From 8aa01de647ccfbc489328b245c09f379e4615074 Mon Sep 17 00:00:00 2001 From: Gregory Jefferis Date: Thu, 14 May 2020 18:31:54 +0100 Subject: [PATCH] redown --- docs/404.html | 154 ++++++++++ docs/LICENSE.html | 43 ++- docs/SUPPORT.html | 43 ++- docs/authors.html | 42 ++- docs/bootstrap-toc.css | 60 ++++ docs/bootstrap-toc.js | 159 +++++++++++ docs/index.html | 43 +-- docs/news/index.html | 93 +++--- docs/pkgdown.css | 161 ++++++++++- docs/pkgdown.js | 15 +- docs/pkgdown.yml | 3 +- docs/reference/Dmel.html | 71 ++--- docs/reference/DsecI.html | 68 +++-- docs/reference/Dsim.html | 71 ++--- docs/reference/Dvir.html | 71 ++--- docs/reference/FCWB.html | 68 ++--- docs/reference/FCWBNP.surf.html | 65 +++-- docs/reference/IBN.html | 64 ++--- docs/reference/IBNWB.html | 64 ++--- docs/reference/IS2.html | 61 ++-- docs/reference/IS2.surf.html | 62 ++-- docs/reference/IS2NP.surf.html | 62 ++-- docs/reference/JFRC2.html | 68 ++--- docs/reference/JFRC2013.html | 80 +++--- docs/reference/JFRC2NP.surf.html | 87 +++--- docs/reference/JRC2018.html | 267 ++++++++++++++++++ docs/reference/JRCFIB2018F.html | 197 +++++++++++++ docs/reference/JRCVNC2018.html | 215 ++++++++++++++ docs/reference/T1.html | 65 +++-- docs/reference/VNCIS1.html | 68 ++--- .../download_jefferislab_registrations.html | 75 ++--- docs/reference/index.html | 104 +++++-- docs/reference/nat.flybrains-package.html | 86 +++--- 33 files changed, 2106 insertions(+), 749 deletions(-) create mode 100644 docs/404.html create mode 100644 docs/bootstrap-toc.css create mode 100644 docs/bootstrap-toc.js create mode 100644 docs/reference/JRC2018.html create mode 100644 docs/reference/JRCFIB2018F.html create mode 100644 docs/reference/JRCVNC2018.html diff --git a/docs/404.html b/docs/404.html new file mode 100644 index 0000000..e407750 --- /dev/null +++ b/docs/404.html @@ -0,0 +1,154 @@ + + + + + + + + +Page not found (404) • nat.flybrains + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + +
+ +
+
+
+

Page not found (404)

+
+ +Content not found. Please use links in the navbar. + +
+ + + +
+ + + +
+
+

Developed by Gregory Jefferis, James Manton.

+
+ +
+

Site built with pkgdown 1.5.1.

+
+ +
+
+ + + + + + + + diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 750e407..876dfc3 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -8,21 +8,29 @@ GNU General Public License • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -30,10 +38,12 @@ + + @@ -44,9 +54,10 @@ + - +
@@ -82,7 +93,6 @@ Help -
+
@@ -334,22 +345,32 @@

+ + + + + diff --git a/docs/SUPPORT.html b/docs/SUPPORT.html index 319c010..a3c3203 100644 --- a/docs/SUPPORT.html +++ b/docs/SUPPORT.html @@ -8,21 +8,29 @@ Getting help with nat.flybrains • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -30,10 +38,12 @@ + + @@ -44,9 +54,10 @@ + - +
@@ -82,7 +93,6 @@ Help -
+
@@ -157,22 +168,32 @@

+ + + + + diff --git a/docs/authors.html b/docs/authors.html index e7adb19..2f6896f 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -8,21 +8,29 @@ Citation and Authors • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -30,10 +38,12 @@ + + @@ -44,9 +54,10 @@ + - +
@@ -82,7 +93,6 @@ Help -
+
@@ -124,17 +135,18 @@

Citation

eprint = {https://www.biorxiv.org/content/early/2014/06/19/006353.full.pdf}, journal = {bioRxiv}, } +

Authors

@@ -144,19 +156,23 @@

Authors

+ + + diff --git a/docs/bootstrap-toc.css b/docs/bootstrap-toc.css new file mode 100644 index 0000000..5a85941 --- /dev/null +++ b/docs/bootstrap-toc.css @@ -0,0 +1,60 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ + +/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */ + +/* All levels of nav */ +nav[data-toggle='toc'] .nav > li > a { + display: block; + padding: 4px 20px; + font-size: 13px; + font-weight: 500; + color: #767676; +} +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 19px; + color: #563d7c; + text-decoration: none; + background-color: transparent; + border-left: 1px solid #563d7c; +} +nav[data-toggle='toc'] .nav > .active > a, +nav[data-toggle='toc'] .nav > .active:hover > a, +nav[data-toggle='toc'] .nav > .active:focus > a { + padding-left: 18px; + font-weight: bold; + color: #563d7c; + background-color: transparent; + border-left: 2px solid #563d7c; +} + +/* Nav: second level (shown on .active) */ +nav[data-toggle='toc'] .nav .nav { + display: none; /* Hide by default, but at >768px, show it */ + padding-bottom: 10px; +} +nav[data-toggle='toc'] .nav .nav > li > a { + padding-top: 1px; + padding-bottom: 1px; + padding-left: 30px; + font-size: 12px; + font-weight: normal; +} +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 29px; +} +nav[data-toggle='toc'] .nav .nav > .active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 28px; + font-weight: 500; +} + +/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */ +nav[data-toggle='toc'] .nav > .active > ul { + display: block; +} diff --git a/docs/bootstrap-toc.js b/docs/bootstrap-toc.js new file mode 100644 index 0000000..1cdd573 --- /dev/null +++ b/docs/bootstrap-toc.js @@ -0,0 +1,159 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ +(function() { + 'use strict'; + + window.Toc = { + helpers: { + // return all matching elements in the set, or their descendants + findOrFilter: function($el, selector) { + // http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/ + // http://stackoverflow.com/a/12731439/358804 + var $descendants = $el.find(selector); + return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])'); + }, + + generateUniqueIdBase: function(el) { + var text = $(el).text(); + var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-'); + return anchor || el.tagName.toLowerCase(); + }, + + generateUniqueId: function(el) { + var anchorBase = this.generateUniqueIdBase(el); + for (var i = 0; ; i++) { + var anchor = anchorBase; + if (i > 0) { + // add suffix + anchor += '-' + i; + } + // check if ID already exists + if (!document.getElementById(anchor)) { + return anchor; + } + } + }, + + generateAnchor: function(el) { + if (el.id) { + return el.id; + } else { + var anchor = this.generateUniqueId(el); + el.id = anchor; + return anchor; + } + }, + + createNavList: function() { + return $(''); + }, + + createChildNavList: function($parent) { + var $childList = this.createNavList(); + $parent.append($childList); + return $childList; + }, + + generateNavEl: function(anchor, text) { + var $a = $(''); + $a.attr('href', '#' + anchor); + $a.text(text); + var $li = $('
  • '); + $li.append($a); + return $li; + }, + + generateNavItem: function(headingEl) { + var anchor = this.generateAnchor(headingEl); + var $heading = $(headingEl); + var text = $heading.data('toc-text') || $heading.text(); + return this.generateNavEl(anchor, text); + }, + + // Find the first heading level (`

