+++ b/unravel/docs/_build/html/_sources/unravel/cluster_stats/index.rst.txt
@@ -1,9 +1,9 @@
-.. _unravel.cluster_stats.index:
+.. _unravel.cluster_stats.mean_IF:
-unravel.cluster_stats.index module
-==================================
+unravel.cluster_stats.mean_IF module
+====================================
-.. automodule:: unravel.cluster_stats.index
+.. automodule:: unravel.cluster_stats.mean_IF
:members:
:undoc-members:
:show-inheritance:
diff --git a/unravel/docs/_build/html/_sources/unravel/cluster_stats/mean_IF.rst.txt b/unravel/docs/_build/html/_sources/unravel/cluster_stats/mean_IF.rst.txt
new file mode 100644
index 00000000..b16c6033
--- /dev/null
+++ b/unravel/docs/_build/html/_sources/unravel/cluster_stats/mean_IF.rst.txt
@@ -0,0 +1,9 @@
+.. _unravel.cluster_stats.index:
+
+unravel.cluster_stats.index module
+==================================
+
+.. automodule:: unravel.cluster_stats.index
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/unravel/docs/_build/html/_sources/unravel/cluster_stats/mean_IF_summary.rst.txt b/unravel/docs/_build/html/_sources/unravel/cluster_stats/mean_IF_summary.rst.txt
new file mode 100644
index 00000000..4dc19497
--- /dev/null
+++ b/unravel/docs/_build/html/_sources/unravel/cluster_stats/mean_IF_summary.rst.txt
@@ -0,0 +1,9 @@
+.. _unravel.cluster_stats.mean_IF_summary:
+
+unravel.cluster_stats.mean_IF_summary module
+============================================
+
+.. automodule:: unravel.cluster_stats.mean_IF_summary
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/unravel/docs/_build/html/_sources/unravel/cluster_stats/toc.rst.txt b/unravel/docs/_build/html/_sources/unravel/cluster_stats/toc.rst.txt
index eef2d48d..29d7b109 100644
--- a/unravel/docs/_build/html/_sources/unravel/cluster_stats/toc.rst.txt
+++ b/unravel/docs/_build/html/_sources/unravel/cluster_stats/toc.rst.txt
@@ -21,6 +21,8 @@ unravel.cluster_stats package
sunburst
table
crop
+ mean_IF
+ mean_IF_summary
effect_sizes/toc
.. automodule:: unravel.cluster_stats
diff --git a/unravel/docs/_build/html/genindex.html b/unravel/docs/_build/html/genindex.html
index 524693d6..00083932 100644
--- a/unravel/docs/_build/html/genindex.html
+++ b/unravel/docs/_build/html/genindex.html
@@ -387,6 +387,8 @@ C
(in module unravel.region_stats.rstats_mean_IF_in_segmented_voxels)
+
calculate_mean_intensity_in_clusters() (in module unravel.cluster_stats.mean_IF)
+calculate_padded_dimensions() (in module unravel.warp.to_fixed)
calculate_regional_densities() (in module unravel.region_stats.rstats)
@@ -421,6 +423,8 @@ C
collapse_hierarchy() (in module unravel.cluster_stats.table)
+
+
-
Config (class in unravel.core.config)
Configuration (class in unravel.core.config)
@@ -549,7 +551,7 @@ G
load_image_metadata_from_txt() (in module unravel.core.img_io)
-load_mask() (in module unravel.voxel_stats.apply_mask)
+ load_mask() (in module unravel.voxel_stats.apply_mask)
+load_nii() (in module unravel.core.img_io)
load_nii_orientation() (in module unravel.core.img_io)
@@ -682,9 +688,13 @@ M
(in module unravel.cluster_stats.group_bilateral_data)
(in module unravel.cluster_stats.index)
+ (in module unravel.cluster_stats.index)
(in module unravel.cluster_stats.legend)
+(in module unravel.cluster_stats.mean_IF)
+(in module unravel.cluster_stats.mean_IF_summary)
(in module unravel.cluster_stats.org_data)
M
unravel.cluster_stats.group_bilateral_data
unravel.cluster_stats.index
+ unravel.cluster_stats.index
unravel.cluster_stats.legend
+unravel.cluster_stats.mean_IF
+unravel.cluster_stats.mean_IF_summary
unravel.cluster_stats.org_data
P
(in module unravel.cluster_stats.group_bilateral_data)
(in module unravel.cluster_stats.index)
+ (in module unravel.cluster_stats.index)
