+
+
+
+
+
+
+Sacha Hadaway-Andreae
+
+
+Inspired by All Contributors. All information is sourced from GitHub. If any changes
diff --git a/searchindex.js b/searchindex.js
index 65aa6135..25e7e50e 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"2D filtering": [[29, "d-filtering"]], "3D Edge-Aware Refined Atlases Derived from the Allen Developing Mouse Brain Atlases": [[46, "d-edge-aware-refined-atlases-derived-from-the-allen-developing-mouse-brain-atlases"]], "3D filtering": [[29, "id1"]], "3D version of the Allen mouse spinal cord atlas": [[46, "d-version-of-the-allen-mouse-spinal-cord-atlas"]], "A mouse brain atlas with barrel field annotations has been added to BrainGlobe": [[3, null]], "A note about the camera position": [[73, "a-note-about-the-camera-position"]], "AZBA: A 3D Adult zebrafish brain atlas": [[46, "azba-a-3d-adult-zebrafish-brain-atlas"]], "About": [[0, null]], "Accessing data": [[0, "accessing-data"]], "Activate the environment": [[104, "activate-the-environment"]], "Actors": [[79, null]], "Adding a new atlas": [[44, null]], "Adding a new supported citation format": [[27, "adding-a-new-supported-citation-format"]], "Adding actors to your scene": [[79, "adding-actors-to-your-scene"]], "Adding new repositories or tools": [[27, "adding-new-repositories-or-tools"]], "Adding/removing actors": [[81, "adding-removing-actors"]], "Additional options": [[61, "additional-options"], [71, "additional-options"]], "Advanced installation": [[78, "advanced-installation"]], "Affine registration": [[75, "affine-registration"]], "Aligning Big Brains & Atlases": [[33, "aligning-big-brains-atlases"]], "Aligning samples for template building": [[127, null]], "Aligning spikes to histology with BrainGlobe": [[113, "aligning-spikes-to-histology-with-brainglobe"]], "Aligning to atlas\u2019s space": [[84, "aligning-to-atlass-space"]], "All cell detection parameters": [[93, null]], "All point information": [[58, "all-point-information"]], "Allen Adult Mouse Brain Atlas": [[46, "allen-adult-mouse-brain-atlas"]], "Allen Human Brain Atlas": [[46, "allen-human-brain-atlas"]], "Allen Morphology": [[102, "allen-morphology"]], "Amphibian": [[46, "amphibian"]], "An Atlas for the regenerative Ambystoma mexicanum (axolotl) has been added to BrainGlobe": [[2, null]], "An atlas for the Blind Mexican Cavefish has been added to BrainGlobe": [[8, null]], "An atlas for the prairie vole Microtus ochrogaster has been added to BrainGlobe": [[12, null]], "Analyse the segmented layer": [[52, "analyse-the-segmented-layer"]], "Analysing brainwide distribution of cells": [[129, null]], "Analysing segmentation from other napari plugins": [[52, null]], "Analysis": [[65, "analysis"]], "Analyze and visualize bulk fluorescence tracing data": [[128, null]], "Analyzing data": [[0, "analyzing-data"]], "Anatomical, annotation and hemispheres stack": [[48, "anatomical-annotation-and-hemispheres-stack"]], "Annotating data": [[96, "annotating-data"]], "Anything else": [[89, "anything-else"]], "Appendix: a note on cellfinder": [[16, "appendix-a-note-on-cellfinder"]], "Arguments": [[61, "arguments"], [71, "arguments"], [98, "arguments"]], "Atlas": [[71, "atlas"]], "Atlas details": [[46, null]], "Atlas generation": [[44, "atlas-generation"]], "Atlas scripts": [[44, "atlas-scripts"]], "Atlases available": [[45, "atlases-available"]], "Automated versioning": [[32, "automated-versioning"]], "Available atlases": [[46, "available-atlases"]], "Axis ordering in spatial arrays": [[22, "axis-ordering-in-spatial-arrays"]], "Basic installation": [[78, "basic-installation"]], "Basic usage": [[61, "basic-usage"], [71, "basic-usage"]], "Before tracing bulk axonal tracks": [[128, "before-tracing-bulk-axonal-tracks"]], "Before tracing probe tracks": [[126, "before-tracing-probe-tracks"]], "Before you start": [[117, "before-you-start"]], "Blind Mexican cavefish brain atlas": [[46, "blind-mexican-cavefish-brain-atlas"]], "Blog": [[11, null]], "BlueBrain Barrel Cortex Atlas": [[46, "bluebrain-barrel-cortex-atlas"]], "Brain registration to an atlas": [[126, "brain-registration-to-an-atlas"], [128, "brain-registration-to-an-atlas"]], "BrainAtlas": [[33, "brainatlas"]], "BrainGlobe": [[109, null]], "BrainGlobe Atlas API (brainglobe-atlasapi)": [[45, null]], "BrainGlobe Tools": [[24, "brainglobe-tools"]], "BrainGlobe