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Page Not Found

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More details

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What do I need to do?

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What do I need to do?

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brainrender

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What do I need to do?

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Why are we adding new atlases?

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PyTorch backend

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What do I need to do?

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Blog#

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-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

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Full changelog

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Full changelog

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Full changelog

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Appendix: a note on

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Full Changelog

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Location

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Courses#<

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Axis ordering in spatial arrays

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Further information

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Default architecture for BrainGlobe Tools

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Workflow for publishing new releases

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Regenerating the Dependency Tree

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citation.format

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cellfinder

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Structure detection

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Specific Repository Developer Documentation

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Test data

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Automated versioning

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ClearFinder

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Community

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BrainGlobe restructuring (version 1) release notes

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brainreg-segmen

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I have not updated to

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Delaying updating

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Full Changelog

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Roadmaps

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Q2 2025#<

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Other ongoing projects (release TBC)

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Other ways to get in touch

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Citation

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Allen Human B

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Command line interface

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Query for hemispheres

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Using the files directly

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainglobe-heatmap/index.html b/documentation/brainglobe-heatmap/index.html index ad8733d2..662427ed 100644 --- a/documentation/brainglobe-heatmap/index.html +++ b/documentation/brainglobe-heatmap/index.html @@ -894,7 +894,7 @@

Citing brainglo

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainglobe-segmentation/index.html b/documentation/brainglobe-segmentation/index.html index be3482f0..64effe86 100644 --- a/documentation/brainglobe-segmentation/index.html +++ b/documentation/brainglobe-segmentation/index.html @@ -791,7 +791,7 @@

Citation

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainglobe-segmentation/user-guide/analysing-external-segmentation.html b/documentation/brainglobe-segmentation/user-guide/analysing-external-segmentation.html index 533dc745..d2cd0fd2 100644 --- a/documentation/brainglobe-segmentation/user-guide/analysing-external-segmentation.html +++ b/documentation/brainglobe-segmentation/user-guide/analysing-external-segmentation.html @@ -824,7 +824,7 @@

Analyse the segmented layer

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainglobe-segmentation/user-guide/index.html b/documentation/brainglobe-segmentation/user-guide/index.html index 5fa3e74b..85d26cde 100644 --- a/documentation/brainglobe-segmentation/user-guide/index.html +++ b/documentation/brainglobe-segmentation/user-guide/index.html @@ -802,7 +802,7 @@

Navigating

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainglobe-space/index.html b/documentation/brainglobe-space/index.html index 3ed8ee47..6380305e 100644 --- a/documentation/brainglobe-space/index.html +++ b/documentation/brainglobe-space/index.html @@ -858,7 +858,7 @@

Easy iteration over projections

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainglobe-utils/citation-module.html b/documentation/brainglobe-utils/citation-module.html index 2f9b2600..4bed6e85 100644 --- a/documentation/brainglobe-utils/citation-module.html +++ b/documentation/brainglobe-utils/citation-module.html @@ -859,7 +859,7 @@

Usage Pattern

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainglobe-utils/image_io.html b/documentation/brainglobe-utils/image_io.html index ee584c35..333c51f2 100644 --- a/documentation/brainglobe-utils/image_io.html +++ b/documentation/brainglobe-utils/image_io.html @@ -809,7 +809,7 @@

Saving images

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainglobe-utils/index.html b/documentation/brainglobe-utils/index.html index bdc9bad9..ae4943bb 100644 --- a/documentation/brainglobe-utils/index.html +++ b/documentation/brainglobe-utils/index.html @@ -762,7 +762,7 @@

User guide

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainglobe-workflows/brainmapper/candidate-detection.html b/documentation/brainglobe-workflows/brainmapper/candidate-detection.html index 6a0feb69..47e72816 100644 --- a/documentation/brainglobe-workflows/brainmapper/candidate-detection.html +++ b/documentation/brainglobe-workflows/brainmapper/candidate-detection.html @@ -750,7 +750,7 @@