    `, then `

    `, etc.) that has more than one element. Defaults to 1 (for `

    `). + getTopLevel: function($scope) { + for (var i = 1; i <= 6; i++) { + var $headings = this.findOrFilter($scope, 'h' + i); + if ($headings.length > 1) { + return i; + } + } + + return 1; + }, + + // returns the elements for the top level, and the next below it + getHeadings: function($scope, topLevel) { + var topSelector = 'h' + topLevel; + + var secondaryLevel = topLevel + 1; + var secondarySelector = 'h' + secondaryLevel; + + return this.findOrFilter($scope, topSelector + ',' + secondarySelector); + }, + + getNavLevel: function(el) { + return parseInt(el.tagName.charAt(1), 10); + }, + + populateNav: function($topContext, topLevel, $headings) { + var $context = $topContext; + var $prevNav; + + var helpers = this; + $headings.each(function(i, el) { + var $newNav = helpers.generateNavItem(el); + var navLevel = helpers.getNavLevel(el); + + // determine the proper $context + if (navLevel === topLevel) { + // use top level + $context = $topContext; + } else if ($prevNav && $context === $topContext) { + // create a new level of the tree and switch to it + $context = helpers.createChildNavList($prevNav); + } // else use the current $context + + $context.append($newNav); + + $prevNav = $newNav; + }); + }, + + parseOps: function(arg) { + var opts; + if (arg.jquery) { + opts = { + $nav: arg + }; + } else { + opts = arg; + } + opts.$scope = opts.$scope || $(document.body); + return opts; + } + }, + + // accepts a jQuery object, or an options object + init: function(opts) { + opts = this.helpers.parseOps(opts); + + // ensure that the data attribute is in place for styling + opts.$nav.attr('data-toggle', 'toc'); + + var $topContext = this.helpers.createChildNavList(opts.$nav); + var topLevel = this.helpers.getTopLevel(opts.$scope); + var $headings = this.helpers.getHeadings(opts.$scope, topLevel); + this.helpers.populateNav($topContext, topLevel, $headings); + } + }; + + $(function() { + $('nav[data-toggle="toc"]').each(function(i, el) { + var $nav = $(el); + Toc.init($nav); + }); + }); +})(); diff --git a/docs/index.html b/docs/index.html index 37497be..1d5dd11 100644 --- a/docs/index.html +++ b/docs/index.html @@ -7,20 +7,21 @@ Additional data for use with the NeuroAnatomy Toolbox (nat) • nat.flybrains - - - + + + + + - - +
    @@ -117,24 +119,24 @@

    Installation

    This package is fully functional but there are presently no plans to release a version to CRAN, since there is a significant amount of data included with the package (and CRAN discourages large packages).

    You can, however, download the tar ball, and run R CMD INSTALL on it, or (highly recommended) use the devtools package to install straight from github:

    - +
    # install devtools package if you don't already have it
+if (!require("remotes")) install.packages("remotes")
+remotes::install_github("natverse/nat.flybrains")
+
+# to install additional/updated registrations 
+# (beyond those distributed as part of the R package)
+# Strongly recommended!
+nat.flybrains::download_jefferislab_registrations()

    Note: Windows users need Rtools and devtools to install this way.

    - + diff --git a/docs/news/index.html b/docs/news/index.html index a600500..50009d3 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -8,21 +8,29 @@ Changelog • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -30,10 +38,12 @@ + + @@ -44,9 +54,10 @@ + - +
    @@ -82,7 +93,6 @@ Help -
    +
    -

    Changelog

    +

    Changelog

    Source: NEWS.md
    +
    +

    +nat.flybrains 1.8.0

    +
      +
    • Add JRCFIB2018F Janleia electron microscopy hemibrain template brain; this will help link EM connectomics and light level anatomical data (#43)
      • +
    • Add JRC2018U intersex template brain and surface, from the Bogovic and Saalfeld average template brains. This intersex template brain from may become the new registration standard. (#41)
      • +
    • Add JRCVNC2018F female template nerve cord and surface, from the Bogovic and Saalfeld average template brains. Thanks to @istvantaisz. (#42)
      • +
    +
    -

    +

    nat.flybrains 1.7.4

    • new github organisation: natverse/nat.flybrains
    • other standard doc features for https://natverse.github.io packages
    • fix DOI link for Dsim brain
      • -
    • decription for JRC2018F brain
      • +
    • description for JRC2018F brain
    -

    +

    nat.flybrains 1.7.3

    • add citation
    -

    +

    nat.flybrains 1.7.2

    • Add JRC2018F female template brain and surface, the first of the Bogovic and Saalfeld average template brains. The intersex template brain from this series may become the new registration standard.
    -

    +

    nat.flybrains 1.7.1

    • Rename IVLP neuropil to WED in accordance with Ito et al 2014 (#37)
      • @@ -142,14 +162,14 @@

    -

    +

    nat.flybrains 1.7

    • add D. sechellia DsecI template and surface model (with Richard Benton)
    -

    +

    nat.flybrains 1.6

    • add information and surfaces for Drosophila melanogaster, virilis and simulans template brains
      • @@ -159,7 +179,7 @@

    -

    +

    nat.flybrains 1.5

    • added functions to support download/update of additional external registrations from github repositories (see ?add_reg_repo and ?update_reg_repos)
      • @@ -168,7 +188,7 @@

    -

    +

    nat.flybrains 1.4

    • package loading adds appropriate directories to the option nat.templatebrains.regdirs.
      • @@ -177,7 +197,7 @@

    -

    +

    nat.flybrains 1.3

    • add T1 mirroring registration
      • @@ -186,14 +206,14 @@

    -

    +

    nat.flybrains 1.2

    • templatebrain definitions and functions moved to nat.templatebrains package
    -

    +

    nat.flybrains 1.1

    • BrainTemplate class is now templatebrain
      • @@ -204,40 +224,31 @@

    - +

    Developed by Gregory Jefferis, James Manton.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.5.1.

    +
    + + diff --git a/docs/pkgdown.css b/docs/pkgdown.css index c03fb08..c01e592 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -17,12 +17,14 @@ html, body { height: 100%; } +body { + position: relative; +} + body > .container { display: flex; height: 100%; flex-direction: column; - - padding-top: 60px; } body > .container .row { @@ -69,6 +71,10 @@ summary { margin-top: calc(-60px + 1em); } +dd { + margin-left: 3em; +} + /* Section anchors ---------------------------------*/ a.anchor { @@ -102,37 +108,135 @@ a.anchor { margin-top: -40px; } -/* Static header placement on mobile devices */ -@media (max-width: 767px) { - .navbar-fixed-top { - position: absolute; - } - .navbar { - padding: 0; - } +/* Navbar submenu --------------------------*/ + +.dropdown-submenu { + position: relative; } +.dropdown-submenu>.dropdown-menu { + top: 0; + left: 100%; + margin-top: -6px; + margin-left: -1px; + border-radius: 0 6px 6px 6px; +} + +.dropdown-submenu:hover>.dropdown-menu { + display: block; +} + +.dropdown-submenu>a:after { + display: block; + content: " "; + float: right; + width: 0; + height: 0; + border-color: transparent; + border-style: solid; + border-width: 5px 0 5px 5px; + border-left-color: #cccccc; + margin-top: 5px; + margin-right: -10px; +} + +.dropdown-submenu:hover>a:after { + border-left-color: #ffffff; +} + +.dropdown-submenu.pull-left { + float: none; +} + +.dropdown-submenu.pull-left>.dropdown-menu { + left: -100%; + margin-left: 10px; + border-radius: 6px 0 6px 6px; +} /* Sidebar --------------------------*/ -#sidebar { +#pkgdown-sidebar { margin-top: 30px; + position: -webkit-sticky; + position: sticky; + top: 70px; } -#sidebar h2 { + +#pkgdown-sidebar h2 { font-size: 1.5em; margin-top: 1em; } -#sidebar h2:first-child { +#pkgdown-sidebar h2:first-child { margin-top: 0; } -#sidebar .list-unstyled li { +#pkgdown-sidebar .list-unstyled li { margin-bottom: 0.5em; } +/* bootstrap-toc tweaks ------------------------------------------------------*/ + +/* All levels of nav */ + +nav[data-toggle='toc'] .nav > li > a { + padding: 4px 20px 4px 6px; + font-size: 1.5rem; + font-weight: 400; + color: inherit; +} + +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 5px; + color: inherit; + border-left: 1px solid #878787; +} + +nav[data-toggle='toc'] .nav > .active > a, +nav[data-toggle='toc'] .nav > .active:hover > a, +nav[data-toggle='toc'] .nav > .active:focus > a { + padding-left: 5px; + font-size: 1.5rem; + font-weight: 400; + color: inherit; + border-left: 2px solid #878787; +} + +/* Nav: second level (shown on .active) */ + +nav[data-toggle='toc'] .nav .nav { + display: none; /* Hide by default, but at >768px, show it */ + padding-bottom: 10px; +} + +nav[data-toggle='toc'] .nav .nav > li > a { + padding-left: 16px; + font-size: 1.35rem; +} + +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 15px; +} + +nav[data-toggle='toc'] .nav .nav > .active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 15px; + font-weight: 500; + font-size: 1.35rem; +} + +/* orcid ------------------------------------------------------------------- */ + .orcid { - height: 16px; + font-size: 16px; + color: #A6CE39; + /* margins are required by official ORCID trademark and display guidelines */ + margin-left:4px; + margin-right:4px; vertical-align: middle; } @@ -222,6 +326,19 @@ a.sourceLine:hover { visibility: visible; } +/* headroom.js ------------------------ */ + +.headroom { + will-change: transform; + transition: transform 200ms linear; +} +.headroom--pinned { + transform: translateY(0%); +} +.headroom--unpinned { + transform: translateY(-100%); +} + /* mark.js ----------------------------*/ mark { @@ -234,3 +351,17 @@ mark { .html-widget { margin-bottom: 10px; } + +/* fontawesome ------------------------ */ + +.fab { + font-family: "Font Awesome 5 Brands" !important; +} + +/* don't display links in code chunks when printing */ +/* source: https://stackoverflow.com/a/10781533 */ +@media print { + code a:link:after, code a:visited:after { + content: ""; + } +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js index eb7e83d..7e7048f 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -2,18 +2,11 @@ (function($) { $(function() { - $("#sidebar") - .stick_in_parent({offset_top: 40}) - .on('sticky_kit:bottom', function(e) { - $(this).parent().css('position', 'static'); - }) - .on('sticky_kit:unbottom', function(e) { - $(this).parent().css('position', 'relative'); - }); + $('.navbar-fixed-top').headroom(); - $('body').scrollspy({ - target: '#sidebar', - offset: 60 + $('body').css('padding-top', $('.navbar').height() + 10); + $(window).resize(function(){ + $('body').css('padding-top', $('.navbar').height() + 10); }); $('[data-toggle="tooltip"]').tooltip(); diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 254fe91..f835abe 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,6 @@ pandoc: 2.3.1 -pkgdown: 1.3.0 +pkgdown: 1.5.1 pkgdown_sha: ~ articles: [] +last_built: 2020-05-14T17:31Z diff --git a/docs/reference/Dmel.html b/docs/reference/Dmel.html index dcf4910..063db55 100644 --- a/docs/reference/Dmel.html +++ b/docs/reference/Dmel.html @@ -8,21 +8,29 @@ Template information and surface model for D. melanogaster reference brain — Dmel • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -30,15 +38,15 @@ - + - + @@ -52,9 +60,10 @@ + - +
    @@ -90,7 +99,6 @@ Help -
    +
    @@ -119,60 +128,56 @@