(in module unravel.cluster_stats.legend)
+(in module unravel.cluster_stats.mean_IF)
+(in module unravel.cluster_stats.mean_IF_summary)
(in module unravel.cluster_stats.org_data)
P
+
+
unravel.image_tools.bbox
@@ -1674,8 +1716,6 @@ U
module
-
unravel.image_tools.DoG
@@ -1998,9 +2038,11 @@ W
unravel.cluster_stats.find_incongruent_clusters module unravel.cluster_stats.group_bilateral_data module unravel.cluster_stats.index module unravel.cluster_stats.mean_IF module unravel.cluster_stats.legend module unravel.cluster_stats.org_data module unravel.cluster_stats.prism module unravel.cluster_stats.table module unravel.cluster_stats.crop module unravel.cluster_stats.index module unravel.cluster_stats.mean_IF_summary module unravel.cluster_stats.effect_sizes package Python Module Index
- unravel.cluster_stats.index
+ unravel.cluster_stats.index
unravel.cluster_stats.legend
+
+
+ unravel.cluster_stats.mean_IF
+
+
+
+ unravel.cluster_stats.mean_IF_summary
+
diff --git a/unravel/docs/_build/html/searchindex.js b/unravel/docs/_build/html/searchindex.js
index 671af18b..6304220d 100644
--- a/unravel/docs/_build/html/searchindex.js
+++ b/unravel/docs/_build/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"3 letter orientation code": [[0, null]], "Add images to sample?? dirs": [[0, "add-images-to-sample-dirs"]], "Additional contributions from": [[1, "additional-contributions-from"]], "All commands": [[0, null]], "Allen brain atlas coloring": [[0, null]], "Analysis steps": [[0, "analysis-steps"]], "Automatic logging of scripts": [[0, null]], "Back up raw data": [[0, "back-up-raw-data"]], "Background subtraction": [[0, null]], "Batch stitching settings": [[0, null]], "CLI usage:": [[98, "cli-usage"]], "Checking changes between versions": [[2, null]], "Cluster correction": [[0, "cluster-correction"]], "Cluster validation": [[0, "cluster-validation"]], "Common commands": [[0, "common-commands"]], "Contact us": [[1, "contact-us"]], "Contents:": [[1, null]], "Data can be distributed across multiple drives": [[0, null]], "Define common variables in a shell script": [[0, "define-common-variables-in-a-shell-script"]], "Developers": [[1, "developers"]], "Edit .bashrc or .zshrc to set up dependencies": [[2, "edit-bashrc-or-zshrc-to-set-up-dependencies"]], "Example experiment folder structure after analysis": [[0, "example-experiment-folder-structure-after-analysis"]], "Example sample?? folder structure after analysis": [[0, "example-sample-folder-structure-after-analysis"]], "Get started with analysis": [[2, "get-started-with-analysis"]], "Getting started": [[1, "getting-started"]], "Guide": [[0, "guide"]], "Help on commands": [[0, "help-on-commands"]], "Helper Functions:": [[28, "helper-functions"]], "If sample orientations vary": [[0, null]], "Indices": [[1, "indices"]], "Installation": [[2, "installation"]], "Installing UNRAVEL on Linux or WSL": [[2, "installing-unravel-on-linux-or-wsl"]], "Listing commands": [[0, "listing-commands"]], "Log exp paths, commands, etc.": [[0, "log-exp-paths-commands-etc"]], "Main Functions:": [[28, "main-functions"]], "Main dependencies": [[1, "main-dependencies"]], "Make a sample_key.csv:": [[0, "make-a-sample-key-csv"]], "Make an exp_notes.txt": [[0, null]], "Make sample folders": [[0, "make-sample-folders"]], "Module contents": [[76, "module-contents"]], "More info on commands": [[0, null]], "Name sample folders like sample01, sample02, \u2026": [[0, null]], "Note x/y and z voxel sizes": [[0, "note-x-y-and-z-voxel-sizes"]], "Open source options for stitching": [[0, null]], "Optional: clean tifs": [[0, "optional-clean-tifs"]], "Optional: editable installation of