Cell candidate detection

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainglobe-workflows/brainmapper/classification.html b/documentation/brainglobe-workflows/brainmapper/classification.html index f8896ea2..86ffeed2 100644 --- a/documentation/brainglobe-workflows/brainmapper/classification.html +++ b/documentation/brainglobe-workflows/brainmapper/classification.html @@ -756,7 +756,7 @@

Cell candidate classification

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainglobe-workflows/brainmapper/cli.html b/documentation/brainglobe-workflows/brainmapper/cli.html index b3edaf85..8961a1a0 100644 --- a/documentation/brainglobe-workflows/brainmapper/cli.html +++ b/documentation/brainglobe-workflows/brainmapper/cli.html @@ -848,7 +848,7 @@

Additional options

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainglobe-workflows/brainmapper/data-requirements.html b/documentation/brainglobe-workflows/brainmapper/data-requirements.html index c71e53d6..dedb65bf 100644 --- a/documentation/brainglobe-workflows/brainmapper/data-requirements.html +++ b/documentation/brainglobe-workflows/brainmapper/data-requirements.html @@ -795,7 +795,7 @@

Organisation

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainglobe-workflows/brainmapper/error-messages.html b/documentation/brainglobe-workflows/brainmapper/error-messages.html index 610d53c1..19f337d9 100644 --- a/documentation/brainglobe-workflows/brainmapper/error-messages.html +++ b/documentation/brainglobe-workflows/brainmapper/error-messages.html @@ -798,7 +798,7 @@

CommandLineInputError: File path: cannot be found.

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainglobe-workflows/brainmapper/index.html b/documentation/brainglobe-workflows/brainmapper/index.html index c445de63..dd10ca7e 100644 --- a/documentation/brainglobe-workflows/brainmapper/index.html +++ b/documentation/brainglobe-workflows/brainmapper/index.html @@ -813,7 +813,7 @@

Notes#<

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainglobe-workflows/brainmapper/output-files.html b/documentation/brainglobe-workflows/brainmapper/output-files.html index 38233935..7ad4100e 100644 --- a/documentation/brainglobe-workflows/brainmapper/output-files.html +++ b/documentation/brainglobe-workflows/brainmapper/output-files.html @@ -792,7 +792,7 @@

Registration

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainglobe-workflows/brainmapper/visualisation.html b/documentation/brainglobe-workflows/brainmapper/visualisation.html index 1e7489a6..1f7e78b2 100644 --- a/documentation/brainglobe-workflows/brainmapper/visualisation.html +++ b/documentation/brainglobe-workflows/brainmapper/visualisation.html @@ -777,7 +777,7 @@

Visualising your results

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainglobe-workflows/index.html b/documentation/brainglobe-workflows/index.html index 0e6ce45f..1c881c1f 100644 --- a/documentation/brainglobe-workflows/index.html +++ b/documentation/brainglobe-workflows/index.html @@ -785,7 +785,7 @@

Installing with

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainreg/index.html b/documentation/brainreg/index.html index f0766b38..87f9f5a0 100644 --- a/documentation/brainreg/index.html +++ b/documentation/brainreg/index.html @@ -836,7 +836,7 @@

Citation

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainreg/installation.html b/documentation/brainreg/installation.html index 08d236b8..a1193385 100644 --- a/documentation/brainreg/installation.html +++ b/documentation/brainreg/installation.html @@ -823,7 +823,7 @@

Download atlas (optional)

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainreg/troubleshooting.html b/documentation/brainreg/troubleshooting.html index 88695149..aefad400 100644 --- a/documentation/brainreg/troubleshooting.html +++ b/documentation/brainreg/troubleshooting.html @@ -786,7 +786,7 @@

Segmentation fault

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainreg/user-guide/brainreg-cli.html b/documentation/brainreg/user-guide/brainreg-cli.html index 887f798e..0e94fc60 100644 --- a/documentation/brainreg/user-guide/brainreg-cli.html +++ b/documentation/brainreg/user-guide/brainreg-cli.html @@ -833,7 +833,7 @@

