Source code for unravel.cluster_stats.org_data
cluster_correction_dir = validation_dir_name # Regular expression to match the part before and after 'q*' to remove any suffix added to the rev_cluster_index<suffix>.nii.gz - pattern = r'(.*q\d+\.\d+)(_.*)' + pattern = r'(.*q\d+\.\d+)(_.+)?' # This also works when there is no "suffix" match = re.match(pattern, cluster_correction_dir) if match: cluster_correction_dir = match.group(1) - suffix = match.group(2)[1:] # Remove the leading underscore + suffix = match.group(2)[1:] if match.group(2) else '' # This gets the string after the q value if there is one else: print("\n [red1]No match found in cluster_org_data\n") diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/recursively_mirror_rev_cluster_indices.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/recursively_mirror_rev_cluster_indices.html index 7ee81b73..d0ece924 100644 --- a/unravel/docs/_build/html/_modules/unravel/cluster_stats/recursively_mirror_rev_cluster_indices.html +++ b/unravel/docs/_build/html/_modules/unravel/cluster_stats/recursively_mirror_rev_cluster_indices.html @@ -359,6 +359,10 @@
Source code for unravel.cluster_stats.recursively_mirror_rev_cluster_indices
cluster_mirror_indices -m RH -v
Use this command after ``cluster_fdr`` to mirror the cluster indices for the other side of the brain before running ``cluster_validation``.
+
+Note:
+ - Use -ax 2 and -s 0 for the CCFv3 2020 atlas.
+ - Use -ax 0 and -s 2 for the 25 um Gubra atlas
"""
import argparse
@@ -380,15 +384,13 @@ Source code for unravel.cluster_stats.recursively_mirror_rev_cluster_indices
parser = argparse.ArgumentParser(formatter_class=SuppressMetavar)
parser.add_argument('-m', '--mas_side', help='Side of the brain corresponding to the mask used for ``vstats`` and ``cluster_fdr`` (RH or LH)', choices=['RH', 'LH'], required=True, action=SM)
parser.add_argument('-p', '--pattern', help='Glob pattern to match files. Default: **/*rev_cluster_index.nii.gz', default='**/*rev_cluster_index.nii.gz', action=SM)
- parser.add_argument('-ax', '--axis', help='Axis to flip the image along. Default: 0', default=0, type=int, action=SM)
- parser.add_argument('-s', '--shift', help='Number of voxels to shift content after flipping. Default: 2', default=2, type=int, action=SM)
+ parser.add_argument('-ax', '--axis', help='Axis to flip the image along. Default: 2', default=2, type=int, action=SM)
+ parser.add_argument('-s', '--shift', help='Number of voxels to shift content after flipping. Default: 0', default=0, 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()
[docs]
diff --git a/unravel/docs/_build/html/_modules/unravel/core/img_io.html b/unravel/docs/_build/html/_modules/unravel/core/img_io.html
index 82a1b824..c9797032 100644
--- a/unravel/docs/_build/html/_modules/unravel/core/img_io.html
+++ b/unravel/docs/_build/html/_modules/unravel/core/img_io.html
@@ -597,6 +597,8 @@
Source code for unravel.core.img_io
def load_single_tif(tif_file):
"""Load a single .tif file using OpenCV and return the ndarray."""
img = cv2.imread(str(tif_file), cv2.IMREAD_UNCHANGED)
+ if img is None:
+ raise ValueError(f"Failed to load image: {tif_file}")
return img
tif_files = sorted(Path(tif_path).parent.glob("*.tif"))
if parallel_loading:
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 bed89196..15cd290d 100644
--- a/unravel/docs/_build/html/_modules/unravel/register/reg_prep.html
+++ b/unravel/docs/_build/html/_modules/unravel/register/reg_prep.html
@@ -356,7 +356,7 @@ Source code for unravel.register.reg_prep
Usage:
------
- reg_prep -i <asterisk>.czi [-e <list of paths to exp dirs>] [-v]
+ reg_prep -i <asterisk>.czi -x <x/y voxel size in microns> -z <z voxel size> [-e <list of paths to exp dirs>] [-v]
Run command from the experiment directory w/ sample?? folder(s), a sample?? folder, or provide -e or -d arguments.