is being restructured, version 1 is on it\u2019s way!": [[16, null]], "BrainGlobe publications": [[112, null]], "BrainGlobe restructuring (version 1) release notes": [[35, "brainglobe-restructuring-version-1-release-notes"]], "BrainGlobe tools with additional developer information": [[30, null]], "BrainGlobe version 1 is here!": [[17, null]], "BrainGlobe version 1 overview": [[39, null]], "BrainGlobe version 1.1.0 is released!": [[5, null]], "BrainGlobe: a Python ecosystem for computational (neuro)anatomy": [[113, "brainglobe-a-python-ecosystem-for-computational-neuro-anatomy"], [113, "id1"]], "BrainGlobe; An Open-Source Platform for Neuroscientists": [[110, "brainglobe-an-open-source-platform-for-neuroscientists"]], "Brainrender: visualising brain data in 3D": [[110, "brainrender-visualising-brain-data-in-3d"]], "Braintracer": [[33, "braintracer"]], "Brainways": [[33, "brainways"]], "Bugs": [[43, "bugs"]], "Bulk axonal track detection": [[128, "bulk-axonal-track-detection"]], "CPU instruction sets": [[88, "cpu-instruction-sets"]], "Can I install from conda-forge?": [[39, "can-i-install-from-conda-forge"]], "Can\u2019t find openCV": [[88, "cant-find-opencv"]], "Cell candidate classification": [[60, null], [89, "cell-candidate-classification"]], "Cell candidate detection": [[59, null], [89, "cell-candidate-detection"]], "Cell classification or training the network is slow": [[90, "cell-classification-or-training-the-network-is-slow"]], "Cell coordinates": [[83, "cell-coordinates"]], "Cell detection": [[29, "cell-detection"], [94, null]], "Cellfinder version 1.3.0 is released!": [[9, null]], "Cellfinder: Harnessing the power of deep learning to map the brain": [[110, "cellfinder-harnessing-the-power-of-deep-learning-to-map-the-brain"]], "Chan Zuckerberg Initiative awards two grants to BrainGlobe": [[110, "chan-zuckerberg-initiative-awards-two-grants-to-brainglobe"]], "Changes at-a-glance": [[39, "changes-at-a-glance"]], "Check that conda is installed": [[104, "check-that-conda-is-installed"]], "Checking orientation": [[73, null]], "Citation": [[45, "citation"], [51, "citation"], [68, "citation"], [77, "citation"]], "Citing brainglobe-heatmap": [[50, "citing-brainglobe-heatmap"]], "Citing cellfinder": [[64, "citing-cellfinder"], [86, "citing-cellfinder"]], "Classification performance": [[9, "classification-performance"]], "ClearFinder": [[33, "clearfinder"]], "Command line interface": [[47, null], [61, null]], "Command line tool": [[71, null]], "Command-line executable": [[36, "command-line-executable"]], "CommandLineInputError: File path: cannot be found.": [[63, "commandlineinputerror-file-path-cannot-be-found"]], "Common problems": [[70, "common-problems"]], "Community": [[34, null]], "Contact": [[43, null]], "Continuous integration": [[31, "continuous-integration"]], "Contributing": [[43, "contributing"], [50, "contributing"]], "Contributors": [[111, "contributors"]], "Conventions": [[22, null], [26, "conventions"]], "Coordinating releases with the documentation and the metapackage": [[25, "coordinating-releases-with-the-documentation-and-the-metapackage"]], "Coronal section": [[106, "coronal-section"]], "Correct orientation": [[73, "correct-orientation"]], "Course materials": [[18, "course-materials"]], "Courses": [[18, null]], "Create the environment": [[104, "create-the-environment"]], "Creating a BrainGlobeAtlas object": [[48, "creating-a-brainglobeatlas-object"]], "Creating a development environment": [[23, "creating-a-development-environment"]], "Current status": [[41, "current-status"], [42, "current-status"]], "Currently supported datasets": [[101, "currently-supported-datasets"]], "Data requirements": [[62, null]], "Debugging common error messages": [[63, null], [88, null]], "December 6th 2023": [[20, null]], "Default architecture for BrainGlobe Tools": 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"Figure options": [[61, "figure-options"]], "Figures": [[65, "figures"]], "Fish": [[46, "fish"]], "Fixing technical problems": [[89, "fixing-technical-problems"]], "Freeform registration": [[75, "freeform-registration"]], "From PyPI, via pip": [[26, "from-pypi-via-pip"]], "Full Changelog": [[17, "full-changelog"], [39, "full-changelog"]], "Full changelog": [[13, "full-changelog"], [14, "full-changelog"], [15, "full-changelog"]], "Full