diff --git a/docs/articles/articles/multiple_somata.html b/docs/articles/articles/multiple_somata.html index 1330497..b9ce78a 100644 --- a/docs/articles/articles/multiple_somata.html +++ b/docs/articles/articles/multiple_somata.html @@ -18,7 +18,7 @@ -
+
-
+

Finding Neurons with Multiple Somata

Gregory Jefferis

-

2018-05-02

+

2018-05-05

- Source: vignettes/articles/multiple_somata.Rmd + Source: vignettes/articles/multiple_somata.Rmd +
-

Intro

@@ -225,6 +225,28 @@

2773 soma +32793 +11614584 +409165 +248515.0 +47320 +-10102.8955 +1 + + +2773 +soma +32793 +11614561 +409733 +247733.0 +49720 +-9630.9375 +2 + + +2773 +soma 58484 1507652 461036 @@ -2334,7 +2356,6 @@

write.table(file=tf, sep="\t", row.names = FALSE) gs_upload(tf, sheet_title = 'multi_soma_neurons') unlink(tf)

-
@@ -2365,5 +2386,7 @@

+ + diff --git a/docs/articles/articles/multiple_somata_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/articles/multiple_somata_files/figure-html/unnamed-chunk-4-1.png index 045d272..05d3169 100644 Binary files a/docs/articles/articles/multiple_somata_files/figure-html/unnamed-chunk-4-1.png and b/docs/articles/articles/multiple_somata_files/figure-html/unnamed-chunk-4-1.png differ diff --git a/docs/articles/index.html b/docs/articles/index.html index c098725..593db09 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -25,6 +25,9 @@ + + + @@ -40,7 +43,7 @@ -
+
@@ -108,12 +112,12 @@ -
-

Articles version 0.5.2

-
-
-
+
+
+

Articles

+
+

All vignettes

@@ -141,6 +145,8 @@

All vignettes

+ + diff --git a/docs/articles/landmarks.html b/docs/articles/landmarks.html index f2d8c95..d893b6d 100644 --- a/docs/articles/landmarks.html +++ b/docs/articles/landmarks.html @@ -18,7 +18,7 @@ -
+
-
+

Landmarks

Gregory Jefferis

-

2018-05-02

+

2018-05-05

- Source: vignettes/landmarks.Rmd + Source: vignettes/landmarks.Rmd +
-

Intro

@@ -1908,7 +1908,6 @@

write.table(cbind(elm.landmarks, xyzm.pixels), 'elm.landmarks-with-mirror.tsv', col.names = T, sep='\t', row.names = F)

If one were then to take the mirror image landmarks in JFRC2013 space and manually pick the corresponding locations in EM space, one should be able to compare two different paths to the same point (one mirroring in FAFB, the other mirroring in JFRC2013) and see whether there is a difference in the calculated position. Differences would presumably reflect the uncertainty in picking positions in the EM volume (and a small contribution from the mirroring uncertainty in JFRC2013, which nevertheless expect to be <1 µm based on analysis in Manton et al 2014).

-
@@ -1938,5 +1937,7 @@

+ + diff --git a/docs/articles/landmarks_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/landmarks_files/figure-html/unnamed-chunk-6-1.png index 80ae81b..99e33f5 100644 Binary files a/docs/articles/landmarks_files/figure-html/unnamed-chunk-6-1.png and b/docs/articles/landmarks_files/figure-html/unnamed-chunk-6-1.png differ diff --git a/docs/articles/making_meshes.html b/docs/articles/making_meshes.html index 2b58954..ba9adfd 100644 --- a/docs/articles/making_meshes.html +++ b/docs/articles/making_meshes.html @@ -18,7 +18,7 @@ -
+
-
+

Making Surface Meshes

Gregory Jefferis

-

2018-05-02

+

2018-05-05

- Source: vignettes/making_meshes.Rmd + Source: vignettes/making_meshes.Rmd +
-

Intro

@@ -151,21 +151,20 @@ 

wire3d(calyx)
 points3d(cxyz, col='red')
 points3d(pntokc[,c('post_node_x','post_node_y','post_node_z')], col='blue')
-