UNRAVEL": [[2, "optional-editable-installation-of-unravel"]], "Output:": [[60, "output"], [60, "id3"], [60, "id5"]], "Overview and steps for voxel-wise stats": [[0, null]], "Parameters:": [[60, "parameters"], [60, "id1"], [60, "id4"]], "Please note the version of UNRAVEL you are using for reproducibility.": [[2, null]], "Python usage:": [[66, "python-usage"], [98, "python-usage"]], "Region-wise stats": [[0, "region-wise-stats"]], "Registration": [[0, "registration"]], "Returns:": [[60, "returns"], [60, "id2"]], "Running batch stitching": [[0, null]], "Segmentation": [[0, "segmentation"]], "Set up": [[0, "set-up"]], "Setting Up Windows Subsystem for Linux (WSL)": [[2, "setting-up-windows-subsystem-for-linux-wsl"]], "Sorting by hierarchy and volume:": [[23, "sorting-by-hierarchy-and-volume"]], "Stitch z-stacks": [[0, "stitch-z-stacks"]], "Subpackages": [[76, "subpackages"]], "Support is welcome for": [[1, "support-is-welcome-for"]], "Syntax": [[0, null]], "T-test usage:": [[20, "t-test-usage"]], "TL;DR": [[2, "tl-dr"]], "Todo": [[0, "id1"], [0, "id2"], [0, "id5"], [2, "id1"]], "Train an Ilastik project": [[0, "train-an-ilastik-project"], [0, null]], "Tukey\u2019s test usage:": [[20, "tukey-s-test-usage"]], "Typical workflow": [[0, "typical-workflow"]], "UN-biased high-Resolution Analysis and Validation of Ensembles using Light sheet images": [[1, "un-biased-high-resolution-analysis-and-validation-of-ensembles-using-light-sheet-images"]], "UNRAVEL visualizer": [[1, "unravel-visualizer"]], "Updating UNRAVEL": [[2, "updating-unravel"]], "Usage": [[6, "usage"], [7, "usage"], [9, "usage"], [11, "usage"], [12, "usage"], [13, "usage"], [14, "usage"], [15, "usage"], [17, "usage"], [18, "usage"], [19, "usage"], [62, "usage"]], "Usage for Tukey\u2019s tests w/ reordering and renaming of conditions:": [[63, "usage-for-tukey-s-tests-w-reordering-and-renaming-of-conditions"]], "Usage for activating sample?? dirs for certain conditions:": [[84, "usage-for-activating-sample-dirs-for-certain-conditions"]], "Usage for atlas to atlas registration:": [[67, "usage-for-atlas-to-atlas-registration"]], "Usage for forward warping atlas to tissue space:": [[100, "usage-for-forward-warping-atlas-to-tissue-space"]], "Usage for inverse warping tissue to atlas space:": [[100, "usage-for-inverse-warping-tissue-to-atlas-space"]], "Usage for printing all non-zero intensities:": [[59, "usage-for-printing-all-non-zero-intensities"]], "Usage for printing the number of voxels for each intensity that is present:": [[59, "usage-for-printing-the-number-of-voxels-for-each-intensity-that-is-present"]], "Usage for printing unique intensities w/ a min cluster size > 100 voxels:": [[59, "usage-for-printing-unique-intensities-w-a-min-cluster-size-100-voxels"]], "Usage for renaming directories:": [[82, "usage-for-renaming-directories"]], "Usage for renaming files:": [[82, "usage-for-renaming-files"]], "Usage for t-tests:": [[63, "usage-for-t-tests"]], "Usage for template to template registration:": [[67, "usage-for-template-to-template-registration"]], "Usage for tissue registration:": [[67, "usage-for-tissue-registration"]], "Usage for toggling all sample?? dirs to active:": [[84, "usage-for-toggling-all-sample-dirs-to-active"]], "Usage for when metadata is extractable:": [[36, "usage-for-when-metadata-is-extractable"]], "Usage for when metadata is not extractable:": [[36, "usage-for-when-metadata-is-not-extractable"]], "Usage for when sample?? is already in the name of files being copied:": [[78, "usage-for-when-sample-is-already-in-the-name-of-files-being-copied"]], "Usage for z-score scaling (if 8 bit is needed):": [[35, "usage-for-z-score-scaling-if-8-bit-is-needed"]], "Usage if running after cluster_validation