documentation": [[77, "full-documentation"]], "Funders": [[108, null]], "Further details": [[104, "further-details"]], "Further help": [[98, "further-help"]], "Further information": [[23, "further-information"]], "Future": [[0, "future"], [41, "future"]], "Future-warning": [[38, "future-warning"]], "Generate training data": [[98, "generate-training-data"]], "Generating Citations for BrainGlobe tools": [[55, null]], "Generating data to retrain the cellfinder classification network": [[96, null]], "Getting started": [[66, "getting-started"], [72, "getting-started"], [122, "getting-started"]], "Gubra\u2019s LSFM mouse brain atlas": [[46, "gubras-lsfm-mouse-brain-atlas"]], "Guiding principles for development": [[24, "guiding-principles-for-development"]], "Histology analysis using napari and BrainGlobe": [[20, "histology-analysis-using-napari-and-brainglobe"], [21, "histology-analysis-using-napari-and-brainglobe"]], "Horizontal section": [[106, "horizontal-section"]], "How are BrainGlobe atlases distributed?": [[44, "how-are-brainglobe-atlases-distributed"]], "How can I be sure I get credited for the atlas I contributed?": [[44, "how-can-i-be-sure-i-get-credited-for-the-atlas-i-contributed"]], "How can I stay updated?": [[16, "how-can-i-stay-updated"]], "How do I install it?": [[6, "how-do-i-install-it"]], "How do I use it?": [[6, "how-do-i-use-it"]], "How do I use the new atlas?": [[2, "how-do-i-use-the-new-atlas"], [3, "how-do-i-use-the-new-atlas"], [8, "how-do-i-use-the-new-atlas"], [12, "how-do-i-use-the-new-atlas"]], "How to generate an atlas programmatically?": [[44, "how-to-generate-an-atlas-programmatically"]], "How to install": [[58, "how-to-install"], [68, "how-to-install"]], "How to use": [[58, "how-to-use"]], "Human": [[46, "human"]], "I have not updated to brainglobe-workflows, and I use the cellfinder CLI": [[37, "i-have-not-updated-to-brainglobe-workflows-and-i-use-the-cellfinder-cli"]], "I have not updated to brainglobe-workflows, but I don\u2019t use the cellfinder CLI": [[37, "i-have-not-updated-to-brainglobe-workflows-but-i-dont-use-the-cellfinder-cli"]], "I previously updated to brainglobe-workflows": [[37, "i-previously-updated-to-brainglobe-workflows"]], "INFO:tensorflow:Error reported to Coordinator: Failed to get convolution algorithm": [[88, "info-tensorflow-error-reported-to-coordinator-failed-to-get-convolution-algorithm"]], "Image IO submodule": [[56, null]], "Image channels": [[62, "image-channels"]], "Image data": [[83, "image-data"]], "Image space definition": [[106, null]], "Image structure": [[62, "image-structure"]], "ImportError: DLL load failed: The specified module could not be found.": [[88, "importerror-dll-load-failed-the-specified-module-could-not-be-found"]], "Improving algorithm performance": [[89, "improving-algorithm-performance"]], "Improving registration performance": [[70, "improving-registration-performance"]], "Incorrect orientation": [[73, "incorrect-orientation"]], "Individual Tool Documentation": [[100, "individual-tool-documentation"]], "Inspecting results": [[44, "inspecting-results"]], "Install miniconda": [[104, "install-miniconda"]], "Installation": [[26, "installation"], [45, "installation"], [50, "installation"], [51, "installation"], [54, "installation"], [56, "installation"], [67, "installation"], [69, "installation"], [86, "installation"], [87, null], [101, "installation"], [104, "installation"], [105, "installation"]], "Installation and download": [[117, "installation-and-download"]], "Installing BrainGlobe": [[100, "installing-brainglobe"]], "Installing Individual Tools": [[100, "installing-individual-tools"]], "Installing NVIDIA drivers": [[105, "installing-nvidia-drivers"]], "Installing PyTorch with GPU support": [[105, "installing-pytorch-with-gpu-support"]], "Installing as part of the metapackage": [[58, null]], "Installing brainmapper": [[87, "installing-brainmapper"]], "Installing brainrender": [[78, null]], "Installing on its own via PyPI": [[58, null]], "Installing the cellfinder package": [[87, "installing-the-cellfinder-package"]], "Installing the command line tool": [[69, null]], "Installing the napari plugin": [[69, null]], "Installing with cellfinder versions older than v1.0.0": [[67, "installing-with-cellfinder-versions-older-than-v1-0-0"]], "Installing within