@@ -383,7 +383,6 @@ Source code for unravel.register.reg_prep
from unravel.core.img_io import load_3D_img, resolve_path, save_as_tifs, save_as_nii
from unravel.core.img_tools import resample, reorient_for_raw_to_nii_conv
from unravel.core.utils import log_command, verbose_start_msg, verbose_end_msg, initialize_progress_bar, get_samples, print_func_name_args_times
-from unravel.segment.copy_tifs import copy_specific_slices
@@ -394,21 +393,19 @@ Source code for unravel.register.reg_prep
parser.add_argument('-p', '--pattern', help='Pattern for sample?? dirs. Use cwd if no matches.', default='sample??', action=SM)
parser.add_argument('-d', '--dirs', help='List of sample?? dir names or paths to dirs to process', nargs='*', default=None, action=SM)
parser.add_argument('-i', '--input', help='Full res image input path relative (rel_path) to ./sample??', required=True, action=SM)
+ parser.add_argument('-x', '--xy_res', help='x/y voxel size in microns of the input image.', required=True, type=float, action=SM) # Set up Default: get via ``io_metadata``
+ parser.add_argument('-z', '--z_res', help='z voxel size in microns of the input image.', required=True, type=float, action=SM) # Set up Default: get via ``io_metadata``
parser.add_argument('-c', '--channel', help='.czi channel number. Default: 0 for autofluo', default=0, type=int, action=SM)
parser.add_argument('-o', '--output', help='Output path. Default: reg_inputs/autofl_50um.nii.gz', default="reg_inputs/autofl_50um.nii.gz", action=SM)
- parser.add_argument('-x', '--xy_res', help='x/y voxel size in microns of the input image. Default: get via metadata', default=None, type=float, action=SM)
- parser.add_argument('-z', '--z_res', help='z voxel size in microns of the input image. Default: get via metadata', default=None, type=float, action=SM)
parser.add_argument('-r', '--reg_res', help='Resample input to this res in um for reg. Default: 50', default=50, type=int, action=SM)
parser.add_argument('-zo', '--zoom_order', help='Order for resampling (scipy.ndimage.zoom). Default: 1', default=1, type=int, action=SM)
- 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. Default: False', action='store_true', default=False)
parser.epilog = __doc__
return parser.parse_args()
-# TODO: Remove args.target_dir since this can be done with ``seg_copy_tifs``
+# TODO: The script works if -x and -z are provided. Fix it so that it works if they are not provided (i.e., get res via ``io_metadata`` output: sample??/parameters/metadata.txt)
@@ -448,11 +445,6 @@ Source code for unravel.register.reg_prep
Configuration.verbose = args.verbose
verbose_start_msg()
- if args.target_dir is not None:
- # Create the target directory for copying the selected slices for ``seg_brain_mask``
- target_dir = Path(args.target_dir)
- target_dir.mkdir(exist_ok=True, parents=True)
-
samples = get_samples(args.dirs, args.pattern, args.exp_paths)
progress, task_id = initialize_progress_bar(len(samples), "[red]Processing samples...")