    Template information and surface model for D. melanogaster reference brain
    -

    The Dmel reference brain is a shape averaged template brain generated using the CMTK avg_adm tool. See https://github.com/jefferislab/MakeAverageBrain for the relevant code.

    The surface model was constructed in Amira by L. Goetz and G. Jefferis using a simple threshold, followed by a surface simplification to ~ 18,000 faces.

    -
    - + +

    Details

    doi:10.5281/zenodo.10591

    -

    See also

    -

    Other Drosophilid-Brains: DsecI, - Dsim, Dvir

    - +

    Other Drosophilid-Brains: +DsecI, +Dsim, +Dvir

    Examples

    - 
    # NOT RUN {
+    
    if (FALSE) {
 # Depends on nat
 plot3d(Dmel.surf)
-# }
    
+}
    - +

    Developed by Gregory Jefferis, James Manton.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.5.1.

    +
    + + diff --git a/docs/reference/DsecI.html b/docs/reference/DsecI.html index 537f02d..507934c 100644 --- a/docs/reference/DsecI.html +++ b/docs/reference/DsecI.html @@ -8,21 +8,29 @@ Template information and surface model for D. sechellia reference brain — DsecI • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -30,8 +38,8 @@ - + - + @@ -54,9 +62,10 @@ + - +
    @@ -92,7 +101,6 @@ Help -
    +
    @@ -121,7 +130,6 @@

    Template information and surface model for D. sechellia reference brain

    -

    The DsecI reference brain is a shape averaged template brain generated using the CMTK avg_adm tool. See https://github.com/jefferislab/MakeAverageBrain for the relevant code.

    @@ -130,48 +138,48 @@

    Template information and surface model for D. sechellia reference brain

    (e^u) followed by a simple threshold (10000), surface simplification to ~ 18,000 faces, default surface smoothing and manual editing in meshlab to remove a small unconnected island of points.

    -
    - + +

    See also

    -

    Other Drosophilid-Brains: Dmel, - Dsim, Dvir

    - +

    Other Drosophilid-Brains: +Dmel, +Dsim, +Dvir

    Examples

    - 
    # NOT RUN {
+    
    if (FALSE) {
 # Depends on nat
 plot3d(DsecI.surf)
 plot3d(DsecI)
-# }
    
+}
    - + + + diff --git a/docs/reference/Dsim.html b/docs/reference/Dsim.html index 5681f08..acc2e30 100644 --- a/docs/reference/Dsim.html +++ b/docs/reference/Dsim.html @@ -8,21 +8,29 @@ Template information and surface model for D. simulans reference brain — Dsim • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -30,15 +38,15 @@ - + - + @@ -52,9 +60,10 @@ + - +
    @@ -90,7 +99,6 @@ Help -
    +
    @@ -119,60 +128,56 @@

    Template information and surface model for D. simulans reference brain

    -

    The Dsim reference brain is a shape averaged template brain generated using the CMTK avg_adm tool. See https://github.com/jefferislab/MakeAverageBrain for the relevant code.

    The surface model was constructed in Amira by L. Goetz and G. Jefferis using a simple threshold, followed by a surface simplification to ~ 18,000 faces.

    -
    - + +

    Details

    doi:10.5281/zenodo.10594

    -

    See also

    -

    Other Drosophilid-Brains: Dmel, - DsecI, Dvir

    - +

    Other Drosophilid-Brains: +Dmel, +DsecI, +Dvir

    Examples

    - 
    # NOT RUN {
+    
    if (FALSE) {
 # Depends on nat
 plot3d(Dsim.surf)
-# }
    
+}
    - + + + diff --git a/docs/reference/Dvir.html b/docs/reference/Dvir.html index 7b89d85..49d64d4 100644 --- a/docs/reference/Dvir.html +++ b/docs/reference/Dvir.html @@ -8,21 +8,29 @@ Template information and surface model for D. virilis reference brain — Dvir • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -30,15 +38,15 @@ - + - + @@ -52,9 +60,10 @@ + - +
    @@ -90,7 +99,6 @@ Help -
    +
    @@ -119,60 +128,56 @@

    Template information and surface model for D. virilis reference brain

    -

    The Dvir reference brain is a shape averaged template brain generated using the CMTK avg_adm tool. See https://github.com/jefferislab/MakeAverageBrain for the relevant code.

    The surface model was constructed in Amira by L. Goetz and G. Jefferis using a simple threshold, followed by a surface simplification to ~ 18,000 faces.

    -
    - + +

    Details

    doi:10.5281/zenodo.10593

    -

    See also

    -

    Other Drosophilid-Brains: Dmel, - DsecI, Dsim

    - +

    Other Drosophilid-Brains: +Dmel, +DsecI, +Dsim

    Examples

    - 
    # NOT RUN {
+    
    if (FALSE) {
 # Depends on nat
 plot3d(Dvir.surf)
-# }
    
+}
    - + + + diff --git a/docs/reference/FCWB.html b/docs/reference/FCWB.html index 404c94a..d3ebdd1 100644 --- a/docs/reference/FCWB.html +++ b/docs/reference/FCWB.html @@ -8,21 +8,29 @@ Template information and Surface model of the FCWB FlyCircuit reference brain — FCWB • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -30,14 +38,14 @@ - + - + @@ -51,9 +59,10 @@ + - +
    @@ -89,7 +98,6 @@ Help -
    +
    @@ -118,21 +127,19 @@

    Template information and Surface model of the FCWB FlyCircuit reference brai

    -

    The FCWB reference brain is a shape averaged template brain generated using the CMTK avg_adm tool. See https://github.com/jefferislab/MakeAverageBrain for the relevant code.

    The FCWB.surf surface model was generated in Amira by constructing an isosurface model based on the FCWB brain.

    - 
    FCWB
    - + +

    Format

    An object of class templatebrain of dimension 1769 x 1026 x 108.