+

We can also compare with the mesh supplied with elmr, which was transformed from JFRC2 space via JFRC2013 to FAFB:

wire3d(calyx)
 plot3d(FAFBNP.surf, "MB_CA_R", alpha=.3)
 view3d(userMatrix=rgl::rotationMatrix(angle = pi, 1,0,0), zoom=0.8)
-

+

And we can also compare the dorsal view as well:

wire3d(calyx)
 plot3d(FAFBNP.surf, "MB_CA_R", alpha=.3)
 view3d(userMatrix=rgl::rotationMatrix(angle = -pi/2, 1,0,0), zoom=0.8)
-

+

It’s clear that there is a mismatch here. This may originate in part from the fact that the JFRC2013 intermediate template has rather flattened MB calyces. The quality of the JFRC2-JFRC2013 bridging registration is likely also a factor.

Finally if one wanted to place this mesh into CATMAID, one could do it as follows:

catmaid_add_volume(calyx, title="fafb14.MB_CA_R", comment="Constructed by GSXEJ from PN-KC synapses directly in FAFB14 space.")
-

@@ -194,5 +193,7 @@

+ + diff --git a/docs/articles/making_meshes_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/making_meshes_files/figure-html/unnamed-chunk-5-1.png index 9b75187..9824be3 100644 Binary files a/docs/articles/making_meshes_files/figure-html/unnamed-chunk-5-1.png and b/docs/articles/making_meshes_files/figure-html/unnamed-chunk-5-1.png differ diff --git a/docs/articles/making_meshes_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/making_meshes_files/figure-html/unnamed-chunk-6-1.png index 28dc606..f9e13f8 100644 Binary files a/docs/articles/making_meshes_files/figure-html/unnamed-chunk-6-1.png and b/docs/articles/making_meshes_files/figure-html/unnamed-chunk-6-1.png differ diff --git a/docs/articles/making_meshes_files/figure-html/unnamed-chunk-7-1.png b/docs/articles/making_meshes_files/figure-html/unnamed-chunk-7-1.png index d6f6e89..f98f40a 100644 Binary files a/docs/articles/making_meshes_files/figure-html/unnamed-chunk-7-1.png and b/docs/articles/making_meshes_files/figure-html/unnamed-chunk-7-1.png differ diff --git a/docs/articles/selecting_random_synapses.html b/docs/articles/selecting_random_synapses.html index 954e506..0a24dd7 100644 --- a/docs/articles/selecting_random_synapses.html +++ b/docs/articles/selecting_random_synapses.html @@ -18,7 +18,7 @@ -
+
-
+

Selecting random synapses

Gregory Jefferis

-

2018-05-02

+

2018-05-05

- Source: vignettes/selecting_random_synapses.Rmd + Source: vignettes/selecting_random_synapses.Rmd +
-

Intro

@@ -182,12 +182,12 @@

That was a little bit clunky but we basically feed the open_fafb function the data one row at a time centering the URL on the postsynaptic node and selecting that node in the CATMAID viewer.

So here are the results

head(synapse_urls)
-
## [1] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=147840&yp=157639&xp=357688&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=493170&active_node_id=2590188" 
-## [2] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=148160&yp=160572&xp=357893&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=487673&active_node_id=2574169" 
-## [3] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=148120&yp=160585&xp=358070&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=487663&active_node_id=2574164" 
-## [4] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=146560&yp=156243&xp=356498&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=590683&active_node_id=2864653" 
-## [5] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=157440&yp=151367&xp=370270&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=1911124&active_node_id=2591427"
-## [6] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=159280&yp=152447&xp=368799&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=479389&active_node_id=2555990"
+
## [1] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=158600&yp=152298&xp=369266&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=493834&active_node_id=2591273"
+## [2] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=149080&yp=149816&xp=357044&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=485999&active_node_id=2571178"
+## [3] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=146600&yp=146171&xp=356114&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=487093&active_node_id=2572894"
+## [4] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=156440&yp=152450&xp=370511&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=494144&active_node_id=2591773"
+## [5] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=159880&yp=150987&xp=369202&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=479254&active_node_id=2555905"
+## [6] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=159160&yp=152131&xp=369553&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=493585&active_node_id=2590874"