@@ -485,11 +477,6 @@ Source code for unravel.register.reg_prep
# Save the prepped autofl image (for ``reg`` if skipping ``seg_brain_mask`` and for applying the brain mask)
save_as_nii(img_resampled, output, args.reg_res, args.reg_res, np.uint16)
- if args.target_dir is not None:
- # Copy specific slices to the target directory
- tif_dir = str(output).replace('.nii.gz', '_tifs')
- copy_specific_slices(sample_path, tif_dir, target_dir, args.slices)
-
progress.update(task_id, advance=1)
verbose_end_msg()
diff --git a/unravel/docs/_build/html/_modules/unravel/segment/copy_tifs.html b/unravel/docs/_build/html/_modules/unravel/segment/copy_tifs.html
index ff0c160c..51c31eb1 100644
--- a/unravel/docs/_build/html/_modules/unravel/segment/copy_tifs.html
+++ b/unravel/docs/_build/html/_modules/unravel/segment/copy_tifs.html
@@ -408,10 +408,7 @@ Source code for unravel.segment.copy_tifs
dest_file = target_dir / f'{sample_path.name}_{file_path.name}'
shutil.copy(file_path, dest_file)
if verbose:
- print(f"Copied {file_path} to {dest_file}")
- else:
- if verbose:
- print(f"File {file_path.name} does not match specified slices and was not copied.")
+ print(f"Copied {file_path} to {dest_file}")
diff --git a/unravel/docs/_build/html/_modules/unravel/voxel_stats/mirror.html b/unravel/docs/_build/html/_modules/unravel/voxel_stats/mirror.html
index 7cfe3534..fb2774f6 100644
--- a/unravel/docs/_build/html/_modules/unravel/voxel_stats/mirror.html
+++ b/unravel/docs/_build/html/_modules/unravel/voxel_stats/mirror.html
@@ -359,8 +359,9 @@ Source code for unravel.voxel_stats.mirror
------
vstats_mirror -v
-Note:
- The current defaults are specific to our version of the Gubra atlas and may need to be adjusted for other atlases.
+Note:
+ - Use -ax 2 and -s 0 for the CCFv3 2020 atlas.
+ - Use -ax 0 and -s 2 for the 25 um Gubra atlas
"""
import argparse
@@ -379,20 +380,18 @@ Source code for unravel.voxel_stats.mirror
def parse_args():
parser = argparse.ArgumentParser(formatter_class=SuppressMetavar)
parser.add_argument('-p', '--pattern', help='Pattern to match files. Default: *.nii.gz', default='*.nii.gz', action=SM)
- parser.add_argument('-ax', '--axis', help='Axis to flip the image along. Default: 0', default=0, type=int, action=SM)
- parser.add_argument('-s', '--shift', help='Number of voxels to shift content after flipping. Default: 2', default=2, type=int, action=SM)
+ parser.add_argument('-ax', '--axis', help='Axis to flip the image along. Default: 2', default=2, type=int, action=SM)
+ parser.add_argument('-s', '--shift', help='Number of voxels to shift content after flipping. Default: 0', default=0, type=int, action=SM)
parser.add_argument('-v', '--verbose', help='Increase verbosity', default=False, action='store_true')
parser.epilog = __doc__
return parser.parse_args()
-# TODO: adapt to work with CCFv3 images if needed
-
[docs]
@print_func_name_args_times()
-def mirror(img, axis=0, shift=2):
+def mirror(img, axis=2, shift=0):
"""Mirror an image along the specified axis and shift the content by the specified number of voxels.
Args:
@@ -402,13 +401,20 @@ Source code for unravel.voxel_stats.mirror
# Flip the image data along the specified axis
flipped_img = np.flip(img, axis=axis)
- # Shift the image data by padding with zeros on the left and cropping on the right
- # This adds 2 voxels of zeros on the left side (beginning) and removes 2 voxels from the right side (end)
- mirrored_img = np.pad(flipped_img, ((shift, 0), (0, 0), (0, 0)), mode='constant', constant_values=0)[:-shift, :, :]
-
- return mirrored_img
+ if shift == 0:
+ return flipped_img
+ else:
+ # Shift the image data by padding with zeros on the left and cropping on the right
+ # This adds 2 voxels of zeros on the left side (beginning) and removes 2 voxels from the right side (end)
+ if axis == 0:
+ mirrored_img = np.pad(flipped_img, ((shift, 0), (0, 0), (0, 0)), mode='constant', constant_values=0)[:-shift, :, :]
+ return mirrored_img
+ else:
+ print('[red1]Logic for shifting content in axeses other than 0 has not been added. Please request this if needed.')