    -

    References

    Ann-Shyn Chiang, Chih-Yung Lin, Chao-Chun Chuang, Hsiu-Ming Chang, @@ -144,11 +151,9 @@

    R Current Biology 21, 1-11. doi:10.1016/j.cub.2010.11.056

    FCWB is available for download at http://dx.doi.org/10.5281/zenodo.10568

    -

    See also

    FCWBNP.surf

    -

    Examples

    FCWB
    #> === Template Brain === 
@@ -165,40 +170,35 @@ 
    Examp
 #>   x = 0, y = 0, z = 0,
 #>   x = 563.9342, y = 326.3877, z = 107.
 #> Description: An intersex averaged brain formed from 17 female and 9 male brains from the FlyCircuit dataset. 
-#> DOI: 10.5281/zenodo.10568
    # NOT RUN {
+#> DOI: 10.5281/zenodo.10568
    if (FALSE) {
 # Depends on nat
 plot3d(FCWB.surf)
-# }
    +} - + + + diff --git a/docs/reference/FCWBNP.surf.html b/docs/reference/FCWBNP.surf.html index 532e1f2..bdfbb7e 100644 --- a/docs/reference/FCWBNP.surf.html +++ b/docs/reference/FCWBNP.surf.html @@ -9,21 +9,29 @@ Surface model of the Insect Brain Name Working Group neuropil segmentation in FCWB space — FCWBNP.surf • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -31,12 +39,12 @@ + - - + @@ -50,9 +58,10 @@ + - +
    @@ -88,7 +97,6 @@ Help -
    +
    @@ -118,13 +127,12 @@

    Surface model of the Insect Brain Name Working Group neuropil segmentation i

    -

    The JFRC2NP.surf model was mapped from JFRC2 to FCWB space using a bridging registration.

    -
    - + +

    References

    Kei Ito, Kazunori Shinomiya, Masayoshi Ito, J. Douglas Armstrong, @@ -134,45 +142,40 @@

    R Strauss, Leslie B. Vosshall, Insect Brain Name Working Group (2013). A systematic nomenclature for the insect brain. Neuron 81 (4), 755-765. doi:10.1016/j.neuron.2013.12.017

    -

    See also

    FCWB

    -

    Examples

    - 
    # NOT RUN {
+    
    if (FALSE) {
 # Depends on nat
 plot3d(FCWBNP.surf)
-# }
    
+}
    - + + + diff --git a/docs/reference/IBN.html b/docs/reference/IBN.html index b0d8f94..e9bba03 100644 --- a/docs/reference/IBN.html +++ b/docs/reference/IBN.html @@ -8,21 +8,29 @@ Template information for the Insect Brain Nomenclature reference brain — IBN • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -30,11 +38,11 @@ - + - + @@ -48,9 +56,10 @@ + - +
    @@ -86,7 +95,6 @@ Help -
    +
    @@ -115,18 +124,16 @@

    Template information for the Insect Brain Nomenclature reference brain

    -

    Template used for the study "A Systematic Nomenclature for the Insect Brain" (doi:10.1016/j.neuron.2013.12.017).

    - 
    IBN
    - + +

    Format

    An object of class templatebrain of dimension 512 x 512 x 135.

    -

    Details

    Constructed from the green channel of serial sections of a Drosophila @@ -148,7 +155,6 @@

    Details section, of 135 total, was recorded with a resolution of 1024 by 1024 pixels and 1.41 micron optical z-slice steps. These were then down-sampled to a resolution of 512 by 512 pixels.

    -

    References

    Kei Ito, Kazunori Shinomiya, Masayoshi Ito, J. Douglas Armstrong, @@ -158,7 +164,6 @@

    R Strauss, Leslie B. Vosshall, Insect Brain Name Working Group (2013). A systematic nomenclature for the insect brain. Neuron 81 (4), 755-765. doi:10.1016/j.neuron.2013.12.017

    -

    Examples

    IBN
    #> === Template Brain === 
@@ -187,35 +192,30 @@ 
    Examp
 #> The image was acquired using a confocal laser-scanning microscope LSM510 (Zeiss) with a 40x water-immersion C-Apochromat objective (NA = 1.2). Each section, of 135 total, was recorded with a resolution of 1024 by 1024 pixels and 1.41 micron optical z-slice steps. These were then down-sampled to a resolution of 512 by 512 pixels. 
 #> DOI:
    - + + + diff --git a/docs/reference/IBNWB.html b/docs/reference/IBNWB.html index 3702c00..270da69 100644 --- a/docs/reference/IBNWB.html +++ b/docs/reference/IBNWB.html @@ -9,21 +9,29 @@ Template information for the Insect Brain Nomenclature Whole Brain reference brain — IBNWB • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -31,16 +39,16 @@ + - - + @@ -54,9 +62,10 @@ + - +
    @@ -92,7 +101,6 @@ Help -
    +
    @@ -122,22 +131,20 @@

    Template information for the Insect Brain Nomenclature Whole Brain reference

    -

    A synthetic whole brain constructed from the Insect Brain Nomenclature template brain. The original confocal stack was duplicated, mirrored about a vertical axis and then displaced by 392 pixels in \(x\) and then merged with the original, with a linear blend in the overlapping region.

    The surface model was constructed in Amira in the Jefferis Lab using a simple median filter, followed by thresholding and a surface simplification.

    - 
    IBNWB
    - + +

    Format

    An object of class templatebrain of dimension 905 x 513 x 136.

    -

    References

    Kei Ito, Kazunori Shinomiya, Masayoshi Ito, J. Douglas Armstrong, @@ -154,11 +161,9 @@

    R Strauss, Leslie B. Vosshall, Insect Brain Name Working Group (2013). A systematic nomenclature for the insect brain. Neuron 81 (4), 755-765. doi:10.1016/j.neuron.2013.12.017

    -

    See also

    IBN

    -

    Examples

    IBNWB
    #> === Template Brain === 
@@ -177,35 +182,30 @@ 
    Examp
 #> Description: A synthetic whole brain constructed from the Insect Brain Nomenclature template brain. The original confocal stack was duplicated, mirrored about a vertical axis and then displaced by 392 pixels in x and then merged with the original, with a linear blend in the overlapping region. 
 #> DOI: 10.5281/zenodo.10569
    - + + + diff --git a/docs/reference/IS2.html b/docs/reference/IS2.html index b0d5bff..32c084c 100644 --- a/docs/reference/IS2.html +++ b/docs/reference/IS2.html @@ -8,21 +8,29 @@ Template information for the IS2 reference brain — IS2 • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -30,10 +38,10 @@ - + - + @@ -47,9 +55,10 @@ + - +
    @@ -85,7 +94,6 @@ Help -
    +
    @@ -114,24 +123,21 @@

    Template information for the IS2 reference brain

    -

    Template information for the IS2 reference brain

    - 
    IS2
    - + +

    Format

    An object of class templatebrain of dimension 768 x 768 x 173.

    -

    References

    Cachero S., Ostrovsky A.D., Yu J.Y., Dickson B.J., and Jefferis G.S.X.E. (2010). Sexual dimorphism in the fly brain. Curr Biol 20 (18), 1589-601. doi:10.1016/j.cub.2010.07.045

    -

    Examples

    IS2
    #> === Template Brain === 
@@ -150,33 +156,30 @@ 
    Examp
 #> Description: IS2 template brain. 
 #> DOI: 10.5281/zenodo.10595
    - + + + diff --git a/docs/reference/IS2.surf.html b/docs/reference/IS2.surf.html index c5e984b..6300e78 100644 --- a/docs/reference/IS2.surf.html +++ b/docs/reference/IS2.surf.html @@ -8,21 +8,29 @@ Surface model of the IS2 reference brain — IS2.surf • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -30,10 +38,10 @@ - + - + @@ -47,9 +55,10 @@ + - +
    @@ -85,7 +94,6 @@ Help -
    +
    @@ -114,51 +123,48 @@

    Surface model of the IS2 reference brain

    -

    Surface model of the IS2 reference brain

    -
    - + +

    References

    Cachero S., Ostrovsky A.D., Yu J.Y., Dickson B.J., and Jefferis G.S.X.E. (2010). Sexual dimorphism in the fly brain. Curr Biol 20 (18), 1589-601. doi:10.1016/j.cub.2010.07.045

    -

    Examples

    - 
    # NOT RUN {
+    
    if (FALSE) {
 # Depends on nat
 plot3d(IS2.surf)
-# }
    
+}
    - + + + diff --git a/docs/reference/IS2NP.surf.html b/docs/reference/IS2NP.surf.html index 78a4835..b5c4ebb 100644 --- a/docs/reference/IS2NP.surf.html +++ b/docs/reference/IS2NP.surf.html @@ -9,21 +9,29 @@ Surface model of the Insect Brain Name Working Group neuropil segmentation in IS2 coordinate space — IS2NP.surf • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -31,12 +39,12 @@ + - - + @@ -50,9 +58,10 @@ + - +
    @@ -88,7 +97,6 @@ Help -
    +
    @@ -118,13 +127,12 @@