Registration options

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainreg/user-guide/brainreg-napari.html b/documentation/brainreg/user-guide/brainreg-napari.html index 4ca6255c..4bbc9fe5 100644 --- a/documentation/brainreg/user-guide/brainreg-napari.html +++ b/documentation/brainreg/user-guide/brainreg-napari.html @@ -822,7 +822,7 @@

Running brainreg

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainreg/user-guide/checking-orientation.html b/documentation/brainreg/user-guide/checking-orientation.html index d77860b2..3866131e 100644 --- a/documentation/brainreg/user-guide/checking-orientation.html +++ b/documentation/brainreg/user-guide/checking-orientation.html @@ -774,7 +774,7 @@

A note about the camera position

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainreg/user-guide/output-files.html b/documentation/brainreg/user-guide/output-files.html index 4da508e4..78fb67dd 100644 --- a/documentation/brainreg/user-guide/output-files.html +++ b/documentation/brainreg/user-guide/output-files.html @@ -757,7 +757,7 @@

Output files

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainreg/user-guide/parameters.html b/documentation/brainreg/user-guide/parameters.html index 3e6161e4..ef773bf3 100644 --- a/documentation/brainreg/user-guide/parameters.html +++ b/documentation/brainreg/user-guide/parameters.html @@ -779,7 +779,7 @@

Freeform registration

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainreg/user-guide/visualisation.html b/documentation/brainreg/user-guide/visualisation.html index eb160f57..77af1b2d 100644 --- a/documentation/brainreg/user-guide/visualisation.html +++ b/documentation/brainreg/user-guide/visualisation.html @@ -769,7 +769,7 @@

Usage#<

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainrender/index.html b/documentation/brainrender/index.html index 6a64c1d6..1352adc6 100644 --- a/documentation/brainrender/index.html +++ b/documentation/brainrender/index.html @@ -805,7 +805,7 @@

Citation

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainrender/installation.html b/documentation/brainrender/installation.html index 451560d2..824f9182 100644 --- a/documentation/brainrender/installation.html +++ b/documentation/brainrender/installation.html @@ -785,7 +785,7 @@

Advanced installation

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainrender/usage/actors.html b/documentation/brainrender/usage/actors.html index 35fe432e..059cc4f5 100644 --- a/documentation/brainrender/usage/actors.html +++ b/documentation/brainrender/usage/actors.html @@ -803,7 +803,7 @@

Adding actors to your scene

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainrender/usage/index.html b/documentation/brainrender/usage/index.html index 85056611..bdfbe081 100644 --- a/documentation/brainrender/usage/index.html +++ b/documentation/brainrender/usage/index.html @@ -764,7 +764,7 @@

Usage#<

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainrender/usage/scene.html b/documentation/brainrender/usage/scene.html index c408d573..39ebb787 100644 --- a/documentation/brainrender/usage/scene.html +++ b/documentation/brainrender/usage/scene.html @@ -830,7 +830,7 @@

Working with cameras

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainrender/usage/using-notebooks.html b/documentation/brainrender/usage/using-notebooks.html index c1a60c63..0af59e1e 100644 --- a/documentation/brainrender/usage/using-notebooks.html +++ b/documentation/brainrender/usage/using-notebooks.html @@ -820,7 +820,7 @@

Embedding renderings in Jupyter notebooks

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainrender/usage/using-your-data/index.html b/documentation/brainrender/usage/using-your-data/index.html index 3e7b6a95..a63ad743 100644 --- a/documentation/brainrender/usage/using-your-data/index.html +++ b/documentation/brainrender/usage/using-your-data/index.html @@ -902,7 +902,7 @@

Supported data types

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainrender/usage/using-your-data/registering-data.html b/documentation/brainrender/usage/using-your-data/registering-data.html index 41cbafe3..d8eff56f 100644 --- a/documentation/brainrender/usage/using-your-data/registering-data.html +++ b/documentation/brainrender/usage/using-your-data/registering-data.html @@ -800,7 +800,7 @@