+ return
+
[docs]
@log_command
diff --git a/unravel/docs/_build/html/_modules/unravel/voxel_stats/whole_to_LR_avg.html b/unravel/docs/_build/html/_modules/unravel/voxel_stats/whole_to_LR_avg.html
index c901d40d..2a38a6fb 100644
--- a/unravel/docs/_build/html/_modules/unravel/voxel_stats/whole_to_LR_avg.html
+++ b/unravel/docs/_build/html/_modules/unravel/voxel_stats/whole_to_LR_avg.html
@@ -391,9 +391,9 @@ Source code for unravel.voxel_stats.whole_to_LR_avg
def parse_args():
parser = argparse.ArgumentParser(formatter_class=SuppressMetavar)
parser.add_argument('-p', '--pattern', help='Pattern to match atlas space input images in the working dir. Default: *.nii.gz', default='*.nii.gz', action=SM)
- parser.add_argument('-k', '--kernel', help='Smoothing kernel radius in mm if > 0. Default: 0 ', default=0, type=float, action=SM)
- parser.add_argument('-ax', '--axis', help='Axis to flip the image along. Default: 0', default=0, type=int, action=SM)
- parser.add_argument('-s', '--shift', help='Number of voxels to shift content after flipping. Default: 2', default=2, type=int, action=SM)
+ parser.add_argument('-k', '--kernel', help='Smoothing kernel radius in mm if > 0. Default: 0', default=0, type=float, action=SM)
+ parser.add_argument('-ax', '--axis', help='Axis to flip the image along. Default: 2', default=2, type=int, action=SM)
+ parser.add_argument('-s', '--shift', help='Number of voxels to shift content after flipping (if atlas is asym.). Default: 0', default=0, type=int, action=SM)
parser.add_argument('-tp', '--parallel', help='Enable parallel processing with thread pools', default=False, action='store_true')
parser.add_argument('-amas', '--atlas_mask', help='path/atlas_mask.nii.gz', default=None, action=SM)
parser.add_argument('-v', '--verbose', help='Increase verbosity', default=False, action='store_true')
diff --git a/unravel/docs/_build/html/searchindex.js b/unravel/docs/_build/html/searchindex.js
index fdaa78cd..2befacd7 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"], [96, "usage"], [97, "usage"]], "Voxel-wise stats": [[0, "voxel-wise-stats"]], "cluster_fdr": [[0, "cluster-fdr"]], "cluster_fdr_range": [[0, "cluster-fdr-range"]], "cluster_mirror_indices": [[0, "cluster-mirror-indices"]], "cluster_summary": [[0, "cluster-summary"]], "cluster_validation": [[0, "id4"]], "env_var.sh": [[0, null]], "img_avg": [[0, "img-avg"]], "reg": [[0, "reg"]], "reg_check": [[0, "reg-check"]], "reg_prep": [[0, "reg-prep"]], "rstats": [[0, "rstats"]], "rstats_summary": [[0, "rstats-summary"]], "seg_brain_mask": [[0, "seg-brain-mask"]], "seg_copy_tifs": [[0, "seg-copy-tifs"], [0, "id3"]], "seg_ilastik": [[0, "seg-ilastik"]], "unravel package": [[76, "unravel-package"]], "unravel.cluster_stats package": [[24, "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"]], 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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