and cluster_org_data:": [[4, "usage-if-running-after-cluster-validation-and-cluster-org-data"]], "Usage if running directly after cluster_validation:": [[4, "usage-if-running-directly-after-cluster-validation"]], "Usage if the atlas is already in native space from warp_to_native:": [[60, "usage-if-the-atlas-is-already-in-native-space-from-warp-to-native"]], "Usage if the native atlas is not available; it is not saved (faster):": [[60, "usage-if-the-native-atlas-is-not-available-it-is-not-saved-faster"]], "Usage to prep for seg_brain_mask:": [[73, "usage-to-prep-for-seg-brain-mask"]], "Usage to prep for seg_ilastik to segment full resolution immunofluorescence images:": [[73, "usage-to-prep-for-seg-ilastik-to-segment-full-resolution-immunofluorescence-images"]], "Usage to prepend sample?? to the name of files being copied:": [[78, "usage-to-prepend-sample-to-the-name-of-files-being-copied"]], "Usage to print all commands and module names:": [[77, "usage-to-print-all-commands-and-module-names"]], "Usage to print common commands and descriptions:": [[77, "usage-to-print-common-commands-and-descriptions"]], "Usage to replace voxels in image with the mean intensity in the brain where mask > 0:": [[85, "usage-to-replace-voxels-in-image-with-the-mean-intensity-in-the-brain-where-mask-0"]], "Usage to zero out voxels in image where mask < 1 (e.g., to preserve signal from segmented microglia clusters):": [[85, "usage-to-zero-out-voxels-in-image-where-mask-1-e-g-to-preserve-signal-from-segmented-microglia-clusters"]], "Usage to zero out voxels in image where mask > 0 (e.g., to exclude voxels representing artifacts):": [[85, "usage-to-zero-out-voxels-in-image-where-mask-0-e-g-to-exclude-voxels-representing-artifacts"]], "Usage w/ a tissue mask (warped to atlas space):": [[95, "usage-w-a-tissue-mask-warped-to-atlas-space"]], "Usage w/ additional options:": [[92, "usage-w-additional-options"]], "Usage w/ an atlas mask (warped to atlas space):": [[95, "usage-w-an-atlas-mask-warped-to-atlas-space"]], "Usage w/ both masks for side-specific z-scoring:": [[95, "usage-w-both-masks-for-side-specific-z-scoring"]], "Usage with CCFv3:": [[3, "usage-with-ccfv3"]], "Usage with a custom atlas:": [[63, "usage-with-a-custom-atlas"]], "Usage with gubra atlas:": [[3, "usage-with-gubra-atlas"]], "Usage:": [[5, "usage"], [16, "usage"], [21, "usage"], [22, "usage"], [23, "usage"], [32, "usage"], [33, "usage"], [34, "usage"], [35, "usage"], [37, "usage"], [38, "usage"], [39, "usage"], [40, "usage"], [41, "usage"], [42, "usage"], [44, "usage"], [45, "usage"], [46, "usage"], [48, "usage"], [49, "usage"], [50, "usage"], [52, "usage"], [53, "usage"], [54, "usage"], [55, "usage"], [56, "usage"], [58, "usage"], [61, "usage"], [64, "usage"], [66, "usage"], [68, 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"count_cells() (in module unravel.cluster_stats.cluster_validation)": [[5, "unravel.cluster_stats.cluster_validation.count_cells", false]], "count_cells_in_regions() (in module unravel.region_stats.rstats)": [[60, "unravel.region_stats.rstats.count_cells_in_regions", false]], "count_files() (in module unravel.segment.ilastik_pixel_classification)": [[74, "unravel.segment.ilastik_pixel_classification.count_files", false]], "cp() (in module unravel.cluster_stats.org_data)": [[17, "unravel.cluster_stats.org_data.cp", false]], "create_design_ttest2() (in module unravel.voxel_stats.vstats)": [[92, "unravel.voxel_stats.vstats.create_design_ttest2", false]], "crop() (in module unravel.core.img_tools)": [[29, "unravel.core.img_tools.crop", false]], "crop_outer_space() (in module unravel.cluster_stats.cluster_validation)": [[5, "unravel.cluster_stats.cluster_validation.crop_outer_space", false]], "custommofncompletecolumn (class in unravel.core.utils)": [[31, 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\ No newline at end of file