@@ -205,7 +205,7 @@

points(col='grey') # and then the ones we did points(random_syn$post_node_x, random_syn$post_node_y, col='red', pch=19)

-

+

Then you can open those urls directly in CATMAID:

for (u in synapse_urls) {
   readline("Press a key to move to open the next synapse (or Esc to cancel).")
@@ -222,7 +222,6 @@ 

 write.table(random_syn, file=tf, sep="\t")
 gs_upload(tf, sheet_title = 'PN61221_rand_synapse_urls')
 unlink(tf)
-
@@ -252,5 +251,7 @@

+ + diff --git a/docs/articles/selecting_random_synapses_files/figure-html/unnamed-chunk-11-1.png b/docs/articles/selecting_random_synapses_files/figure-html/unnamed-chunk-11-1.png index f86fa6d..3d8f7ae 100644 Binary files a/docs/articles/selecting_random_synapses_files/figure-html/unnamed-chunk-11-1.png and b/docs/articles/selecting_random_synapses_files/figure-html/unnamed-chunk-11-1.png differ diff --git a/docs/articles/xform_brain.html b/docs/articles/xform_brain.html index 7d9856d..dad9f53 100644 --- a/docs/articles/xform_brain.html +++ b/docs/articles/xform_brain.html @@ -18,7 +18,7 @@ -
+
-
+

Transforming between FAFB and light level template brains

Gregory Jefferis

-

2018-05-02

+

2018-05-05

- Source: vignettes/xform_brain.Rmd + Source: vignettes/xform_brain.Rmd +
-

Intro

@@ -149,7 +149,7 @@

# ensure that we have all the relevant bridging registrations downloaded Cell07PNs13.fafb=xform_brain(Cell07PNs[1:3], sample=IS2, reference=FAFB) plot(Cell07PNs13.fafb)

-

+

@@ -161,14 +161,14 @@

# that the surface object is called XXXX.surf plot3d(FAFBJFRC2013.surf, alpha=.3, col='grey') plot3d(dense_core_neurons, lwd=2, soma=3000)

-

+

There are also surface objects available for individual neuropil domains that have been pre-transformed using this approach:

FAFBNP.surf=xform_brain(JFRC2NP.surf, sample = JFRC2, reference = FAFB)

and bundled with the elmr package.

We can plot neuropil subsets as follows:

plot3d(FAFBNP.surf, "LH", alpha=0.4)
 plot3d(dense_core_neurons, lwd=2, soma=3000)
-

+

@@ -196,7 +196,6 @@

## Description: ## DOI:

This becomes quite useful when particular pieces of data are reused extensively in an interactive R session, especially if they are already distributed in tagged form.

-

@@ -228,5 +227,7 @@

+ + diff --git a/docs/articles/xform_brain_files/figure-html/unnamed-chunk-3-1.png b/docs/articles/xform_brain_files/figure-html/unnamed-chunk-3-1.png index 4d02a8c..6c57da7 100644 Binary files a/docs/articles/xform_brain_files/figure-html/unnamed-chunk-3-1.png and b/docs/articles/xform_brain_files/figure-html/unnamed-chunk-3-1.png differ diff --git a/docs/articles/xform_brain_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/xform_brain_files/figure-html/unnamed-chunk-4-1.png index 6c91d1a..51c6d2a 100644 Binary files a/docs/articles/xform_brain_files/figure-html/unnamed-chunk-4-1.png and b/docs/articles/xform_brain_files/figure-html/unnamed-chunk-4-1.png differ diff --git a/docs/articles/xform_brain_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/xform_brain_files/figure-html/unnamed-chunk-6-1.png index 96ab2c5..1d066f5 100644 Binary files a/docs/articles/xform_brain_files/figure-html/unnamed-chunk-6-1.png and b/docs/articles/xform_brain_files/figure-html/unnamed-chunk-6-1.png differ diff --git a/docs/authors.html b/docs/authors.html index f0fb286..4b1b0a3 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -25,6 +25,9 @@ + + + @@ -101,6 +104,7 @@ +
@@ -108,8 +112,8 @@ -
-
+
+