napari": [[58, null]], "Instructions": [[52, "instructions"]], "Instructors": [[20, "instructors"], [21, "instructors"]], "Introduction": [[0, "introduction"], [19, "introduction"], [23, "introduction"], [52, "introduction"], [54, "introduction"], [62, "introduction"], [77, "introduction"], [90, "introduction"], [104, "introduction"], [105, "introduction"], [126, "introduction"], [128, "introduction"]], "Introduction to the BrainGlobe codebase for developers": [[24, null]], "Issues": [[41, "issues"], [42, "issues"]], "Kim Lab Developmental CCF (P56)": [[46, "kim-lab-developmental-ccf-p56"]], "Leadership": [[111, "leadership"]], "Loading data": [[72, "loading-data"], [94, "loading-data"], [96, "loading-data"]], "Loading images": [[56, "loading-images"]], "Loading the data": [[83, "loading-the-data"]], "Location": [[20, "location"], [21, "location"]], "MagellanMapper": [[33, "magellanmapper"]], "Main updates": [[5, "main-updates"], [9, "main-updates"]], "Mandatory": [[61, "mandatory"], [71, "mandatory"], [93, "mandatory"], [97, "mandatory"]], "Mandatory parameters": [[94, "mandatory-parameters"]], "Matching resolution and offset": [[84, "matching-resolution-and-offset"]], "Matching space resolutions and offsets": [[54, "matching-space-resolutions-and-offsets"]], "Materials": [[19, "materials"], [20, "materials"], [21, "materials"]], "Max Planck zebrafish brain atlas": [[46, "max-planck-zebrafish-brain-atlas"]], "May 2024": [[41, null]], "Media": [[110, null]], "Metadata": [[48, "metadata"]], "Methodology": [[29, "methodology"]], "Methods": [[81, "methods"]], "Misc options": [[71, "misc-options"], [93, "misc-options"], [97, "misc-options"]], "More details": [[0, "more-details"], [45, "more-details"]], "Mouse": [[46, "mouse"]], "MouseLight": [[102, "mouselight"]], "Mpin Zebrafish": [[102, "mpin-zebrafish"]], "Napari plugin": [[72, null]], "Navigating": [[53, "navigating"]], "Network": [[97, "network"]], "Neuromorpho": [[102, "neuromorpho"]], "Neuron morphology": [[83, "neuron-morphology"]], "New brainmapper napari widget released": [[6, null]], "NiftyReg": [[75, "niftyreg"]], "Notes": [[64, "notes"]], "November 2023": [[42, null]], "Numerical results": [[58, "numerical-results"]], 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exporting": [[81, "rendering-and-exporting"]], "Rendering data": [[103, null]], "Rendering your scene in a separate window": [[82, "rendering-your-scene-in-a-separate-window"]], "Requirements": [[69, null], [87, "requirements"], [105, "requirements"]], "Results": [[58, "results"]], "Retraining the cellfinder classification network": [[121, null]], "Retraining the network for new data": [[97, null]], "Retraining the pre-trained network": [[98, null]], "Roadmaps": [[40, null]], "Run training": [[97, "run-training"]], "Running brainmapper": [[116, null]], "Running brainreg": [[72, "running-brainreg"]], "Running cellfinder": [[94, "running-cellfinder"]], "Running the cell candidate detection and classification separately": [[91, "running-the-cell-candidate-detection-and-classification-separately"]], "Saving data": [[94, "saving-data"]], "Saving images": [[56, "saving-images"]], "Saving the results": [[91, "saving-the-results"]], "Scene": [[81, null]], "Screenshots": [[85, "screenshots"]], "Segmentation fault": [[70, "segmentation-fault"]], "Segmenting 2/3D structures": [[125, null]], "Segmenting a 1D track": [[124, null]], "Segmenting your feature of interest": [[52, "segmenting-your-feature-of-interest"]], "Set parameters": [[97, "set-parameters"]], "Setting additional parameters": [[72, "setting-additional-parameters"]], "Setting parameters": [[94, "setting-parameters"]], "Setting up": [[107, null], [117, null]], "Setting up registration": [[72, "setting-up-registration"]], "Setting up your GPU": [[105, null]], "Setup your conda environment": [[104, "setup-your-conda-environment"]], "Silicon probe tracking": [[126, null]], "Slicing plane position": [[50, "slicing-plane-position"]], "Smoothed version of the Kim et al. mouse reference atlas": [[46, "smoothed-version-of-the-kim-et-al-mouse-reference-atlas"]], "Software built by the community": [[33, null]], "Specific Issues": [[90, "specific-issues"]], "Specific Repository Developer Documentation": [[30, null]], "Specific actor classes": [[79, "specific-actor-classes"]], "Specific