+Search.setIndex({"alltitles": {"3 letter orientation code": [[0, null]], "Add images to sample?? dirs": [[0, "add-images-to-sample-dirs"]], "Additional contributions from": [[1, "additional-contributions-from"]], "All commands": [[0, null]], "Allen brain atlas coloring": [[0, null]], "Analysis steps": [[0, "analysis-steps"]], "Automatic logging of scripts": [[0, null]], "Back up raw data": [[0, "back-up-raw-data"]], "Background subtraction": [[0, null]], "Batch stitching settings": [[0, null]], "CLI usage:": [[100, "cli-usage"]], "Checking changes between versions": [[2, null]], "Cluster correction": [[0, "cluster-correction"]], "Cluster validation": [[0, "cluster-validation"]], "Common commands": [[0, "common-commands"]], "Contact us": [[1, "contact-us"]], "Contents:": [[1, null]], "Data can be distributed across multiple drives": [[0, null]], "Define common variables in a shell script": [[0, "define-common-variables-in-a-shell-script"]], "Developers": [[1, "developers"]], "Edit .bashrc or .zshrc to set up dependencies": [[2, "edit-bashrc-or-zshrc-to-set-up-dependencies"]], "Example experiment folder structure after analysis": [[0, "example-experiment-folder-structure-after-analysis"]], "Example sample?? folder structure after analysis": [[0, "example-sample-folder-structure-after-analysis"]], "Get started with analysis": [[2, "get-started-with-analysis"]], "Getting started": [[1, "getting-started"]], "Guide": [[0, "guide"]], "Help on commands": [[0, "help-on-commands"]], "Helper Functions:": [[30, "helper-functions"]], "If sample orientations vary": [[0, null]], "Indices": [[1, "indices"]], "Installation": [[2, "installation"]], "Installing UNRAVEL on Linux or WSL": [[2, "installing-unravel-on-linux-or-wsl"]], "Listing commands": [[0, "listing-commands"]], "Log exp paths, commands, etc.": [[0, "log-exp-paths-commands-etc"]], "Main Functions:": [[30, "main-functions"]], "Main dependencies": [[1, "main-dependencies"]], "Make a sample_key.csv:": [[0, "make-a-sample-key-csv"]], "Make an exp_notes.txt": [[0, null]], "Make sample folders": [[0, "make-sample-folders"]], "Module contents": [[78, "module-contents"]], "More info on commands": [[0, null]], "Name sample folders like sample01, sample02, \u2026": [[0, null]], "Note x/y and z voxel sizes": [[0, "note-x-y-and-z-voxel-sizes"]], "Open source options for stitching": [[0, null]], "Optional: clean tifs": [[0, "optional-clean-tifs"]], "Optional: editable installation of UNRAVEL": [[2, "optional-editable-installation-of-unravel"]], "Output:": [[62, "output"], [62, "id3"], [62, "id5"]], "Overview and steps for voxel-wise stats": [[0, null]], "Parameters:": [[62, "parameters"], [62, "id1"], [62, "id4"]], "Please note the version of UNRAVEL you are using for reproducibility.": [[2, null]], "Python usage:": [[68, "python-usage"], [100, "python-usage"]], "Region-wise stats": [[0, "region-wise-stats"]], "Registration": [[0, "registration"]], "Returns:": [[62, "returns"], [62, "id2"]], "Running batch stitching": [[0, null]], "Segmentation": [[0, "segmentation"]], "Set up": [[0, "set-up"]], "Setting Up Windows Subsystem for Linux (WSL)": [[2, "setting-up-windows-subsystem-for-linux-wsl"]], "Sorting by hierarchy and volume:": [[25, "sorting-by-hierarchy-and-volume"]], "Stitch z-stacks": [[0, "stitch-z-stacks"]], "Subpackages": [[78, "subpackages"]], "Support is welcome for": [[1, "support-is-welcome-for"]], "Syntax": [[0, null]], "T-test usage:": [[22, "t-test-usage"]], "TL;DR": [[2, "tl-dr"]], "Todo": [[0, "id1"], [0, "id2"], [0, "id5"], [2, "id1"]], "Train