    Surface model of the Insect Brain Name Working Group neuropil segmentation i

    -

    Surface model of the Insect Brain Name Working Group neuropil segmentation in IS2 coordinate space

    -
    - + +

    References

    Kei Ito, Kazunori Shinomiya, Masayoshi Ito, J. Douglas Armstrong, @@ -134,39 +142,37 @@

    R Strauss, Leslie B. Vosshall, Insect Brain Name Working Group (2013). A systematic nomenclature for the insect brain. Neuron 81 (4), 755-765. doi:10.1016/j.neuron.2013.12.017

    -

    Examples

    - 
    # NOT RUN {
+    
    if (FALSE) {
 # Depends on nat
 plot3d(IS2NP.surf)
-# }
    
+}
    - + + + diff --git a/docs/reference/JFRC2.html b/docs/reference/JFRC2.html index 59abc5e..75488f0 100644 --- a/docs/reference/JFRC2.html +++ b/docs/reference/JFRC2.html @@ -8,21 +8,29 @@ Template information and surface model for the JFRC2 reference brain — JFRC2 • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -30,8 +38,8 @@ - + - + @@ -54,9 +62,10 @@ + - +
    @@ -92,7 +101,6 @@ Help -
    +
    @@ -121,7 +130,6 @@

    Template information and surface model for the JFRC2 reference brain

    -

    The JFRC2 reference brain is a spatially calibrated version of the original FlyLight reference brain (JFRC), which was delivered uncalibrated. This in turn was derived from a single female brain stained with nc82, that was @@ -130,15 +138,14 @@

    Template information and surface model for the JFRC2 reference brain

    The JFRC2.surf surface model was constructed in Amira in the Jefferis Lab using a simple threshold, followed by a surface simplification.

    - 
    JFRC2
    - + +

    Format

    An object of class templatebrain of dimension 1024 x 512 x 218.

    -

    References

    Arnim Jenett, Gerald M. Rubin, Teri-T.B. Ngo, David Shepherd, Christine Murphy, Heather Dionne, Barret D. Pfeiffer, @@ -148,11 +155,9 @@

    R Konrad Rokicki, Todd Safford, Kshiti Shaw, Julie H. Simpson, Allison Sowell, Susana Tae, Yang Yu, Christopher T. Zugates (2012). A GAL4-Driver Line Resource for Drosophila Neurobiology. Cell Reports 2 (4), 991 - 1001. doi:10.1016/j.celrep.2012.09.011

    -

    See also

    JFRC2NP.surf

    -

    Examples

    JFRC2
    #> === Template Brain === 
@@ -169,40 +174,35 @@ 
    Examp
 #>   x = 0, y = 0, z = 0,
 #>   x = 636.396, y = 317.887, z = 134.9931.
 #> Description: The JFRC2 reference brain is a refractive-index-corrected version of the original FlyLight reference brain (JFRC). 
-#> DOI: 10.5281/zenodo.10567
    # NOT RUN {
+#> DOI: 10.5281/zenodo.10567
    if (FALSE) {
 # Depends on nat
 plot3d(JFRC2.surf)
-# }
    +} - + + + diff --git a/docs/reference/JFRC2013.html b/docs/reference/JFRC2013.html index a3ea678..54e1860 100644 --- a/docs/reference/JFRC2013.html +++ b/docs/reference/JFRC2013.html @@ -8,21 +8,29 @@ Template information and surface model for the JFRC2013 reference brain — JFRC2013 • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -30,8 +38,8 @@ - + - + @@ -59,9 +67,10 @@ + - +
    @@ -97,7 +106,6 @@ Help -
    +
    @@ -126,7 +135,6 @@

    Template information and surface model for the JFRC2013 reference brain

    -

    The JFRC2013 reference brain is a single female brain. It is a spatially calibrated version of the brain used in Aso et al. 2014, "The neuronal architecture of the mushroom body provides a logic for @@ -140,17 +148,17 @@

    Template information and surface model for the JFRC2013 reference brain

    microscope with 20 x magnification. The downsampling has shrunk the z direction, such that the brain appears flattened when compared with the original.

    - 
    JFRC2013
 
 JFRC2013DS
    - + +

    Format

    An object of class templatebrain of dimension 1450 x 725 x 436.

    - +

    An object of class templatebrain of dimension 1184 x 592 x 218.

    Calibration

    The isotropic calibration of 0.38 microns is based on a @@ -159,7 +167,6 @@

    No attempt was made to correct for this shrinkage artefact.

    -

    References

    Aso, Y., Sitaraman, D., Ichinose, T., Kaun, K. R., Vogt, K., @@ -169,10 +176,9 @@

    R Rubin, G. M. (2014b). Mushroom body output neurons encode valence and guide memory-based action selection in Drosophila. Elife 3, e04580. doi:10.7554/eLife.04577

    -

    Examples

    - 
    dim(JFRC2013)
    #> [1] 1450  725  436
    voxdims(JFRC2013)
    #> [1] 0.38 0.38 0.38
    boundingbox(JFRC2013)
    #>        [,1]   [,2]  [,3]
+    
    dim(JFRC2013)
    #> [1] 1450  725  436
    voxdims(JFRC2013)
    #> [1] 0.38 0.38 0.38
    boundingbox(JFRC2013)
    #>        [,1]   [,2]  [,3]
 #> [1,]   0.00   0.00   0.0
 #> [2,] 550.62 275.12 165.3
 #> attr(,"class")
@@ -191,12 +197,13 @@ 
    Examp
 #>   x = 550.62, y = 275.12, z = 165.3.
 #> Description: The JFRC2013 reference brain is a spatially calibrated version of the brain used in Aso et al. 2014, "The neuronal architecture of the mushroom body provides a logic for associative learning". 
 #> DOI: 10.7554/eLife.04577
    
-
    # NOT RUN {
-library(nat)
-plot3d(JFRC2013)
-plot3d(JFRC2013.surf)
-plot3d(JFRC2013.surf, col='red', alpha=0.3)
-# }
    dim(JFRC2013DS)
    #> [1] 1184  592  218
    voxdims(JFRC2013DS)
    #> [1] 0.46 0.46 0.46
    boundingbox(JFRC2013DS)
    #>        [,1]   [,2]  [,3]
+if (FALSE) {
+library(nat)
+plot3d(JFRC2013)
+plot3d(JFRC2013.surf)
+plot3d(JFRC2013.surf, col='red', alpha=0.3)
+}
+dim(JFRC2013DS)
    #> [1] 1184  592  218
    voxdims(JFRC2013DS)
    #> [1] 0.46 0.46 0.46
    boundingbox(JFRC2013DS)
    #>        [,1]   [,2]  [,3]
 #> [1,]   0.00   0.00  0.00
 #> [2,] 544.18 271.86 99.82
 #> attr(,"class")
@@ -216,35 +223,30 @@ 
    Examp
 #> Description: This is a downsampled version of the JFRC2013 reference brain, designed for use with images taken on a microscope with 20 x magnification. The downsampling has shrunk the z direction, such that the brain appears flattened when compared with the original. 
 #> DOI: 10.7554/eLife.04577
    
   
    
-  
 
+
       
    
       
    
   
    Developed by Gregory Jefferis, James Manton.
    
 
    
 
 
    
-  
    Site built with pkgdown 1.3.0.
    
+  
    Site built with pkgdown 1.5.1.
    
 
    
+
       
    
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/JFRC2NP.surf.html b/docs/reference/JFRC2NP.surf.html
index c2a354b..d237355 100644
--- a/docs/reference/JFRC2NP.surf.html
+++ b/docs/reference/JFRC2NP.surf.html
@@ -9,21 +9,29 @@
 Surface model of the Insect Brain Name Working Group neuropil segmentation in
 JFRC2 coordinate space — JFRC2NP.surf • nat.flybrains
 
+
 
-
+
 
 
-
-
+
+
+
+
+
+
+
 
 
-
+
+
 
 
-
+
 
-
-
+
+
+
 
 
 
@@ -31,12 +39,12 @@
 
 
 
+
 
-
 
-
+
 
 
 
@@ -50,9 +58,10 @@
 
 
 
+
   
 
-  
+  
     
    
       
    
       
 
@@ -88,7 +97,6 @@
   Help
 
       
-      
       
    
 
       
+
       
 
 
    
@@ -118,20 +127,20 @@ 
    Surface model of the Insect Brain Name Working Group neuropil segmentation i
     
    
 
     
    
-    
     
    Surface model of the Insect Brain Name Working Group neuropil segmentation in
 JFRC2 coordinate space
    
-    
     
    
 
-        
+
+
     
    Details
    
 
     
    Note that the supplementary information for the Insect Brain Name
   working group only includes neuropil information in the IBN
   space, which can be downloaded from
   ftp://flybase.org/flybase/associated_files/InsectBrainNomenclature_RawData.zip.
    