+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"], [96, "usage"], [97, "usage"]], "Voxel-wise stats": [[0, "voxel-wise-stats"]], "cluster_fdr": [[0, "cluster-fdr"]], "cluster_fdr_range": [[0, "cluster-fdr-range"]], "cluster_mirror_indices": [[0, "cluster-mirror-indices"]], "cluster_summary": [[0, "cluster-summary"]], "cluster_validation": [[0, "id4"]], "env_var.sh": [[0, null]], "img_avg": [[0, "img-avg"]], "reg": [[0, "reg"]], "reg_check": [[0, "reg-check"]], "reg_prep": [[0, "reg-prep"]], "rstats": [[0, "rstats"]], "rstats_summary": [[0, "rstats-summary"]], "seg_brain_mask": [[0, "seg-brain-mask"]], "seg_copy_tifs": [[0, "seg-copy-tifs"], [0, "id3"]], "seg_ilastik": [[0, "seg-ilastik"]], "unravel package": [[76, "unravel-package"]], "unravel.cluster_stats package": [[24, "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": [[9, "module-unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative"]], "unravel.cluster_stats.fdr module": [[11, "module-unravel.cluster_stats.fdr"]], "unravel.cluster_stats.fdr_range module": [[12, "module-unravel.cluster_stats.fdr_range"]], "unravel.cluster_stats.find_incongruent_clusters module": [[13, "module-unravel.cluster_stats.find_incongruent_clusters"]], "unravel.cluster_stats.group_bilateral_data module": [[14, "module-unravel.cluster_stats.group_bilateral_data"]], "unravel.cluster_stats.index module": [[15, "module-unravel.cluster_stats.index"]], "unravel.cluster_stats.legend module": [[16, "module-unravel.cluster_stats.legend"]], "unravel.cluster_stats.org_data module": [[17, "module-unravel.cluster_stats.org_data"]], "unravel.cluster_stats.prism module": [[18, "module-unravel.cluster_stats.prism"]], "unravel.cluster_stats.recursively_mirror_rev_cluster_indices module": [[19, "module-unravel.cluster_stats.recursively_mirror_rev_cluster_indices"]], "unravel.cluster_stats.stats module": [[20, "module-unravel.cluster_stats.stats"]], "unravel.cluster_stats.stats_table module": [[21, "module-unravel.cluster_stats.stats_table"]], "unravel.cluster_stats.sunburst module": [[22, "module-unravel.cluster_stats.sunburst"]], "unravel.cluster_stats.table module": [[23, "module-unravel.cluster_stats.table"]], "unravel.core package": [[30, "unravel-core-package"]], "unravel.core.argparse_utils module": [[25, "module-unravel.core.argparse_utils"]], "unravel.core.argparse_utils_rich module": [[26, "module-unravel.core.argparse_utils_rich"]], "unravel.core.config module": [[27, "module-unravel.core.config"]], "unravel.core.img_io module": [[28, "module-unravel.core.img_io"]], "unravel.core.img_tools module": [[29, "module-unravel.core.img_tools"]], "unravel.core.utils module": [[31, "module-unravel.core.utils"]], "unravel.image_io package": [[43, "unravel-image-io-package"]], "unravel.image_io.h5_to_tifs module": [[32, "module-unravel.image_io.h5_to_tifs"]], "unravel.image_io.img_to_npy module": [[33, "module-unravel.image_io.img_to_npy"]], "unravel.image_io.io_img module": [[34, "module-unravel.image_io.io_img"]], "unravel.image_io.io_nii module": [[35, "module-unravel.image_io.io_nii"]], "unravel.image_io.metadata module": [[36, "module-unravel.image_io.metadata"]], "unravel.image_io.nii_hd module": [[37, "module-unravel.image_io.nii_hd"]], "unravel.image_io.nii_info module": [[38, "module-unravel.image_io.nii_info"]], "unravel.image_io.nii_to_tifs module": [[39, "module-unravel.image_io.nii_to_tifs"]], "unravel.image_io.nii_to_zarr module": [[40, "module-unravel.image_io.nii_to_zarr"]], "unravel.image_io.reorient_nii module": [[41, "module-unravel.image_io.reorient_nii"]], "unravel.image_io.tif_to_tifs module": [[42, "module-unravel.image_io.tif_to_tifs"]], "unravel.image_io.zarr_to_nii