Authors

@@ -138,6 +142,8 @@

Authors

+ + diff --git a/docs/docsearch.css b/docs/docsearch.css new file mode 100644 index 0000000..c524034 --- /dev/null +++ b/docs/docsearch.css @@ -0,0 +1,145 @@ +/* Docsearch -------------------------------------------------------------- */ +/* + Source: https://github.com/algolia/docsearch/ + License: MIT +*/ + +.algolia-autocomplete { + display: block; + -webkit-box-flex: 1; + -ms-flex: 1; + flex: 1 +} + +.algolia-autocomplete .ds-dropdown-menu { + width: 100%; + min-width: none; + max-width: none; + padding: .75rem 0; + background-color: #fff; + background-clip: padding-box; + border: 1px solid rgba(0, 0, 0, .1); + box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175); +} + +@media (min-width:768px) { + .algolia-autocomplete .ds-dropdown-menu { + width: 175% + } +} + +.algolia-autocomplete .ds-dropdown-menu::before { + display: none +} + +.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] { + padding: 0; + background-color: rgb(255,255,255); + border: 0; + max-height: 80vh; +} + +.algolia-autocomplete .ds-dropdown-menu .ds-suggestions { + margin-top: 0 +} + +.algolia-autocomplete .algolia-docsearch-suggestion { + padding: 0; + overflow: visible +} + +.algolia-autocomplete .algolia-docsearch-suggestion--category-header { + padding: .125rem 1rem; + margin-top: 0; + font-size: 1.3em; + font-weight: 500; + color: #00008B; + border-bottom: 0 +} + +.algolia-autocomplete .algolia-docsearch-suggestion--wrapper { + float: none; + padding-top: 0 +} + +.algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column { + float: none; + width: auto; + padding: 0; + text-align: left +} + +.algolia-autocomplete .algolia-docsearch-suggestion--content { + float: none; + width: auto; + padding: 0 +} + +.algolia-autocomplete .algolia-docsearch-suggestion--content::before { + display: none +} + +.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header { + padding-top: .75rem; + margin-top: .75rem; + border-top: 1px solid rgba(0, 0, 0, .1) +} + +.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column { + display: block; + padding: .1rem 1rem; + margin-bottom: 0.1; + font-size: 1.0em; + font-weight: 400 + /* display: none */ +} + +.algolia-autocomplete .algolia-docsearch-suggestion--title { + display: block; + padding: .25rem 1rem; + margin-bottom: 0; + font-size: 0.9em; + font-weight: 400 +} + +.algolia-autocomplete .algolia-docsearch-suggestion--text { + padding: 0 1rem .5rem; + margin-top: -.25rem; + font-size: 0.8em; + font-weight: 400; + line-height: 1.25 +} + +.algolia-autocomplete .algolia-docsearch-footer { + float: none; + width: auto; + height: auto; + padding: .75rem 1rem 0; + font-size: .95rem; + line-height: 1; + color: #767676; + background-color: rgb(255, 255, 255); + border-top: 1px solid rgba(0, 0, 0, .1) +} + +.algolia-autocomplete .algolia-docsearch-footer--logo { + display: inline; + overflow: visible; + color: inherit; + text-indent: 0; + background: 0 0 +} + +.algolia-autocomplete .algolia-docsearch-suggestion--highlight { + color: #FF8C00; + background: rgba(232, 189, 54, 0.1) +} + + +.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight { + box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5) +} + +.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content { + background-color: rgba(192, 192, 192, .15) +} diff --git a/docs/index.html b/docs/index.html index be1110e..cc65fea 100644 --- a/docs/index.html +++ b/docs/index.html @@ -198,5 +198,7 @@