-    
    However Arnim Jenett, Kazunori Shinomiya and Kei Ito generated a full brain
+
+
    However Arnim Jenett, Kazunori Shinomiya and Kei Ito generated a full brain
   segmentation based on the JFRC2 template (used by the Virtual
   Fly Brain project and internally at Janelia Farm for several years.)
    
 
    This surface model was generated in Amira from the segmentation in the file
@@ -140,7 +149,6 @@ 
    Details
   repository https://github.com/VirtualFlyBrain/DrosAdultBRAINdomains.
   The original full size model was then simplified to reduce the number of
   vertices resulting
    
-    
     
    References
    
 
     
    Kei Ito, Kazunori Shinomiya, Masayoshi Ito, J. Douglas Armstrong,
@@ -150,11 +158,9 @@ 
    R
   Strauss, Leslie B. Vosshall, Insect Brain Name Working Group (2013). A
   systematic nomenclature for the insect brain. Neuron 81 (4), 755-765.
   doi:10.1016/j.neuron.2013.12.017
    
-    
     
    See also
    
 
     
    JFRC2
    
-    
 
     
    Examples
    
     
    # list the materials for the different surface regions
@@ -234,64 +240,59 @@ 
    Examp
 #> SCL_L       SCL_L 73 #C926CC
 #> EPA_L       EPA_L 74 #28CC3E
 #> GA_L         GA_L 75 #141666
    
-
    # NOT RUN {
+if (FALSE) {
 # plot the surface
 plot3d(JFRC2NP.surf)
 
 # calculate volumes ond surface areas for all regions
-if(require("RvtkStatismo") && require("tidyr") && require("ggplot2") && require("stringr")){
+if(require("RvtkStatismo") && require("tidyr") && require("ggplot2") && require("stringr")){
   # convert each region to a mesh3d object, note that we use simplify=FALSE
   # to stop sapply mangling the result
-  meshes=sapply(JFRC2NP.surf$RegionList,
-    function(r) as.mesh3d(subset(JFRC2NP.surf, r)), simplify=FALSE)
+  meshes=sapply(JFRC2NP.surf$RegionList,
+    function(r) as.mesh3d(subset(JFRC2NP.surf, r)), simplify=FALSE)
 
   # now calculate information for each mesh
   # NB vtkMeshInfo returns a list so we need to convert to a vector
   # to end up with a nice matrix output
-  vs=sapply(meshes, function(x) unlist(vtkMeshInfo(x)))
+  vs=sapply(meshes, function(x) unlist(vtkMeshInfo(x)))
 
   # now make that into a tidy data.frame and plot
-  df=data.frame(key=colnames(vs), t(vs),
-                region=sub("_[LR]", "", colnames(vs)),
-                side=str_match(colnames(vs), "_([LR])")[,2])
+  df=data.frame(key=colnames(vs), t(vs),
+                region=sub("_[LR]", "", colnames(vs)),
+                side=str_match(colnames(vs), "_([LR])")[,2])
 
   df2=gather(df, measure, value, volume:surfaceArea)
-  library(ggplot2)
+  library(ggplot2)
   qplot( value, region, data=df2, col=side, facets = . ~ measure) + scale_x_log10()
 
 }
 
-# }
    
+}
    - + + + diff --git a/docs/reference/JRC2018.html b/docs/reference/JRC2018.html new file mode 100644 index 0000000..767611b --- /dev/null +++ b/docs/reference/JRC2018.html @@ -0,0 +1,267 @@ + + + + + + + + +Template information and surface models for the JRC2018 reference brains — JRC2018F • nat.flybrains + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Template information and surface models for the JRC2018 reference brains

    + Source: R/JRC2018.R + +
    + +
    +

    The JRC2018F reference brain is an average template + brain constructed from brains labelled with brp-SNAP, dehydrated, and + mounted in DPX and imaged at 0.19 x 0.19 x 0.38 microns. The image was + downsampled in XY to result in a 0.38 micron isotropic voxel size, which we + take to be the standard JRC2018F space.

    +

    The JRC2018U reference brain was constructed as for + JRC2018F brain but pooling both male and female brains.

    +

    JRC2018F.surf, JRC2018U.surf were generated in + Amira from a 2 micron downsampled, Lanczos filtered 8 bit version of the + respective template brain. A surface was then generated with a threshold + level of 20 in case of brains this was then smoothed and downsampled. See + data-raw/JFRC2018_FEMALE_surface.hx, + data-raw/JRC2018_UNISEX_surface.hx for details.

    +
    + + 
    JRC2018F
+
+JRC2018U
+
+JRC2018F.surf
+
+JRC2018U.surf
    + + +

    Format

    + +

    An object of class templatebrain of dimension 1652 x 768 x 479.

    +

    An object of class templatebrain of dimension 1652 x 773 x 456.

    +

    An object of class hxsurf (inherits from list) of length 4.

    +

    An object of class hxsurf (inherits from list) of length 4.

    +

    Details

    + +

    For the central brain, Bogovic and Saalfeld used 36 female + individuals (72 images including left-right flips) for the female template, + 26 male individuals (52 image with left-right flips) for the male template, + and the union of both for the unisex brain template: 62 individuals (124 + images with left-right flips).

    +

    Downloaded from + https://www.janelia.org/open-science/jrc-2018-brain-templates

    +

    References

    + +

    An unbiased template of the Drosophila brain and ventral nerve + cord John A Bogovic, Hideo Otsuna, Larissa Heinrich, Masayoshi Ito, + Jennifer Jeter, Geoffrey W Meissner, Aljoscha Nern, Jennifer Colonell, Oz + Malkesman, Kei Ito, Stephan Saalfeld bioRxiv 376384; doi: + doi:10.1101/376384

    +

    See also

    + +

    JRCVNC2018

    + +

    Examples

    + 
    dim(JRC2018F)
    #> [1] 1652  768  479
    voxdims(JRC2018F)
    #> [1] 0.38 0.38 0.38
    boundingbox(JRC2018F)
    #>        [,1]   [,2]   [,3]
+#> [1,]   0.00   0.00   0.00
+#> [2,] 627.38 291.46 181.64
+#> attr(,"class")
+#> [1] "boundingbox"
    JRC2018F
    #> === Template Brain === 
+#> Name: JRC2018F 
+#> Short Name: JRC2018F 
+#> Type: Average template brain 
+#> Sex:  F 
+#> Dimensions:1652 x 768 x 479 voxels
+#> Voxel size:
+#>   x = 0.38 microns
+#>   y = 0.38 microns
+#>   z = 0.38 microns
+#> Bounding box (microns):
+#>   x = 0, y = 0, z = 0,
+#>   x = 627.38, y = 291.46, z = 181.64.
+#> Description: Average template brain constructed from brains labelled with brp-SNAP presynaptic marker,
+#>     dehydrated, and mounted in DPX and then imaged by confocal microscope. 
+#> DOI: https://doi.org/10.1101/376384
    
+if (FALSE) {
+library(nat)
+plot3d(JRC2018F)
+plot3d(JRC2018F.surf)
+plot3d(JRC2018F.surf, col='red', alpha=0.3)
+}
+dim(JRC2018U)
    #> [1] 1652  773  456
    voxdims(JRC2018U)
    #> [1] 0.38 0.38 0.38
    boundingbox(JRC2018U)
    #>        [,1]   [,2]  [,3]
+#> [1,]   0.00   0.00   0.0
+#> [2,] 627.38 293.36 172.9
+#> attr(,"class")
+#> [1] "boundingbox"
    JRC2018U
    #> === Template Brain === 
+#> Name: JRC2018U 
+#> Short Name: JRC2018U 
+#> Type: Average template brain 
+#> Sex:  Intersex 
+#> Dimensions:1652 x 773 x 456 voxels
+#> Voxel size:
+#>   x = 0.38 microns
+#>   y = 0.38 microns
+#>   z = 0.38 microns
+#> Bounding box (microns):
+#>   x = 0, y = 0, z = 0,
+#>   x = 627.38, y = 293.36, z = 172.9.
+#> Description: Average template brain constructed from brains labelled with brp-SNAP presynaptic marker,dehydrated, and mounted in DPX and then imaged by confocal microscope. There were 36 female individuals (72 images including left-right flips) and 26 male individuals (52 image with left-right flips) for a total of 62 individuals (124 images with left-right flips). 
+#> DOI: https://doi.org/10.1101/376384
    
+if (FALSE) {
+library(nat)
+plot3d(JRC2018U)
+plot3d(JRC2018U.surf)
+plot3d(JRC2018U.surf, col='red', alpha=0.3)
+}
    +
    + +
    + + +
    +
    +

    Developed by Gregory Jefferis, James Manton.