module": [[44, "module-unravel.image_io.zarr_to_nii"]], "unravel.image_tools package": [[57, "unravel-image-tools-package"]], "unravel.image_tools.DoG module": [[45, "module-unravel.image_tools.DoG"]], "unravel.image_tools.atlas package": [[47, "unravel-image-tools-atlas-package"]], "unravel.image_tools.atlas.relabel_nii module": [[46, "module-unravel.image_tools.atlas.relabel_nii"]], "unravel.image_tools.atlas.wireframe module": [[48, "module-unravel.image_tools.atlas.wireframe"]], "unravel.image_tools.avg module": [[49, "module-unravel.image_tools.avg"]], "unravel.image_tools.bbox module": [[50, "module-unravel.image_tools.bbox"]], "unravel.image_tools.extend module": [[51, "module-unravel.image_tools.extend"]], "unravel.image_tools.max module": [[52, "module-unravel.image_tools.max"]], "unravel.image_tools.pad module": [[53, "module-unravel.image_tools.pad"]], "unravel.image_tools.rb module": [[54, "module-unravel.image_tools.rb"]], "unravel.image_tools.resample module": [[55, "module-unravel.image_tools.resample"]], "unravel.image_tools.spatial_averaging module": [[56, "module-unravel.image_tools.spatial_averaging"]], "unravel.image_tools.transpose_axes module": [[58, "module-unravel.image_tools.transpose_axes"]], "unravel.image_tools.unique_intensities module": [[59, "module-unravel.image_tools.unique_intensities"]], "unravel.region_stats package": [[65, "unravel-region-stats-package"]], 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\ No newline at end of file
diff --git a/unravel/docs/_build/html/unravel/cluster_stats/recursively_mirror_rev_cluster_indices.html b/unravel/docs/_build/html/unravel/cluster_stats/recursively_mirror_rev_cluster_indices.html
index 0939b54a..4bfdc9bd 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/recursively_mirror_rev_cluster_indices.html
+++ b/unravel/docs/_build/html/unravel/cluster_stats/recursively_mirror_rev_cluster_indices.html
@@ -497,6 +497,13 @@ Usage#<
cluster_mirror_indices -m RH -v
Use this command after cluster_fdr to mirror the cluster indices for the other side of the brain before running cluster_validation.
+
+Note
+
+Use -ax 2 and -s 0 for the CCFv3 2020 atlas.
Use -ax 0 and -s 2 for the 25 um Gubra atlas
+
-
diff --git a/unravel/docs/_build/html/unravel/register/reg_prep.html b/unravel/docs/_build/html/unravel/register/reg_prep.html
index 85f442d5..870bcd65 100644
--- a/unravel/docs/_build/html/unravel/register/reg_prep.html
+++ b/unravel/docs/_build/html/unravel/register/reg_prep.html
@@ -494,7 +494,7 @@
Usage:#
-reg_prep -i <asterisk>.czi [-e <list of paths to exp dirs>] [-v]
+reg_prep -i <asterisk>.czi -x <x/y voxel size in microns> -z <z voxel size> [-e <list of paths to exp dirs>] [-v]
Run command from the experiment directory w/ sample?? folder(s), a sample?? folder, or provide -e or -d arguments.
diff --git a/unravel/docs/_build/html/unravel/voxel_stats/mirror.html b/unravel/docs/_build/html/unravel/voxel_stats/mirror.html
index f56db7c9..c9d9bf8a 100644
--- a/unravel/docs/_build/html/unravel/voxel_stats/mirror.html
+++ b/unravel/docs/_build/html/unravel/voxel_stats/mirror.html
@@ -498,7 +498,10 @@ Usage:#
Note
-The current defaults are specific to our version of the Gubra atlas and may need to be adjusted for other atlases.
+
+Use -ax 2 and -s 0 for the CCFv3 2020 atlas.
Use -ax 0 and -s 2 for the 25 um Gubra atlas