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zi#iT0;>o_ZT9U(S1RE&t4)n3>I}Y$G&7n5xTaK;~EZ$tDN>nqzq~X4nl6vvu9gCFq zJI5)9@V*qm3e_^PnX-_jxA?2$*PebyI8~Q0$OLlV5vv+NAEg@lnrK&U-fGM wj$mp-6KmMW#4;K)rZ+6zsfu^GOPsz(GjIeOBFkXlC8}k?9JMepu}|p#0540AeEWixo2S6!i3q6LSl4 zQtj>ai&E1w^YapO;)_cXON#X;Z{+owe23?ZMh@{BLN&69SL|XiC4)V7N`^rXDVjE~ I;Pdte0Lw*Dh5!Hn delta 97 zcmaFAhw<}nM%D(_sV`zTvR3klMEIAM6qJ?}TXE?sI0uI*q-Ex$Zr;cv#>nXl<4)el a<2BimkDJp6NyKIH20ji{kSource code for unravel.region_stats.rstats
     rstats -s rel_path/segmentation_image.nii.gz -m path/atlas_split.nii.gz -c Saline --dirs sample14 sample36
 
 Outputs:
-    - CSV file with cell counts, region volumes, or cell densities for each region
+    - CSV files in ./sample??/regional_stats/ with cell counts, region volumes, or cell densities for each region
 
 Notes 
     - Regarding --type, also use 'counts' or 'cell_desities' for object counts or object densities
@@ -403,7 +403,7 @@ 
Source code for unravel.region_stats.rstats
     parser.add_argument('-t', '--type', help='Type of measurement (options: counts, volumes, cell_densities [default])', default='cell_densities', action=SM)
     parser.add_argument('-c', '--condition', help='One word name for group (prepended to sample ID for rstats_summary)', required=True, action=SM)
     parser.add_argument('-s', '--seg_img_path', help='rel_path/segmentation_image.nii.gz (can be glob pattern)', required=True, action=SM)
-    parser.add_argument('-a', '--atlas_path', help='rel_path/native_atlas_split.nii.gz (only use this option if this file exists; left label IDs increased by 20,000)', default=None, action=SM)
+    parser.add_argument('-a', '--atlas_path', help='rel_path/native_atlas_split.nii.gz (use this -a if this exists from ``warp_to_native``, otherwise use -m ; "split" == left label IDs increased by 20,000)', default=None, action=SM)
     parser.add_argument('-m', '--moving_img', help='path/atlas_image.nii.gz to warp from atlas space', default=None, action=SM)
     parser.add_argument('-md', '--metadata', help='path/metadata.txt. Default: ./parameters/metadata.txt', default="./parameters/metadata.txt", action=SM)
     parser.add_argument('-cc', '--connect', help='Connected component connectivity (6, 18, or 26). Default: 6', type=int, default=6, action=SM)
diff --git a/unravel/docs/_build/html/_modules/unravel/register/reg_prep.html b/unravel/docs/_build/html/_modules/unravel/register/reg_prep.html
index a30c7f35..bed89196 100644
--- a/unravel/docs/_build/html/_modules/unravel/register/reg_prep.html
+++ b/unravel/docs/_build/html/_modules/unravel/register/reg_prep.html
@@ -403,7 +403,6 @@ 
Source code for unravel.register.reg_prep
     parser.add_argument('-td', '--target_dir', help='path/target_dir name to copy specific slices for seg_brain_mask (see usage)', default=None, action=SM)
     parser.add_argument('-s', '--slices', help='List of slice numbers to copy, e.g., 0000 0400 0800', nargs='*', type=str, default=[])
     parser.add_argument('-mi', '--miracl', help="Include reorientation step to mimic MIRACL's tif to .nii.gz conversion", action='store_true', default=False)
-    parser.add_argument('-v', '--verbose', help='Increase verbosity.', action='store_true', default=False)
     parser.add_argument('-v', '--verbose', help='Increase verbosity. Default: False', action='store_true', default=False)
     parser.epilog = __doc__
     return parser.parse_args()