Matching resolution and offset

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/brainrender/usage/videos-animations-and-exporting-to-html.html b/documentation/brainrender/usage/videos-animations-and-exporting-to-html.html index acda782a..12f1cd11 100644 --- a/documentation/brainrender/usage/videos-animations-and-exporting-to-html.html +++ b/documentation/brainrender/usage/videos-animations-and-exporting-to-html.html @@ -847,7 +847,7 @@

Exporting to html

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/cellfinder/index.html b/documentation/cellfinder/index.html index 5bef406b..82decf9a 100644 --- a/documentation/cellfinder/index.html +++ b/documentation/cellfinder/index.html @@ -819,7 +819,7 @@

Citing cellfinder

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/cellfinder/installation.html b/documentation/cellfinder/installation.html index 1e04da19..83c552ea 100644 --- a/documentation/cellfinder/installation.html +++ b/documentation/cellfinder/installation.html @@ -783,7 +783,7 @@

Installing brai

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/cellfinder/troubleshooting/error-messages.html b/documentation/cellfinder/troubleshooting/error-messages.html index 45519b6f..285de8dd 100644 --- a/documentation/cellfinder/troubleshooting/error-messages.html +++ b/documentation/cellfinder/troubleshooting/error-messages.html @@ -836,7 +836,7 @@

CPU instruction sets

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/cellfinder/troubleshooting/index.html b/documentation/cellfinder/troubleshooting/index.html index 9c3e2abe..1cc3cc29 100644 --- a/documentation/cellfinder/troubleshooting/index.html +++ b/documentation/cellfinder/troubleshooting/index.html @@ -798,7 +798,7 @@

Anything else

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/cellfinder/troubleshooting/speed-up.html b/documentation/cellfinder/troubleshooting/speed-up.html index fd992f3f..8cf6fa02 100644 --- a/documentation/cellfinder/troubleshooting/speed-up.html +++ b/documentation/cellfinder/troubleshooting/speed-up.html @@ -829,7 +829,7 @@

Cell classification or training the network is slow

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/cellfinder/user-guide/cellfinder-core.html b/documentation/cellfinder/user-guide/cellfinder-core.html index 0d2a0fb8..98a937e1 100644 --- a/documentation/cellfinder/user-guide/cellfinder-core.html +++ b/documentation/cellfinder/user-guide/cellfinder-core.html @@ -917,7 +917,7 @@

Training the network

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/cellfinder/user-guide/cellfinder-download.html b/documentation/cellfinder/user-guide/cellfinder-download.html index adfba09b..6ce7972d 100644 --- a/documentation/cellfinder/user-guide/cellfinder-download.html +++ b/documentation/cellfinder/user-guide/cellfinder-download.html @@ -742,7 +742,7 @@

Downloading the pre-trained model in advance

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/cellfinder/user-guide/napari-plugin/all-cell-detection-parameters.html b/documentation/cellfinder/user-guide/napari-plugin/all-cell-detection-parameters.html index cd317618..9946b36e 100644 --- a/documentation/cellfinder/user-guide/napari-plugin/all-cell-detection-parameters.html +++ b/documentation/cellfinder/user-guide/napari-plugin/all-cell-detection-parameters.html @@ -799,7 +799,7 @@

Misc options

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/cellfinder/user-guide/napari-plugin/cell-detection.html b/documentation/cellfinder/user-guide/napari-plugin/cell-detection.html index 2a6c461f..a9c00472 100644 --- a/documentation/cellfinder/user-guide/napari-plugin/cell-detection.html +++ b/documentation/cellfinder/user-guide/napari-plugin/cell-detection.html @@ -815,7 +815,7 @@

Saving data

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/cellfinder/user-guide/napari-plugin/index.html b/documentation/cellfinder/user-guide/napari-plugin/index.html index 678ec0b7..4c18869b 100644 --- a/documentation/cellfinder/user-guide/napari-plugin/index.html +++ b/documentation/cellfinder/user-guide/napari-plugin/index.html @@ -745,7 +745,7 @@

cellfinder napari plugin

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/cellfinder/user-guide/napari-plugin/training-data-generation.html b/documentation/cellfinder/user-guide/napari-plugin/training-data-generation.html index adc50815..294438f2 100644 --- a/documentation/cellfinder/user-guide/napari-plugin/training-data-generation.html +++ b/documentation/cellfinder/user-guide/napari-plugin/training-data-generation.html @@ -806,7 +806,7 @@