an Ilastik project": [[0, "train-an-ilastik-project"], [0, null]], "Tukey\u2019s test usage:": [[22, "tukey-s-test-usage"]], "Typical workflow": [[0, "typical-workflow"]], "UN-biased high-Resolution Analysis and Validation of Ensembles using Light sheet images": [[1, "un-biased-high-resolution-analysis-and-validation-of-ensembles-using-light-sheet-images"]], "UNRAVEL visualizer": [[1, "unravel-visualizer"]], "Updating UNRAVEL": [[2, "updating-unravel"]], "Usage": [[6, "usage"], [7, "usage"], [9, "usage"], [11, "usage"], [12, "usage"], [13, "usage"], [14, "usage"], [17, "usage"], [19, "usage"], [20, "usage"], [21, "usage"], [64, "usage"]], "Usage for Tukey\u2019s tests w/ reordering and renaming of conditions:": [[18, "usage-for-tukey-s-tests-w-reordering-and-renaming-of-conditions"], [65, "usage-for-tukey-s-tests-w-reordering-and-renaming-of-conditions"]], "Usage for activating sample?? dirs for certain conditions:": [[86, "usage-for-activating-sample-dirs-for-certain-conditions"]], "Usage for atlas to atlas registration:": [[69, "usage-for-atlas-to-atlas-registration"]], "Usage for forward warping atlas to tissue space:": [[102, "usage-for-forward-warping-atlas-to-tissue-space"]], "Usage for inverse warping tissue to atlas space:": [[102, "usage-for-inverse-warping-tissue-to-atlas-space"]], "Usage for printing all non-zero intensities:": [[61, "usage-for-printing-all-non-zero-intensities"]], "Usage for printing the number of voxels for each intensity that is present:": [[61, "usage-for-printing-the-number-of-voxels-for-each-intensity-that-is-present"]], "Usage for printing unique intensities w/ a min cluster size > 100 voxels:": [[61, "usage-for-printing-unique-intensities-w-a-min-cluster-size-100-voxels"]], "Usage for renaming directories:": [[84, "usage-for-renaming-directories"]], "Usage for renaming files:": [[84, "usage-for-renaming-files"]], "Usage for t-tests:": [[18, "usage-for-t-tests"], [65, "usage-for-t-tests"]], "Usage for template to template registration:": [[69, "usage-for-template-to-template-registration"]], "Usage for tissue registration:": [[69, "usage-for-tissue-registration"]], "Usage for toggling all sample?? dirs to active:": [[86, "usage-for-toggling-all-sample-dirs-to-active"]], "Usage for when metadata is extractable:": [[38, "usage-for-when-metadata-is-extractable"]], "Usage for when metadata is not extractable:": [[38, "usage-for-when-metadata-is-not-extractable"]], "Usage for when sample?? is already in the name of files being copied:": [[80, "usage-for-when-sample-is-already-in-the-name-of-files-being-copied"]], "Usage for z-score scaling (if 8 bit is needed):": [[37, "usage-for-z-score-scaling-if-8-bit-is-needed"]], "Usage if running after cluster_validation and cluster_org_data:": [[4, "usage-if-running-after-cluster-validation-and-cluster-org-data"]], "Usage if running directly after cluster_validation:": [[4, "usage-if-running-directly-after-cluster-validation"]], "Usage if the atlas is already in native space from warp_to_native:": [[62, "usage-if-the-atlas-is-already-in-native-space-from-warp-to-native"]], "Usage if the native atlas is not available; it is not saved (faster):": [[62, "usage-if-the-native-atlas-is-not-available-it-is-not-saved-faster"]], "Usage to prep for seg_brain_mask:": [[75, "usage-to-prep-for-seg-brain-mask"]], "Usage to prep for seg_ilastik to segment full resolution immunofluorescence images:": [[75, "usage-to-prep-for-seg-ilastik-to-segment-full-resolution-immunofluorescence-images"]], "Usage to prepend sample?? to the name of files being copied:": [[80, "usage-to-prepend-sample-to-the-name-of-files-being-copied"]], "Usage to print all