Dev status

+ + diff --git a/docs/jquery.sticky-kit.min.js b/docs/jquery.sticky-kit.min.js index e2a3c6d..1c16271 100644 --- a/docs/jquery.sticky-kit.min.js +++ b/docs/jquery.sticky-kit.min.js @@ -1,5 +1,7 @@ +/* Sticky-kit v1.1.2 | WTFPL | Leaf Corcoran 2015 | */ /* - Sticky-kit v1.1.2 | WTFPL | Leaf Corcoran 2015 | http://leafo.net + Source: https://github.com/leafo/sticky-kit + License: MIT */ (function(){var b,f;b=this.jQuery||window.jQuery;f=b(window);b.fn.stick_in_parent=function(d){var A,w,J,n,B,K,p,q,k,E,t;null==d&&(d={});t=d.sticky_class;B=d.inner_scrolling;E=d.recalc_every;k=d.parent;q=d.offset_top;p=d.spacer;w=d.bottoming;null==q&&(q=0);null==k&&(k=void 0);null==B&&(B=!0);null==t&&(t="is_stuck");A=b(document);null==w&&(w=!0);J=function(a,d,n,C,F,u,r,G){var v,H,m,D,I,c,g,x,y,z,h,l;if(!a.data("sticky_kit")){a.data("sticky_kit",!0);I=A.height();g=a.parent();null!=k&&(g=g.closest(k)); if(!g.length)throw"failed to find stick parent";v=m=!1;(h=null!=p?p&&a.closest(p):b("
"))&&h.css("position",a.css("position"));x=function(){var c,f,e;if(!G&&(I=A.height(),c=parseInt(g.css("border-top-width"),10),f=parseInt(g.css("padding-top"),10),d=parseInt(g.css("padding-bottom"),10),n=g.offset().top+c+f,C=g.height(),m&&(v=m=!1,null==p&&(a.insertAfter(h),h.detach()),a.css({position:"",top:"",width:"",bottom:""}).removeClass(t),e=!0),F=a.offset().top-(parseInt(a.css("margin-top"),10)||0)-q, diff --git a/docs/pkgdown.css b/docs/pkgdown.css index fcd97bb..c5ab586 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -217,3 +217,11 @@ a.sourceLine:hover { .hasCopyButton:hover button.btn-copy-ex { visibility: visible; } + +/* mark.js ----------------------------*/ + +mark { + background-color: rgba(255, 255, 51, 0.5); + border-bottom: 2px solid rgba(255, 153, 51, 0.3); + padding: 1px; +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js index 362b060..16d5750 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -33,6 +33,45 @@ $(function() { }); }); +$(document).ready(function() { + // do keyword highlighting + /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */ + var mark = function() { + + var referrer = document.URL ; + var paramKey = "q" ; + + if (referrer.indexOf("?") !== -1) { + var qs = referrer.substr(referrer.indexOf('?') + 1); + var qs_noanchor = qs.split('#')[0]; + var qsa = qs_noanchor.split('&'); + var keyword = ""; + + for (var i = 0; i < qsa.length; i++) { + var currentParam = qsa[i].split('='); + + if (currentParam.length !== 2) { + continue; + } + + if (currentParam[0] == paramKey) { + keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20")); + } + } + + if (keyword !== "") { + $(".contents").unmark({ + done: function() { + $(".contents").mark(keyword); + } + }); + } + } + }; + + mark(); +}); + function paths(pathname) { var pieces = pathname.split("/"); pieces.shift(); // always starts with / @@ -99,3 +138,37 @@ if(Clipboard.isSupported()) { }); } +/* Search term highlighting ------------------------------*/ + +function matchedWords(hit) { + var words = []; + + var hierarchy = hit._highlightResult.hierarchy; + // loop to fetch from lvl0, lvl1, etc. + for (var idx in hierarchy) { + words = words.concat(hierarchy[idx].matchedWords); + } + + var content = hit._highlightResult.content; + if (content) { + words = words.concat(content.matchedWords); + } + + // return unique words + var words_uniq = [...new Set(words)]; + return words_uniq; +} + +function updateHitURL(hit) { + + var words = matchedWords(hit); + var url = ""; + + if (hit.anchor) { + url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor; + } else { + url = hit.url + '?q=' + escape(words.join(" ")); + } + + return url; +} diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index ab8c5a9..3701f78 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,6 +1,6 @@ pandoc: 1.19.2.1 -pkgdown: 0.1.0.9000 -pkgdown_sha: 966bc9d667ab87806ef684bab22e39effe62c8a5 +pkgdown: 1.0.0 +pkgdown_sha: ~ articles: multiple_somata: articles/multiple_somata.html landmarks: landmarks.html diff --git a/docs/reference/FAFB.html b/docs/reference/FAFB.html index 46eab55..0af2022 100644 --- a/docs/reference/FAFB.html +++ b/docs/reference/FAFB.html @@ -25,6 +25,9 @@ + + + +