Exporting data for training

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/cellfinder/user-guide/napari-plugin/training-the-network.html b/documentation/cellfinder/user-guide/napari-plugin/training-the-network.html index fc792091..65fe46c1 100644 --- a/documentation/cellfinder/user-guide/napari-plugin/training-the-network.html +++ b/documentation/cellfinder/user-guide/napari-plugin/training-the-network.html @@ -832,7 +832,7 @@

Run training

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/cellfinder/user-guide/training/index.html b/documentation/cellfinder/user-guide/training/index.html index a7590257..f3b78f53 100644 --- a/documentation/cellfinder/user-guide/training/index.html +++ b/documentation/cellfinder/user-guide/training/index.html @@ -888,7 +888,7 @@

Further help

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/cellfinder/user-guide/training/using-supplied-data.html b/documentation/cellfinder/user-guide/training/using-supplied-data.html index f39b1d94..c4c616f1 100644 --- a/documentation/cellfinder/user-guide/training/using-supplied-data.html +++ b/documentation/cellfinder/user-guide/training/using-supplied-data.html @@ -778,7 +778,7 @@

Using supplied training data

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/index.html b/documentation/index.html index bcb6f65f..7e0f1d25 100644 --- a/documentation/index.html +++ b/documentation/index.html @@ -810,7 +810,7 @@

Individual Tool Documentation

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/morphapi/index.html b/documentation/morphapi/index.html index 8334a1c8..2c3c5125 100644 --- a/documentation/morphapi/index.html +++ b/documentation/morphapi/index.html @@ -780,7 +780,7 @@

Usage#<

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/morphapi/usage/downloading-data.html b/documentation/morphapi/usage/downloading-data.html index b16259fa..3e6af7ae 100644 --- a/documentation/morphapi/usage/downloading-data.html +++ b/documentation/morphapi/usage/downloading-data.html @@ -851,7 +851,7 @@

Mpin Zebrafish

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/morphapi/usage/rendering-data.html b/documentation/morphapi/usage/rendering-data.html index 9cd0124d..2fdbaa5f 100644 --- a/documentation/morphapi/usage/rendering-data.html +++ b/documentation/morphapi/usage/rendering-data.html @@ -745,7 +745,7 @@

Rendering data

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/setting-up/conda.html b/documentation/setting-up/conda.html index 260ce5e1..c9a44bc9 100644 --- a/documentation/setting-up/conda.html +++ b/documentation/setting-up/conda.html @@ -857,7 +857,7 @@

Further details

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/setting-up/gpu.html b/documentation/setting-up/gpu.html index 39ac01b1..c73c3ee4 100644 --- a/documentation/setting-up/gpu.html +++ b/documentation/setting-up/gpu.html @@ -794,7 +794,7 @@

Installing PyTorch with GPU support

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/setting-up/image-definition.html b/documentation/setting-up/image-definition.html index 94dbd066..b137a2eb 100644 --- a/documentation/setting-up/image-definition.html +++ b/documentation/setting-up/image-definition.html @@ -793,7 +793,7 @@

Voxel sizes

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/documentation/setting-up/index.html b/documentation/setting-up/index.html index 324bbbdd..ccfe5ce4 100644 --- a/documentation/setting-up/index.html +++ b/documentation/setting-up/index.html @@ -747,7 +747,7 @@

Setting up

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/funders.html b/funders.html index 159ec438..40e428ef 100644 --- a/funders.html +++ b/funders.html @@ -635,7 +635,7 @@

Funders#<

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/genindex.html b/genindex.html index 59f8970b..660c2d26 100644 --- a/genindex.html +++ b/genindex.html @@ -552,7 +552,7 @@

Index

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/index.html b/index.html index 30ffea14..55e9cddd 100644 --- a/index.html +++ b/index.html @@ -616,7 +616,7 @@