applications": [[122, "specific-applications"]], "Speeding up cellfinder": [[90, null]], "Standalone installation": [[51, "standalone-installation"]], "Standard space options": [[61, "standard-space-options"]], "Start training": [[98, "start-training"]], "Starting the plugin": [[72, "starting-the-plugin"]], "Streamlines": [[83, "streamlines"]], "Structure detection": [[29, "structure-detection"]], "Suggested schedule": [[19, "suggested-schedule"]], "Supported data types": [[83, "supported-data-types"]], "Talks": [[113, null]], "TensorFlow backend": [[9, "tensorflow-backend"]], "Test data": [[31, "test-data"]], "Testing": [[31, null]], "The SpaceConvention class": [[54, "the-spaceconvention-class"]], "The best neuroscience stories from April 2020": [[110, "the-best-neuroscience-stories-from-april-2020"]], "Theory": [[98, "theory"]], "Things that look like errors, but aren\u2019t:": [[88, 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59, 61, 71, 75, 85, 88, 91, 93, 97, 98, 99, 104, 106, 112, 114, 116, 120, 121, 122, 126, 127, 128, 129], "20": [5, 45, 46, 58, 60, 91, 112, 116, 129], "200": 58, "2000": 50, "2015": [60, 88, 97, 98], "2016": 68, "2017": 88, "2019": [46, 88, 101], "2020": [45, 46, 51, 55, 64, 68, 112, 113, 116], "2021": [2, 11, 46, 64, 77, 86, 110, 112, 113], "2022": [50, 51, 64, 68, 112], "2023": [8, 11, 18, 40, 41, 46, 112, 113], "2024": [3, 11, 12, 18, 40, 46, 55, 112], "207203665153": [58, 114], "20\u03bcm": [46, 126], "21": [11, 112], "21105": [45, 51, 55, 64, 68, 112], "212": 112, "2158": 58, "2194": 58, "22": 116, "222": 112, "23": [23, 112], "230": 72, "23408mib": 88, "24": [11, 22, 112], "24187mib": 88, "2441": 58, "245": [6, 58, 114], "247": 42, "25": [5, 45], "250": 115, "251": 112, "2528": 58, "255": 44, "256391": [58, 114], "2577": [58, 114], "258": 112, "25\u03bcm": [3, 46, 71], "26": 112, "2663": 99, "2667": [58, 114], "2668": [45, 51, 64, 68, 112], "2763": 58, "28": 112, "2800": 117, 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101, 103, 112, 119, 121, 122, 124, 126, 127, 128, 129, 130, 131], "3ng7n33r": 111, "3x3": 127, "4": [4, 10, 26, 42, 45, 50, 54, 59, 75, 88, 90, 91, 93, 98, 99, 112, 126, 128], "40": [9, 45, 48, 130], "4000": 48, "403": 112, "407": 112, "4080": 90, "40\u03bcm": 46, "41": [88, 112], "412": [6, 58, 114], "418": 88, "42": [22, 99, 112, 116], "421": [58, 114], "422": 112, "424": 112, "43": 112, "435693645163": [58, 114], "437": 58, "439": [58, 114], "44": 112, "444": 58, "44971595174": [58, 114], "45": [19, 112, 119], "450": 105, "456": 84, "457": 112, "46": 42, "460": 58, "460668": [58, 114], "461": 112, "468": 112, "47": 99, "477": 112, "48": 112, "480": 112, "481": 112, "492384": [58, 114], "494": 112, "497": [58, 114], "4983": 112, "4d": 112, "4iar": 111, "4\u03bcm": 46, "5": [4, 5, 6, 10, 19, 25, 45, 46, 50, 51, 54, 55, 58, 60, 61, 64, 68, 71, 75, 86, 91, 98, 99, 102, 105, 106, 112, 114, 116, 120], "50": [5, 45, 48, 60, 91, 97, 98, 99, 130], "500": [45, 102], "5000": [48, 50, 98], "500\u03bcm": 46, "5040": 112, "5058": 112, "50gb": 69, "50\u03bcm": 46, "528": 84, "5281": 50, "53": [88, 112], "531": 112, "532": 112, "534717": [58, 114], "535": 112, "54": [45, 51, 64, 68, 112], "543": 112, "547": 112, "550306": 88, "558": 112, "55w": 88, "56": 88, "560": 112, "56008346531": [58, 114], "561": [6, 58, 114], "565467": 88, "568": 112, "573": 112, "57638": [58, 114], "579125235589": [58, 114], "586": 58, "5891814": 50, "594": 112, "597768": [58, 114], "598": 112, "5pm": 20, "5\u03bcm": [117, 126], "6": [25, 42, 45, 50, 59, 75, 91, 93, 112, 119, 125, 127], "60": 130, "60000": 63, "601": 112, "6050": 99, "607": 112, "609": 112, "61": 112, "611487": [58, 114], "613": 112, "614387": [58, 114], "6173": 99, "637": 112, "639": 112, "64": [9, 60, 91, 104], "643": [58, 114], "644904": [58, 114], "65751": [77, 112], "663": 58, "679": 58, "6814116984": [58, 114], "686": [6, 58, 114], "690": 58, "6th": 18, "7": [25, 68, 104, 112, 127], "71": 42, "722443": 112, "723": 58, "733": 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112, 118, 124, 125, 126, 127, 128, 129, 130, 131], "And": 15, "As": [1, 11, 15, 16, 24, 25, 26, 27, 29, 38, 53, 64, 65, 82, 88, 89, 90, 96, 106, 119, 124, 125], "At": [27, 44, 52, 85, 130], "Be": [5, 14, 62], "By": [0, 14, 15, 24, 44, 49, 55, 71, 85, 92, 94, 103, 