templatebrain for assembled FAFB full adult female brain EM volume

- Source: R/elmr-data.R + Source: R/elmr-data.R +
+

FAFB Current default assembly of FAFB (an alias for FAFB13 since 2016-12-07)

@@ -139,6 +145,7 @@

templatebrain for assembled FAFB full adult female brain EM volume

FAFB11 Assembly v11 of FAFB full adult female brain EM volume (2016-02-09)

+

Details

@@ -154,8 +161,8 @@

Details

See also

-

templatebrain, - xform_brain

+

templatebrain, + xform_brain

Examples

@@ -205,6 +212,8 @@

Contents

+ + diff --git a/docs/reference/FAFB.surf.html b/docs/reference/FAFB.surf.html index b23731b..7e679b5 100644 --- a/docs/reference/FAFB.surf.html +++ b/docs/reference/FAFB.surf.html @@ -25,6 +25,9 @@ + + + +

FAFB brain and neuropil surface objects

- Source: R/elmr-data.R + Source: R/elmr-data.R +
+

FAFB13.surf describes the neuropil surface of the FAFB13 brain.

@@ -143,6 +149,7 @@

FAFB brain and neuropil surface objects

FAFBNP.surf is a surface object for the Ito et al (2014) neuropil regions in the default FAFB space (currently FAFB14)

+

Details

@@ -163,7 +170,7 @@

Details

See also

-

FAFB template brain

+

FAFB template brain

Examples

@@ -222,6 +229,8 @@

Contents

+ + diff --git a/docs/reference/dense_core_neurons-1.png b/docs/reference/dense_core_neurons-1.png index 6be1b61..1a6564a 100644 Binary files a/docs/reference/dense_core_neurons-1.png and b/docs/reference/dense_core_neurons-1.png differ diff --git a/docs/reference/dense_core_neurons.html b/docs/reference/dense_core_neurons.html index 184c37e..43deeda 100644 --- a/docs/reference/dense_core_neurons.html +++ b/docs/reference/dense_core_neurons.html @@ -25,6 +25,9 @@ + + + @@ -104,6 +107,7 @@ +
@@ -111,16 +115,19 @@ -
+

Sample EM tracings (homologous pair of neurons wrapping around lateral horn)

- Source: R/elmr-data.R + Source: R/elmr-data.R +
+

Sample EM tracings (homologous pair of neurons wrapping around lateral horn)

