brainglobe/cellfinder-visualize

This repository has been archived on 07/Dec/2023
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Python
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BSD 3-Clause "New...
Created over 2 years ago
Updated 11 months ago

brainglobe/cellfinder-visualize

brainglobe

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brainrender

a python based software for visualization of neuroanatomical and morphological data.

cellfinder

Automated 3D cell detection in very large images

brainglobe-atlasapi

A lightweight python module to interact with atlases for systems neuroscience

brainreg

Automated 3D brain registration with support for multiple species and atlases.

slicereg

A 2D-3D histological brain slice registration application for mouse, rat, zebrafish brains.

brainglobe-heatmap

Rendering anatomical heatmaps with brainrender and matplotlib

brainglobe-segmentation

Segmentation of anatomical structures in a common coordinate space

cellfinder-napari

Efficient cell detection in large images using cellfinder in napari

cellfinder-core

Standalone cellfinder cell detection algorithm

brainrender-napari

A napari plugin to render BrainGlobe atlases and associated data as layers.

morphapi

A lightweight python package to download neuronal morphologies

brainreg-napari

Automated 3D brain registration in napari with support for multiple species and atlases.

brainglobe-napari-io

Read and write files from the BrainGlobe neuroanatomy suite

brainglobe-registration

Registration to BrainGlobe atlases in napari using Elastix

bg-brainrender-gui

A GUI built on brainrender: visualise brain regions, neurons and labelled cells.

bg-atlasgen

Tools for packaging atlases for use with BrainGlobe

brainglobe-utils

Shared general purpose tools for the BrainGlobe project

brainrender_paper

Code for recreating the figures in the brainrender paper (Claudi et al. 2020)

probeplanner

Helps plan where to put things in brains

BrainGlobe

General information, resources and dicussions for the BrainGlobe project.

brainglobe-meta

(Meta-)package repository for BrainGlobe's Python tools for computational neuroanatomy.

brainglobe.github.io

brainglobe.info website

imio

Loading and saving of image data.

napari-brainreg

Visualise brainreg registration output

bgviewer

Visualisation and exploration of brain atlases

brainrender-docs

brainglobe-workflows

Workflows that utilise BrainGlobe tools to perform data analysis and visualisation.

brainglobe-template-builder

Build unbiased anatomical templates from individual images

napari-cellfinder

brainglobe-space

Anatomical space conventions made easy.

bg-gitbook

Mirror of the brainglobe GitBook page

napari-brainreg-standard

Visualise brainreg registration output in standard space

actions

Re-usable GitHub Action scripts

brainglobe-web

brainglobe.info website

brainglobe-stitch

A napari plugin for stitching large tiled 3D imaging datasets

.github

Common templates for BrainGlobe repositories.

course-dec-2023

Materials for the BrainGlobe & napari course at the Sainsbury Wellcome Centre

slides-roadmap-oct-2023

napari-experimental

micrometa

Parsing of whole-brain microscopy metadata