128], "For": [0, 5, 9, 14, 15, 17, 22, 23, 25, 26, 27, 32, 38, 44, 46, 48, 50, 52, 53, 55, 56, 57, 62, 63, 70, 72, 73, 79, 85, 89, 91, 92, 106, 117, 118, 120, 121, 124, 125, 130], "If": [1, 2, 3, 4, 5, 7, 8, 10, 12, 13, 14, 15, 17, 20, 21, 23, 25, 36, 37, 38, 39, 43, 44, 45, 46, 48, 50, 51, 52, 53, 55, 58, 60, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 75, 76, 77, 78, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 94, 96, 97, 98, 99, 100, 102, 104, 106, 111, 115, 116, 118, 120, 121, 124, 125, 126, 127, 131], "In": [0, 2, 5, 7, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 32, 37, 38, 43, 44, 46, 48, 49, 50, 52, 55, 73, 77, 78, 79, 83, 88, 89, 90, 97, 98, 106, 111, 114, 117, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 131], "Into": 118, "It": [0, 6, 7, 10, 11, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 32, 33, 38, 39, 41, 42, 46, 52, 56, 58, 64, 67, 79, 81, 88, 94, 98, 100, 101, 102, 114, 115, 117, 123, 126, 127, 128], "NOT": 25, "No": [14, 128], "Not": 85, "On": [5, 78, 88, 104, 120, 124, 125], "One": [6, 11, 16, 23, 25, 103, 112], "Or": [23, 48, 56], "Such": 12, "That": [50, 85], "The": [0, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 15, 16, 17, 22, 23, 24, 25, 26, 27, 29, 32, 33, 36, 37, 38, 39, 41, 42, 44, 45, 46, 48, 49, 50, 53, 55, 56, 57, 58, 59, 60, 61, 62, 63, 65, 66, 67, 68, 69, 71, 72, 73, 74, 75, 77, 81, 84, 85, 86, 87, 89, 91, 92, 93, 94, 95, 97, 98, 99, 102, 103, 104, 105, 106, 108, 109, 111, 112, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 131], "Then": [25, 27, 78, 90, 94, 102, 123, 127, 129, 130, 131], "There": [10, 16, 23, 39, 41, 46, 48, 52, 53, 56, 61, 69, 70, 72, 94, 98, 118], "These": [3, 11, 24, 25, 26, 28, 32, 40, 44, 46, 55, 58, 62, 65, 72, 83, 89, 90, 91, 98, 105, 106, 114, 118, 122, 130, 131], "To": [0, 3, 6, 12, 16, 26, 27, 29, 30, 31, 32, 37, 44, 47, 48, 50, 52, 54, 58, 59, 60, 61, 63, 65, 66, 68, 69, 71, 72, 73, 75, 76, 77, 78, 81, 82, 84, 85, 87, 88, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 114, 116, 117, 118, 119, 124, 126, 127, 128], "Will": [11, 55, 111], "With": [0, 13, 26, 38, 78, 117, 126], "_": [27, 102], "__can": 81, "__file__": 85, "__init__": 27, "__main__": 44, "__name__": 44, "__version__": 44, "_cudadeviceproperti": 90, "_prepare_authors_field": 27, "a0": [45, 46], "aart": 112, "abba": 33, "abdu": [11, 111], "abisi": 111, "abl": [24, 26, 37, 52, 69, 72, 99, 126], "ablot": 111, "about": [15, 16, 17, 23, 24, 26, 27, 39, 43, 44, 54, 55, 65, 67, 68, 83, 84, 85, 87, 100, 102, 109, 112, 113, 115, 116, 120, 121, 124, 125, 131], "abov": [25, 26, 27, 37, 38, 39, 44, 48, 50, 53, 59, 65, 84, 88, 93, 100, 106, 118, 129], "absenc": 112, "absolut": [23, 127], "absorb": [10, 11], "abstract": [26, 27, 55], "ac": 112, "academ": 55, 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"add_additional_refer": 44, "add_brain_region": [81, 82, 85, 119], "add_label": 81, "add_silhouett": 81, "add_structure_to_view": 44, "add_to_view": 44, "addit": [0, 14, 17, 22, 23, 27, 31, 32, 38, 44, 46, 48, 54, 68, 74, 76, 77, 78, 81, 84, 88, 94, 117, 118, 124, 128, 131], "addition": [0, 24, 53], "additional_depend": 32, "address": [0, 15, 16, 84], "adher": [22, 23], "adjac": 29, "adjust": [9, 53, 60, 89, 118, 120, 124, 125, 129, 130], "adkin": 112, "admba_3d_e11_5_mouse_16um": [45, 46], "admba_3d_e13_5_mouse_16um": [45, 46], "admba_3d_e15_5_mouse_16um": [45, 46], "admba_3d_e18_5_mouse_16um": [45, 46], "admba_3d_p14_mouse_16": [45, 46], "admba_3d_p28_mouse_16": [45, 46], "admba_3d_p4_mouse_16": [45, 46], "admba_3d_p56_mouse_25um": [45, 46], "admin": [25, 104, 105], "administ": 90, "adolf": 112, "adopt": [12, 26], "adrien": 111, "adult": [3, 11, 33, 42, 45, 82, 112], "advanc": [3, 5, 11, 20, 21, 64, 69, 77, 86, 87, 112], "advantag": [11, 16, 24], "advertis": 33, "advic": [11, 14, 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118, 130], "zsh": 23, "zulip": [16, 23, 40, 43], "zyx": 22, "\u00e7etin": 112, "\u00e9": 112, "\u00f6": 112, "\u00f6nc\u00fcl": 112, "\u00f6zt\u00fcrk": 112, "\u00f8vsthu": 112, "\u00fcnai": 112, "\u0161tih": 112, "\u03bcm": 50}, "titles": ["About", "bg-atlasapi and bg-atlasgen have merged under a new name", "An Atlas for the regenerative Ambystoma mexicanum (axolotl) has been added to BrainGlobe", "A mouse brain atlas with barrel field