    +
    + +
    +

    Site built with pkgdown 1.5.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/JRCFIB2018F.html b/docs/reference/JRCFIB2018F.html new file mode 100644 index 0000000..d9c36fe --- /dev/null +++ b/docs/reference/JRCFIB2018F.html @@ -0,0 +1,197 @@ + + + + + + + + +Template information for the JRCFIB2018F aka hemibrain dataset — JRCFIB2018F • nat.flybrains + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Template information for the JRCFIB2018F aka hemibrain dataset

    + Source: R/JRCFIB2018F.R + +
    + +
    +

    The JRCFIB2018F reference brain is a stitched FIB SEM + volume completed at HHMI Janelia Research Campus in 2018.

    +

    The JRCFIB2018Fraw reference brain is uncalibrated (i.e. has units + of raw pixels), whereas JRCFIB2018F has units of microns and voxel + dimensions of 8x8x8 * 1E-3 microns (i.e. 8 nm isotropic voxels).

    +
    + + + +

    References

    + +

    A Connectome of the Adult Drosophila Central Brain Shan + Xu, C; Januszewski, Michal; Lu, Zhiyuan; Takemura, Shin-Ya; Hayworth, + Kenneth; Huang, Gary; Shinomiya, Kazunori; Maitin-Shepard, Jeremy; + Ackerman, David; Berg, Stuart; Blakely, Tim; Bogovic, John; Clements, Jody; + Dolafi, Tom; Hubbard, Philip; Kainmueller, Dagmar; Katz, William; Kawase, + Takashi; Khairy, Khaled; Leavitt, Laramie; Li, Peter H; Lindsey, Larry; + Neubarth, Nicole; Olbris, Donald J; Otsuna, Hideo; Troutman, Eric T; + Umayam, Lowell; Zhao, Ting; Ito, Masayoshi; Goldammer, Jens; Wolff, Tanya; + Svirskas, Robert; Schlegel, Philipp; Neace, Erika R; Knecht, Christopher J; + Alvarado, Chelsea X; Bailey, Dennis; Ballinger, Samantha; Borycz, Jolanta + A; Canino, Brandon; Cheatham, Natasha; Cook, Michael; Dreyer, Marisa; + Duclos, Octave; Eubanks, Bryon; Fairbanks, Kelli; Finley, Samantha; + Forknall, Nora; Francis, Audrey; Hopkins, Gary Patrick; Joyce, Emily M; + Kim, Sungjin; Kirk, Nicole A; Kovalyak, Julie; Lauchie, Shirley A; Lohff, + Alanna; Maldonado, Charli; Manley, Emily A; McLin, Sari; Mooney, Caroline; + Ndama, Miatta; Ogundeyi, Omotara; Okeoma, Nneoma; Ordish, Christopher; + Padilla, Nicholas; Patrick, Christopher; Paterson, Tyler; Phillips, Elliott + E; Phillips, Emily M; Rampally, Neha; Ribeiro, Caitlin; Robertson, + Madelaine K; Rymer, Jon Thomson; Ryan, Sean M; Sammons, Megan; Scott, Anne + K; Scott, Ashley L; Shinomiya, Aya; Smith, Claire; Smith, Kelsey; Smith, + Natalie L; Sobeski, Margaret A; Suleiman, Alia; Swift, Jackie; Takemura, + Satoko; Talebi, Iris; Tarnogorska, Dorota; Tenshaw, Emily; Tokhi, Temour; + Walsh, John J; Yang, Tansy; Horne, Jane Anne; Li, Feng; Parekh, Ruchi; + Rivlin, Patricia K; Jayaraman, Vivek; Ito, Kei; Saalfeld, Stephan; George, + Reed; Meinertzhagen, Ian; Rubin, Gerald M; Hess, Harald F; Scheffer, Louis + K; Jain, Viren; Plaza, Stephen M + bioRxiv + doi:10.1101/2020.01.21.911859.

    + +
    + +
    + + +
    +
    +

    Developed by Gregory Jefferis, James Manton.

    +
    + +
    +

    Site built with pkgdown 1.5.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/JRCVNC2018.html b/docs/reference/JRCVNC2018.html new file mode 100644 index 0000000..0c7a394 --- /dev/null +++ b/docs/reference/JRCVNC2018.html @@ -0,0 +1,215 @@ + + + + + + + + +Template information and surface models for JRC2018 VNC templates — JRCVNC2018 • nat.flybrains + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Template information and surface models for JRC2018 VNC templates

    + Source: R/JRC2018.R + +
    + +
    +

    The JRCVNC2018F reference VNC was constructed as for + JRC2018F brain based on 36 individuals, with a resolution of + 0.4 x 0.4 x 0.4 microns.

    +

    JRCVNC2018F.surf, was generated in + Amira from a 2 micron downsampled, Lanczos filtered version of the + respective template brain. A surface was then generated with a threshold + level of 2800 and then smoothed and downsampled.

    +
    + + 
    JRCVNC2018F
+
+JRCVNC2018F.surf
    + + +

    Format

    + +

    An object of class templatebrain of dimension 660 x 1342 x 358.

    +

    An object of class hxsurf (inherits from list) of length 4.

    +

    References

    + +

    An unbiased template of the Drosophila brain and ventral nerve + cord John A Bogovic, Hideo Otsuna, Larissa Heinrich, Masayoshi Ito, + Jennifer Jeter, Geoffrey W Meissner, Aljoscha Nern, Jennifer Colonell, Oz + Malkesman, Kei Ito, Stephan Saalfeld bioRxiv 376384; doi: + doi:10.1101/376384

    +

    See also

    + +

    JRCVNC2018F

    + +

    Examples

    + 
    JRCVNC2018F
    #> === Template Brain === 
+#> Name: JRCVNC2018F 
+#> Short Name: JRCVNC2018F 
+#> Type: Average template VNC 
+#> Sex:  F 
+#> Dimensions:660 x 1342 x 358 voxels
+#> Voxel size:
+#>   x = 0.4 microns
+#>   y = 0.4 microns
+#>   z = 0.4 microns
+#> Bounding box (microns):
+#>   x = 0, y = 0, z = 0,
+#>   x = 263.6, y = 536.4, z = 142.8.
+#> Description: Average template VNC constructed from VNC labelled with brp-SNAP presynaptic marker,
+#>     dehydrated, and mounted in DPX and then imaged by confocal microscope. 
+#> DOI: https://doi.org/10.1101/376384
    dim(JRCVNC2018F)
    #> [1]  660 1342  358
    voxdims(JRCVNC2018F)
    #> [1] 0.4 0.4 0.4
    boundingbox(JRCVNC2018F)
    #>       [,1]  [,2]  [,3]
+#> [1,]   0.0   0.0   0.0
+#> [2,] 263.6 536.4 142.8
+#> attr(,"class")
+#> [1] "boundingbox"
    
+if (FALSE) {
+library(nat)
+plot3d(JRCVNC2018F)
+plot3d(JRCVNC2018F.surf)
+plot3d(JRCVNC2018F.surf, col='red', alpha=0.3)
+}
    +
    + +
    + + +
    +
    +

    Developed by Gregory Jefferis, James Manton.

    +
    + +
    +

    Site built with pkgdown 1.5.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/T1.html b/docs/reference/T1.html index b5dcb7e..9c39c0b 100644 --- a/docs/reference/T1.html +++ b/docs/reference/T1.html @@ -8,21 +8,29 @@ Template information and surface model for the T1 reference brain — T1 • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -30,12 +38,12 @@ - + - + @@ -49,9 +57,10 @@ + - +
    @@ -87,7 +96,6 @@ Help -
    +
    @@ -116,19 +125,17 @@

    Template information and surface model for the T1 reference brain

    -

    Template information and surface model for the T1 reference brain

    The surface model was constructed in Amira in the Jefferis Lab using a simple threshold, followed by a surface simplification.