commands and module names:": [[79, "usage-to-print-all-commands-and-module-names"]], "Usage to print common commands and descriptions:": [[79, "usage-to-print-common-commands-and-descriptions"]], "Usage to replace voxels in image with the mean intensity in the brain where mask > 0:": [[87, "usage-to-replace-voxels-in-image-with-the-mean-intensity-in-the-brain-where-mask-0"]], "Usage to zero out voxels in image where mask < 1 (e.g., to preserve signal from segmented microglia clusters):": [[87, "usage-to-zero-out-voxels-in-image-where-mask-1-e-g-to-preserve-signal-from-segmented-microglia-clusters"]], "Usage to zero out voxels in image where mask > 0 (e.g., to exclude voxels representing artifacts):": [[87, "usage-to-zero-out-voxels-in-image-where-mask-0-e-g-to-exclude-voxels-representing-artifacts"]], "Usage w/ a tissue mask (warped to atlas space):": [[97, "usage-w-a-tissue-mask-warped-to-atlas-space"]], "Usage w/ additional options:": [[94, "usage-w-additional-options"]], "Usage w/ an atlas mask (warped to atlas space):": [[97, "usage-w-an-atlas-mask-warped-to-atlas-space"]], "Usage w/ both masks for side-specific z-scoring:": [[97, "usage-w-both-masks-for-side-specific-z-scoring"]], "Usage with CCFv3:": [[3, "usage-with-ccfv3"]], "Usage with a custom atlas:": [[65, "usage-with-a-custom-atlas"]], "Usage with gubra atlas:": [[3, "usage-with-gubra-atlas"]], "Usage:": [[5, "usage"], [15, "usage"], [16, "usage"], [23, "usage"], [24, "usage"], [25, "usage"], [34, "usage"], [35, "usage"], [36, "usage"], [37, "usage"], [39, "usage"], [40, "usage"], [41, "usage"], [42, "usage"], [43, "usage"], [44, "usage"], [46, "usage"], [47, "usage"], [48, "usage"], [50, "usage"], [51, 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"seg_ilastik": [[0, "seg-ilastik"]], "unravel package": [[78, "unravel-package"]], "unravel.cluster_stats package": [[26, "unravel-cluster-stats-package"]], "unravel.cluster_stats.brain_model module": [[3, "module-unravel.cluster_stats.brain_model"]], "unravel.cluster_stats.cluster_summary module": [[4, "module-unravel.cluster_stats.cluster_summary"]], "unravel.cluster_stats.cluster_validation module": [[5, "module-unravel.cluster_stats.cluster_validation"]], "unravel.cluster_stats.crop module": [[6, "module-unravel.cluster_stats.crop"]], "unravel.cluster_stats.effect_sizes package": [[10, "unravel-cluster-stats-effect-sizes-package"]], "unravel.cluster_stats.effect_sizes.effect_sizes module": [[7, "module-unravel.cluster_stats.effect_sizes.effect_sizes"]], "unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute module": [[8, "module-unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute"]], "unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative module": 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\ No newline at end of file
diff --git a/unravel/docs/_build/html/unravel/cluster_stats/brain_model.html b/unravel/docs/_build/html/unravel/cluster_stats/brain_model.html
index 9956b052..fcd3da81 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/brain_model.html
+++ b/unravel/docs/_build/html/unravel/cluster_stats/brain_model.html
@@ -351,7 +351,7 @@
unravel.cluster_stats.brain_model module unravel.cluster_stats.find_incongruent_clusters module unravel.cluster_stats.group_bilateral_data module unravel.cluster_stats.index module unravel.cluster_stats.mean_IF module unravel.cluster_stats.legend module unravel.cluster_stats.org_data module unravel.cluster_stats.prism module unravel.cluster_stats.sunburst module unravel.cluster_stats.table module unravel.cluster_stats.crop module unravel.cluster_stats.index module unravel.cluster_stats.mean_IF_summary module unravel.cluster_stats.effect_sizes package