annotations has been added to BrainGlobe", "bg-space has been renamed", "BrainGlobe version 1.1.0 is released!", "New brainmapper napari widget released", "Plans for brainrender", "An atlas for the Blind Mexican Cavefish has been added to BrainGlobe", "Cellfinder version 1.3.0 is released!", "imio will be merging into brainglobe-utils", "Blog", "An atlas for the prairie vole Microtus ochrogaster has been added to BrainGlobe", "Version 1 of brainreg and brainglobe-segmentation released", "cellfinder has moved: version 1 of brainglobe-workflows released", "cellfinder-core and cellfinder-napari have merged", "BrainGlobe is being restructured, version 1 is on it\u2019s way!", "BrainGlobe version 1 is here!", "Courses", "Whole brain microscopy analysis with BrainGlobe and napari", "December 6th 2023", "October 7th-8th 2024", "Conventions", "Developer\u2019s guide", "Introduction to the BrainGlobe codebase for developers", "Publishing new releases", "brainglobe-meta", "brainglobe-utils", "brainglobe-workflows", "cellfinder.core", "Specific Repository Developer Documentation", "Testing", "Tooling", "Software built by the community", "Community", "Releases", "Version 1: changes to registration and segmentation tools", "Version 1: changes to the cellfinder backend and plugin", "Version 1: Cellfinder migration and brainglobe-workflows", "BrainGlobe version 1 overview", "Roadmaps", "May 2024", "November 2023", "Contact", "Adding a new atlas", "BrainGlobe Atlas API (brainglobe-atlasapi)", "Atlas details", "Command line interface", "Python API", "Using the files directly", "brainglobe-heatmap", "brainglobe-segmentation", "Analysing segmentation from other napari plugins", "Prerequisites", "brainglobe-space", "Generating Citations for BrainGlobe tools", "Image IO submodule", "brainglobe-utils", "brainmapper cell transformation widget", "Cell candidate detection", "Cell candidate classification", "Command line interface", "Data requirements", "Debugging common error messages", "brainmapper command line tool", "Output files", "Visualisation", "brainglobe-workflows", "brainreg", "Requirements", "Troubleshooting", "Command line tool", "Napari plugin", "Checking orientation", "Output files", "Registration parameters", "Visualising brainreg output", "brainrender", "Installing brainrender", "Actors", "Usage", "Scene", "Using Notebooks", "Using your own data in brainrender", "Registering data", "Videos, animations and exporting to html", "cellfinder", "Installation", "Debugging common error messages", "Troubleshooting", "Speeding up cellfinder", "cellfinder.core API", "Downloading the pre-trained model in advance", "All cell detection parameters", "Cell detection", "cellfinder napari plugin", "Generating data to retrain the cellfinder classification network", "Retraining the network for new data", "Retraining the pre-trained network", "Using supplied training data", "Documentation", "morphapi", "Downloading data", "Rendering data", "Using conda", "Setting up your GPU", "Image space definition", "Setting up", "Funders", "BrainGlobe", "Media", "People", "BrainGlobe publications", "Talks", "Exploring the numerical results", "Whole brain cell detection and registration with the brainmapper command line tool", "Running brainmapper", "Setting up", "Visualising the results", "Visualising your data in brainrender", "Detecting cells in 3D with cellfinder", "Retraining the cellfinder classification network", "Tutorials", "Download an atlas through napari", "Segmenting a 1D track", "Segmenting 2/3D structures", "Silicon probe tracking", "Aligning samples for template building", "Analyze and visualize bulk fluorescence tracing data", "Analysing brainwide distribution of cells", "Registering a whole-brain image to an atlas", "Visualise an atlas in napari"], "titleterms": {"": [16, 23, 46, 84], "0": [5, 9, 67], "1": [5, 9, 13, 14, 16, 17, 35, 36, 37, 38, 39], "1d": 124, "2": 125, "2020": 110, "2023": [20, 42], "2024": [21, 41, 42], "2025": 41, "24": 63, "2d": 29, "3": 9, "3d": [29, 46, 110, 120, 125], "6th": 20, "7th": 21, "8th": 21, "A": [3, 46, 73], "On": 25, "The": [54, 88, 110], "These": 110, "To": [23, 53, 91], "_fmt": 27, "about": [0, 73], "access": 0, "activ": 104, "actor": [79, 81], "ad": [2, 3, 8, 12, 27, 44, 79, 81], "addit": [30, 61, 71, 72], "adult": 46, "advanc": [78, 