+

Details

@@ -160,6 +167,8 @@

Contents

+ + diff --git a/docs/reference/distal_to-1.png b/docs/reference/distal_to-1.png index cded5ee..c30efa6 100644 Binary files a/docs/reference/distal_to-1.png and b/docs/reference/distal_to-1.png differ diff --git a/docs/reference/distal_to.html b/docs/reference/distal_to.html index 10bdcc7..7cbe658 100644 --- a/docs/reference/distal_to.html +++ b/docs/reference/distal_to.html @@ -25,6 +25,9 @@ + + + @@ -104,6 +107,7 @@ +
@@ -111,16 +115,19 @@ -
+

Return indices of points in a neuron distal to a given node

- Source: R/ngraph.R + Source: R/ngraph.R +
+

Return indices of points in a neuron distal to a given node

+ 
distal_to(x, node.idx = NULL, node.pointno = NULL, root.idx = NULL,
   root.pointno = NULL)
@@ -156,7 +163,7 @@

Value

See also

-

subset.neuron, prune

+

subset.neuron, prune

Examples

@@ -199,6 +206,8 @@

Contents

+ + diff --git a/docs/reference/elm.landmarks.html b/docs/reference/elm.landmarks.html index fb0d41e..e88f2f4 100644 --- a/docs/reference/elm.landmarks.html +++ b/docs/reference/elm.landmarks.html @@ -25,6 +25,9 @@ + + + +

ELM Landmarks created by Bock & Saalfeld groups at Janelia

- Source: R/elmr-data.R + Source: R/elmr-data.R +
+

These are used to map locations in EM (FAFB) space to JFRC2013 (aka DPX) space, in conjunction with a thin plate spline library.

@@ -131,6 +137,7 @@

ELM Landmarks created by Bock & Saalfeld groups at Janelia

elm.landmarks.13 contains the landmark positions used for the FAFB13 assembly (from March to Sep 2017) as a historical record.

+

Details

@@ -189,6 +196,8 @@

Contents

+ + diff --git a/docs/reference/elmr-package.html b/docs/reference/elmr-package.html index 50c6a6d..133b958 100644 --- a/docs/reference/elmr-package.html +++ b/docs/reference/elmr-package.html @@ -25,6 +25,9 @@ + + + +

Bridge light and EM flybrain datasets

- Source: R/elmr-package.R + Source: R/elmr-package.R +
+

elmr builds on the nat and catmaid packages to provide tools to read, analyse, plot, transform and convert @@ -129,6 +135,7 @@

Bridge light and EM flybrain datasets

generated at the HHMI Janelia Research Campus (groups of Davi Bock, Stephan Saalfeld and many collaborators).

+

Interesting functions/data

@@ -225,6 +232,8 @@

Contents

+ + diff --git a/docs/reference/fafb_world_mapper.html b/docs/reference/fafb_world_mapper.html index 53d8de7..cd8ffed 100644 --- a/docs/reference/fafb_world_mapper.html +++ b/docs/reference/fafb_world_mapper.html @@ -25,6 +25,9 @@ + + + +

Convert coordinates between different FAFB assemblies

- Source: R/fafb_mapper.R + Source: R/fafb_mapper.R +
+

fafb_world_mapper provides a low-level interface to map coordinates based on the tem-services API available from inside the @@ -131,6 +137,7 @@

Convert coordinates between different FAFB assemblies

End users are not presently expected to use this directly. Instead they should use xform_brain to transform data. See examples.

+ 
fafb_world_mapper(xyz, from, to,
   baseurl = "http://tem-services.int.janelia.org:8080/render-ws/v1/owner/flyTEM/project/FAFB00/stack",
@@ -197,6 +204,8 @@ 
Contents
+ + diff --git a/docs/reference/fetchn_fafb.html b/docs/reference/fetchn_fafb.html index 88b35c9..53542d5 100644 --- a/docs/reference/fetchn_fafb.html +++ b/docs/reference/fetchn_fafb.html @@ -25,6 +25,9 @@ + + + +

Fetch neurons from FAFB CATMAID server, transforming them as appropriate

- Source: R/nblast_fafb.R + Source: R/nblast_fafb.R +
+

fetchn_fafb is a thin wrapper around the catmaid::read.neurons.catmaid function with the @@ -133,6 +139,7 @@

Fetch neurons from FAFB CATMAID server, transforming them as appropriate

dotprops representation suitable for nblast.