diff --git a/unravel/docs/_build/html/searchindex.js b/unravel/docs/_build/html/searchindex.js
index 049031e1..fdaa78cd 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"]], "Overview and steps for voxel-wise stats": [[0, null]], "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"]], "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": [[3, "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 a custom atlas:": [[63, "usage-with-a-custom-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, "usage"], [69, "usage"], [70, "usage"], [72, "usage"], [74, "usage"], [79, "usage"], [80, "usage"], [81, "usage"], [86, "usage"], [87, "usage"], [88, "usage"], [89, "usage"], [92, "usage"], [93, "usage"], [94, "usage"], 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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:": [[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, 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"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": [[3, "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, 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"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, 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[0, 1, 4, 45, 77], "your": [0, 1, 2, 31, 77], "z": [1, 6, 13, 28, 29, 36, 41, 43, 55, 56, 60, 67, 70, 76, 85, 89, 91, 93, 94, 96, 98], "z_dim": 28, "z_map": 89, "z_re": [5, 6, 28, 29, 32, 42, 55, 60, 70, 98], "z_score": [0, 1, 76, 91], "z_to_p": [89, 90, 91], "z_voxel_s": [32, 42], "zarr": [0, 28, 34, 40, 44, 56, 85, 93, 96, 98], "zarr_path": 28, "zarr_to_ndarrai": [43, 44, 76], "zarr_to_nii": [1, 43, 76], "zeiss": 0, "zen": 0, "zero": [0, 12, 41, 56, 57, 76, 91], "zero_origin": 41, "zetastitch": 0, "zhao": 1, "zlib1g": 2, "zmax": [5, 28, 29], "zmin": [5, 28, 29], "zo": 55, "zoom": [0, 29, 70], "zoom_ord": [29, 55, 70, 98], "zscore": 35, "zscore_rang": 35, "zshrc": [0, 1, 77], "zyx": [32, 42], "\u00b5m": 0}, "titles": ["Guide", "UN-biased high-Resolution Analysis and Validation of Ensembles using Light sheet images", "Installation", "unravel.cluster_stats.brain_model module", "unravel.cluster_stats.cluster_summary module", "unravel.cluster_stats.cluster_validation module", 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"rstats_mean_if_summari": 63, "rstats_summari": [0, 64], "run": [0, 4], "sampl": [0, 78, 84], "sample01": 0, "sample02": 0, "sample_kei": 0, "save": 60, "scale": 35, "score": [35, 95], "script": 0, "seg_brain_mask": [0, 73], "seg_copy_tif": 0, "seg_ilastik": [0, 73], "segment": [0, 72, 73, 74, 75, 85], "set": [0, 2], "sh": 0, "sheet": 1, "shell": 0, "side": 95, "signal": 85, "size": [0, 59], "sort": 23, "sourc": 0, "space": [60, 95, 100], "spatial_averag": 56, "specif": 95, "stack": 0, "start": [1, 2], "stat": [0, 20], "stats_tabl": 21, "step": 0, "stitch": 0, "structur": 0, "subpackag": 76, "subsystem": 2, "subtract": 0, "sunburst": 22, "support": 1, "syntax": 0, "t": [20, 63], "tabl": 23, "templat": 67, "test": [20, 63], "tif": 0, "tif_to_tif": 42, "tissu": [67, 95, 100], "tl": 2, "to_atla": 96, "to_fix": 97, "to_n": 98, "todo": [0, 2], "toggl": 84, "toggle_sampl": 84, "train": 0, "transpose_ax": 58, "tukei": [20, 63], "txt": 0, "typic": 0, "u": 1, "un": 1, "uniqu": 59, 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85], "voxel_stat": [85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95], "vstat": [0, 92], "vstats_prep": [0, 93], "vstats_whole_to_avg": 0, "vstats_z_scor": 0, "w": [59, 63, 92, 95], "warp": [95, 96, 97, 98, 99, 100], "warp_to_n": 60, "welcom": 1, "when": [36, 78], "where": 85, "whole_to_lr_avg": 94, "window": 2, "wirefram": 48, "wise": 0, "workflow": 0, "wsl": 2, "x": 0, "y": 0, "you": 2, "z": [0, 35, 95], "z_score": 95, "zarr_to_nii": 44, "zero": [59, 85], "zshrc": 2}})
\ No newline at end of file
diff --git a/unravel/docs/_build/html/unravel/region_stats/rstats.html b/unravel/docs/_build/html/unravel/region_stats/rstats.html
index c045f4eb..251f93a0 100644
--- a/unravel/docs/_build/html/unravel/region_stats/rstats.html
+++ b/unravel/docs/_build/html/unravel/region_stats/rstats.html
@@ -504,7 +504,7 @@ 
Usage if the native atlas is not available; it is not saved (faster):
 

 
Outputs:
    
-
  • CSV file with cell counts, region volumes, or cell densities for each region
    • 
+
  • CSV files in ./sample??/regional_stats/ with cell counts, region volumes, or cell densities for each region
    • 
 

 

 
Notes