92], "affin": 75, "aid": 110, "al": 46, "algorithm": [88, 89], "align": [33, 84, 113, 127], "all": [58, 93], "allen": [46, 102], "ambystoma": 2, "amphibian": 46, "an": [2, 8, 12, 44, 110, 123, 126, 128, 130, 131], "analys": 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BrainGlobe", "Version 1 of brainreg and brainglobe-segmentation released", "cellfinder has moved: version 1 of brainglobe-workflows released", "cellfinder-core and cellfinder-napari have merged", "BrainGlobe is being restructured, version 1 is on it\u2019s way!", "BrainGlobe version 1 is here!", "Courses", "Whole brain microscopy analysis with BrainGlobe and napari", "December 6th 2023", "October 7th-8th 2024", "Conventions", "Developer\u2019s guide", "Introduction to the BrainGlobe codebase for developers", "Publishing new releases", "brainglobe-meta", "brainglobe-utils", "brainglobe-workflows", "cellfinder.core", "Specific Repository Developer Documentation", "Testing", "Tooling", "Software built by the community", "Community", "Releases", "Version 1: changes to registration and segmentation tools", "Version 1: changes to the cellfinder backend and plugin", "Version 1: Cellfinder migration and brainglobe-workflows", "BrainGlobe version 1 overview", "Roadmaps", "May 2024", "November 2023", "Contact", "Adding a new atlas", "BrainGlobe Atlas API (brainglobe-atlasapi)", "Atlas details", "Command line interface", "Python API", "Using the files directly", "brainglobe-heatmap", "brainglobe-segmentation", "Analysing segmentation from other napari plugins", "Prerequisites", "brainglobe-space", "Generating Citations for BrainGlobe tools", "Image IO submodule", "brainglobe-utils", "brainmapper cell transformation widget", "Cell candidate detection", "Cell candidate classification", "Command line interface", "Data requirements", "Debugging common error messages", "brainmapper command line tool", "Output files", "Visualisation", "brainglobe-workflows", "brainreg", "Requirements", "Troubleshooting", "Command line tool", "Napari plugin", "Checking orientation", "Output files", "Registration parameters", "Visualising brainreg output", "brainrender", "Installing brainrender", "Actors", "Usage", "Scene", "Using Notebooks", "Using your own data in brainrender", "Registering data", "Videos, animations and exporting to html", "cellfinder", "Installation", "Debugging common error messages", "Troubleshooting", "Speeding up cellfinder", "cellfinder.core API", "Downloading the pre-trained model in advance", "All cell detection parameters", "Cell detection", "cellfinder napari plugin", "Generating data to retrain the cellfinder classification network", "Retraining the network for new data", "Retraining the pre-trained network", "Using supplied training data", "Documentation", "morphapi", "Downloading data", "Rendering data", "Using conda", "Setting up your GPU", "Image space definition", "Setting up", "Funders", "BrainGlobe", "Media", "People", "BrainGlobe publications", "Talks", "Exploring the numerical results", "Whole brain cell detection and registration with the brainmapper command line tool", "Running brainmapper", "Setting up", "Visualising the results", "Visualising your data in brainrender", "Detecting cells in 3D with cellfinder", "Retraining the cellfinder classification network", "Tutorials", "Download an atlas through napari", "Segmenting a 1D track", "Segmenting 2/3D structures", "Silicon probe tracking", "Aligning samples for template building", "Analyze and visualize bulk fluorescence tracing data", "Analysing brainwide distribution of cells", "Registering a whole-brain image to an atlas", "Visualise an atlas in napari"], "titleterms": {"": [16, 23, 46, 84], "0": [5, 9, 67], "1": [5, 9, 13, 14, 16, 17, 35, 36, 37, 38, 39], "1d": 124, "2": 125, "2020": 110, "2023": [20, 42], "2024": [21, 41, 42], "2025": 41, "24": 63, "2d": 29, "3": 9, "3d": [29, 46, 110, 120, 125], "6th": 20, "7th": 21, "8th": 21, "A": [3, 46, 73], "On": 25, "The": [54, 88, 110], "These": 110, "To": [23, 53, 91], "_fmt": 27, "about": [0, 73], "access": 0, "activ": 104, "actor": [79, 81], "ad": [2, 3, 8, 12, 27, 44, 79, 81], "addit": [30, 61, 71, 72], "adult": 46, "advanc": [78, 92], "affin": 75, "aid": 110, "al": 46, "algorithm": [88, 89], "align": [33, 84, 113, 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