BrainGlobe

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/media.html b/media.html index 47739024..a3c59c48 100644 --- a/media.html +++ b/media.html @@ -679,7 +679,7 @@

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/people.html b/people.html index f0f3a2e9..0a1be2b9 100644 --- a/people.html +++ b/people.html @@ -1358,6 +1358,15 @@

Contributors https://github.com/Robkozol

+
+
+
+
+Roberto
+
+ +https://github.com/RobertoDF
+

Inspired by All Contributors. All information is sourced from GitHub. If any changes @@ -1442,7 +1451,7 @@

Contributors

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/publications.html b/publications.html index 4a41230c..fc59f0fe 100644 --- a/publications.html +++ b/publications.html @@ -807,7 +807,7 @@

Publications citing BrainGlobe

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/search.html b/search.html index 2ebdb8ae..13f3b63e 100644 --- a/search.html +++ b/search.html @@ -580,7 +580,7 @@

Search

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/searchindex.js b/searchindex.js index 8e2c7b63..8c88d562 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"2D filtering": [[23, "d-filtering"]], "3D Edge-Aware Refined Atlases Derived from the Allen Developing Mouse Brain Atlases": [[40, "d-edge-aware-refined-atlases-derived-from-the-allen-developing-mouse-brain-atlases"]], "3D filtering": [[23, "id1"]], "3D version of the Allen mouse spinal cord atlas": [[40, "d-version-of-the-allen-mouse-spinal-cord-atlas"]], "A note about the camera position": [[66, "a-note-about-the-camera-position"]], "AZBA: A 3D Adult Zebrafish Brain Atlas": [[40, "azba-a-3d-adult-zebrafish-brain-atlas"]], "About": [[0, null]], "Accessing data": [[0, "accessing-data"]], "Activate the environment": [[97, "activate-the-environment"]], "Actors": [[72, null]], "Adding a new atlas": [[38, null]], "Adding a new supported citation format": [[21, "adding-a-new-supported-citation-format"]], "Adding actors to your 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"titles": ["About", "bg-atlasapi and bg-atlasgen have merged under a new name", "bg-space has been renamed", "BrainGlobe version 1.1.0 is 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", "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!", "December 6th 2023", "Courses", "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", "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", "Segmenting a 1D track", "Segmenting 2/3D structures", "Silicon probe tracking", "Analyze and visualize bulk fluorescence tracing data", "Registering a whole-brain image to an atlas", "Visualise an atlas in napari"], "titleterms": {"": [12, 17, 40, 77], "0": [3, 6, 60], "1": [3, 6, 9, 10, 12, 13, 29, 30, 31, 32, 33], "1d": 116, "2": 117, "2020": 103, "2023": [14, 36], "2024": [35, 36], "2025": 35, "24": 56, "2d": 23, "3": 6, "39": 40, "3d": [23, 40, 103, 113, 117], "6th": 14, "A": [40, 66], "On": 19, "The": [48, 81, 103], "These": 103, "To": [17, 47, 84], "_fmt": 21, "about": [0, 66], "access": 0, "activ": 97, "actor": [72, 74], "ad": [5, 21, 38, 72, 74], "addit": [24, 54, 64, 65], "adult": 40, "advanc": [71, 85], "affin": 68, "aid": 103, "al": 40, 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-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/tutorials/brainmapper/exploring-the-numerical-results.html b/tutorials/brainmapper/exploring-the-numerical-results.html index c95a1380..feccda86 100644 --- a/tutorials/brainmapper/exploring-the-numerical-results.html +++ b/tutorials/brainmapper/exploring-the-numerical-results.html @@ -719,7 +719,7 @@

Exploring the numerical results

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/tutorials/brainmapper/index.html b/tutorials/brainmapper/index.html index 8a2843e5..491f3c89 100644 --- a/tutorials/brainmapper/index.html +++ b/tutorials/brainmapper/index.html @@ -689,7 +689,7 @@

Tutorial

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/tutorials/brainmapper/running-brainmapper.html b/tutorials/brainmapper/running-brainmapper.html index 39316e45..a3c69106 100644 --- a/tutorials/brainmapper/running-brainmapper.html +++ b/tutorials/brainmapper/running-brainmapper.html @@ -679,7 +679,7 @@