    - 
    T1
    - + +

    Format

    An object of class templatebrain of dimension 768 x 768 x 165.

    -

    References

    Jai Y. Yu, Makoto I. Kanai, Ebru Demir, Gregory S. X. E. Jefferis, Barry J. Dickson (2010). @@ -137,7 +144,6 @@

    R

    Jai Y. Yu, Makoto I. Kanai, Ebru Demir, Gregory S. X. E. Jefferis, Barry J. Dickson (2010). Cellular Organization of the Neural Circuit that Drives Drosophila Courtship Behavior. Current Biology 20 (18), 1602-1614. doi:10.1016/j.cub.2010.08.025

    -

    Examples

    T1
    #> === Template Brain === 
@@ -154,38 +160,35 @@ 
    Examp
 #>   x = 0, y = 0, z = 0,
 #>   x = 420.9968, y = 420.9968, z = 164.
 #> Description: BrainBase 
-#> DOI: 10.5281/zenodo.10590
    # NOT RUN {
+#> DOI: 10.5281/zenodo.10590
    if (FALSE) {
 # Depends on nat
 plot3d(T1.surf)
-# }
    +} - + + + diff --git a/docs/reference/VNCIS1.html b/docs/reference/VNCIS1.html index 52f11b2..b8e4ce7 100644 --- a/docs/reference/VNCIS1.html +++ b/docs/reference/VNCIS1.html @@ -8,21 +8,29 @@ Template information and surface model for the VNCIS1 reference neuropil — VNCIS1 • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -30,12 +38,12 @@ - + - + @@ -49,9 +57,10 @@ + - +
    @@ -87,7 +96,6 @@ Help -
    +
    @@ -116,26 +125,23 @@

    Template information and surface model for the VNCIS1 reference neuropil

    -

    The VNCIS1 template is a shape-averaged, intersex template containing the D. melanogaster adult ventral nerve cord (more properly the thoracico-abdominal ganglion) generated using the CMTK avg_adm tool.

    - 
    VNCIS1
    - + +

    Format

    An object of class templatebrain of dimension 1024 x 768 x 163.

    -

    References

    Cachero S., Ostrovsky A.D., Yu J.Y., Dickson B.J., and Jefferis G.S.X.E. (2010). Sexual dimorphism in the fly brain. Curr Biol 20 (18), 1589-601. doi:10.1016/j.cub.2010.07.045

    -

    Examples

    VNCIS1
    #> === Template Brain === 
@@ -153,44 +159,42 @@ 
    Examp
 #>   x = 439.9851, y = 329.8813, z = 171.6938.
 #> Description: See http://dx.doi.org/10.1016/j.cub.2010.07.045 for details 
 #> DOI: 10.5281/zenodo.13884
    
-# originally calculated thus:
-
    # NOT RUN {
+# originally calculated thus:
+if (FALSE) {
 as.templatebrain(
   "/GD/projects/CommonNeuroanatomy/VNCIS1/VNCIS1.nrrd",
   type="Average", sex='Intersex',
   doi="http://doi.org/10.5281/zenodo.13884",
   description = "See http://dx.doi.org/10.1016/j.cub.2010.07.045 for details")
-# }
    plot3d(VNCIS1.surf)
+}
+plot3d(VNCIS1.surf)
 # slightly different display
 plot3d(VNCIS1)
    - + + + diff --git a/docs/reference/download_jefferislab_registrations.html b/docs/reference/download_jefferislab_registrations.html index 9089efd..8c0e252 100644 --- a/docs/reference/download_jefferislab_registrations.html +++ b/docs/reference/download_jefferislab_registrations.html @@ -8,21 +8,29 @@ Download (or update) and install Jefferis lab registrations — download_jefferislab_registrations • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -30,12 +38,12 @@ - + - + @@ -49,9 +57,10 @@ + - +
    @@ -87,7 +96,6 @@ Help -
    +
    @@ -116,16 +125,16 @@

    Download (or update) and install Jefferis lab registrations

    - -

    Uses nat.templatebrains::download_reg_repo to download git +

    Uses nat.templatebrains::download_reg_repo to download git repositories containing bridging and mirroring registrations for Drosophila melanogaster, simulans and virilis template brains.

    -
    - 
    download_jefferislab_registrations(repos = c("BridgingRegistrations",
-  "MirrorRegistrations", "DrosophilidBridgingRegistrations"))
    - + 
    download_jefferislab_registrations(
+  repos = c("BridgingRegistrations", "MirrorRegistrations",
+    "DrosophilidBridgingRegistrations")
+)
    +

    Arguments

    @@ -135,7 +144,7 @@

    Arg from.

    - +

    References

    For a full description and sample applications of these registrations, @@ -144,52 +153,46 @@

    R James D. Manton, Aaron D. Ostrovsky, Lea Goetz, Marta Costa, Torsten Rohlfing, Gregory S. X. E. Jefferis bioRxiv doi: 10.1101/006353

    -

    See also

    https://github.com/jefferislab/BridgingRegistrations, https://github.com/jefferislab/MirrorRegistrations, and https://github.com/jefferislab/DrosophilidBridgingRegistrations.

    download_reg_repo

    -

    Examples

    - 
    # NOT RUN {
+    
    if (FALSE) {
 # to download just one of these repositories do e.g.:
 download_jefferislab_registrations("Mirror")
 
 # to download your own registration repositories for use do
 download_reg_repo("https://github.com/myuser/myrepo")
-# }
    
+}
    - + + + diff --git a/docs/reference/index.html b/docs/reference/index.html index 8ef59a7..8ebc820 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -8,21 +8,29 @@ Function reference • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -30,10 +38,12 @@ + + @@ -44,9 +54,10 @@ + - +
    @@ -82,7 +93,6 @@ Help -
    +
    @@ -123,6 +134,11 @@

    Provides an overview of key features and data/functions in the package as well.

    + + + + + @@ -138,6 +154,11 @@

    How to download additional data beyond those bundled with this package

    + + + + + @@ -152,6 +173,11 @@

    Template objects and surface models for a range of Drosophila template brains.

    + + + + + @@ -225,9 +251,9 @@

    JRC2018F

    +

    JRC2018F JRC2018U JRC2018F.surf JRC2018U.surf

    -

    Template information and surface model for the JRC2018F reference brain

    +

    Template information and surface models for the JRC2018 reference brains

    @@ -242,12 +268,42 @@

    Templates and surface meshes for the ventral nerve cord (i.e. Thoracico-Abdominal Ganglion).

    + + + + +

    VNCIS1

    Template information and surface model for the VNCIS1 reference neuropil

    + + + +

    JRCVNC2018F JRCVNC2018F.surf

    + +

    Template information and surface models for JRC2018 VNC templates

    + + + + +

    Drosophila EM Template Brains

    +

    Template objects and surface models for Drosophila electron microscopy volumes

    + + + + + + + + + + +

    JRCFIB2018F

    + +

    Template information for the JRCFIB2018F aka hemibrain dataset

    @@ -256,6 +312,11 @@

    Template and brain surface models for Drosophilids other than D. melanogaster.

    + + + + + @@ -279,31 +340,30 @@

    -

    Contents

    -     +

    + + + diff --git a/docs/reference/nat.flybrains-package.html b/docs/reference/nat.flybrains-package.html index d702474..1c7c321 100644 --- a/docs/reference/nat.flybrains-package.html +++ b/docs/reference/nat.flybrains-package.html @@ -9,21 +9,29 @@ Additional flybrain-specific data and tools for use with the NeuroAnatomy Toolbox (nat) — nat.flybrains-package • nat.flybrains + - + - - + + + + + + + - + + - + - - + + + @@ -31,13 +39,13 @@ + - - + @@ -51,9 +59,10 @@ + - +
    @@ -89,7 +98,6 @@ Help -
    +
    @@ -119,14 +128,13 @@

    Additional flybrain-specific data and tools for use with the NeuroAnatomy

    -

    This package provides data, such as template brain information and registrations, along with extra functions to extend nat towards easy use for researchers working with fly data.

    -
    - + +

    Template brains

    Information on a number of template brains is @@ -138,9 +146,9 @@

    Bridging registrations

    A number of registrations for bridging data @@ -151,10 +159,10 @@

    Mirroring registrations

    A number of registrations for mirroring @@ -163,59 +171,43 @@

    Additional registrations

    See the nat.templatebrains package documentation for details of how to add extra registrations.

    -

    See also

    -

    nat, nat.templatebrains

    - +

    nat, nat.templatebrains

    - + + +