Running brainma

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/tutorials/brainmapper/setting-up.html b/tutorials/brainmapper/setting-up.html index 816db6f6..6aa9e843 100644 --- a/tutorials/brainmapper/setting-up.html +++ b/tutorials/brainmapper/setting-up.html @@ -691,7 +691,7 @@

Before you start

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/tutorials/brainmapper/visualising-the-results.html b/tutorials/brainmapper/visualising-the-results.html index 1aa6b803..95800a9d 100644 --- a/tutorials/brainmapper/visualising-the-results.html +++ b/tutorials/brainmapper/visualising-the-results.html @@ -670,7 +670,7 @@

Visualising the results

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/tutorials/brainmapper/visualising-your-data-in-brainrender.html b/tutorials/brainmapper/visualising-your-data-in-brainrender.html index 9e9dc433..89ebf4c5 100644 --- a/tutorials/brainmapper/visualising-your-data-in-brainrender.html +++ b/tutorials/brainmapper/visualising-your-data-in-brainrender.html @@ -671,7 +671,7 @@

Visualising your data in brainrender

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/tutorials/cellfinder-detection.html b/tutorials/cellfinder-detection.html index ffa48996..fae1d4c7 100644 --- a/tutorials/cellfinder-detection.html +++ b/tutorials/cellfinder-detection.html @@ -678,7 +678,7 @@

Detecting cells in 3D with cellfinder

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/tutorials/cellfinder-retraining.html b/tutorials/cellfinder-retraining.html index 9b57dea1..6b67562b 100644 --- a/tutorials/cellfinder-retraining.html +++ b/tutorials/cellfinder-retraining.html @@ -683,7 +683,7 @@

Retraining the cellfinder classification network

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/tutorials/index.html b/tutorials/index.html index b1aed9ad..e5e3e938 100644 --- a/tutorials/index.html +++ b/tutorials/index.html @@ -760,7 +760,7 @@

Specific applications

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/tutorials/segmenting-1d-tracks.html b/tutorials/segmenting-1d-tracks.html index fac4de10..d4d88574 100644 --- a/tutorials/segmenting-1d-tracks.html +++ b/tutorials/segmenting-1d-tracks.html @@ -708,7 +708,7 @@

Segmenting a 1D track

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/tutorials/segmenting-3d-structures.html b/tutorials/segmenting-3d-structures.html index 8b5bc76d..eddbed5b 100644 --- a/tutorials/segmenting-3d-structures.html +++ b/tutorials/segmenting-3d-structures.html @@ -689,7 +689,7 @@

Segmenting 2/3D structures

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/tutorials/silicon-probe-tracking.html b/tutorials/silicon-probe-tracking.html index 96fd9153..04d31b1f 100644 --- a/tutorials/silicon-probe-tracking.html +++ b/tutorials/silicon-probe-tracking.html @@ -753,7 +753,7 @@

Visualize the probe track with brainrender

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/tutorials/tracing-tracking.html b/tutorials/tracing-tracking.html index 6aa37658..6bc86424 100644 --- a/tutorials/tracing-tracking.html +++ b/tutorials/tracing-tracking.html @@ -751,7 +751,7 @@

Bulk axonal track detection

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/tutorials/tutorial-whole-brain-registration.html b/tutorials/tutorial-whole-brain-registration.html index 1bc0f94b..f4800b2d 100644 --- a/tutorials/tutorial-whole-brain-registration.html +++ b/tutorials/tutorial-whole-brain-registration.html @@ -693,7 +693,7 @@

Registering a whole-brain image to an atlas

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.

diff --git a/tutorials/visualise-atlas-napari.html b/tutorials/visualise-atlas-napari.html index bd01c028..08b3e961 100644 --- a/tutorials/visualise-atlas-napari.html +++ b/tutorials/visualise-atlas-napari.html @@ -671,7 +671,7 @@

Visualise an atlas in napari

-Created using Sphinx 7.4.5. +Created using Sphinx 7.4.7.