+ 
fetchn_fafb(skids, mirror = TRUE, conn = NULL,
   reference = nat.flybrains::FCWB)
@@ -206,6 +213,8 @@ 
Contents
+ + diff --git a/docs/reference/index.html b/docs/reference/index.html index ff59b4d..6dfba86 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -25,6 +25,9 @@ + + + @@ -101,6 +104,7 @@ +
@@ -108,175 +112,173 @@ -
-
+
+

Reference

-
- +
- - - - + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-

Package Help

-

Provides an overview of key functions and classes

-
-

elmr-package

-

Bridge light and EM flybrain datasets

-

Fetching and searching neurons

-

Fetch and transform neurons or NBLAST them

-
-

fetchn_fafb() fetchdp_fafb()

-

Fetch neurons from FAFB CATMAID server, transforming them as appropriate

-

nblast_fafb()

-

NBLAST EM tracing against FlyCircuit (or other databases of) neurons

-

Working with neuron structures

-

-
-

distal_to()

-

Return indices of points in a neuron distal to a given node

-

simplify_neuron()

-

Simplify a neuron to the longest tree with n branch points

-

stitch_neuron()

-

Stitch two neurons together at their closest endpoints

-

stitch_neurons()

-

Stitch multiple fragments into single neuron using nearest endpoints

-

unspike()

-

Remove artefactual spikes in neuron tracing due to registration errors

-

Interacting with CATMAID server

-

-
-

open_fafb()

-

Open FAFB CATMAID in browser at a given XYZ location

-

Summarising tracer contributions

-

-
-

summarise_contribution() suggest_authorship() write_authors() write_ack()

-

Summarise tracer contributions / suggest authorship for set of neurons

-

Support functions

-

Functions intended primarily for developer use

-
-

tpsreg() xformpoints(<tpsreg>)

-

Thin plate spline registrations via nat::xform and friends

-

fafb_world_mapper()

-

Convert coordinates between different FAFB assemblies

-

Data

-

Data objects

-
-

FAFB

-

templatebrain for assembled FAFB full adult female brain EM volume

-

FAFB.surf

-

FAFB brain and neuropil surface objects

-

elm.landmarks

-

ELM Landmarks created by Bock & Saalfeld groups at Janelia

-

dense_core_neurons

-

Sample EM tracings (homologous pair of neurons wrapping around lateral horn)

-
+ + + +

Package Help

+

Provides an overview of key functions and classes

+ + + + + +

elmr-package

+ +

Bridge light and EM flybrain datasets

+ + + + +

Fetching and searching neurons

+

Fetch and transform neurons or NBLAST them

+ + + + + +

fetchn_fafb() fetchdp_fafb()

+ +

Fetch neurons from FAFB CATMAID server, transforming them as appropriate

+ + + +

nblast_fafb()

+ +

NBLAST EM tracing against FlyCircuit (or other databases of) neurons

+ + + + +

Working with neuron structures

+

+ + + + + +

distal_to()

+ +

Return indices of points in a neuron distal to a given node

+ + + +

simplify_neuron()

+ +

Simplify a neuron to the longest tree with n branch points

+ + + +

stitch_neuron()

+ +

Stitch two neurons together at their closest endpoints

+ + + +

stitch_neurons()

+ +

Stitch multiple fragments into single neuron using nearest endpoints

+ + + +

unspike()

+ +

Remove artefactual spikes in neuron tracing due to registration errors

+ + + + +

Interacting with CATMAID server

+

+ + + + + +

open_fafb()

+ +

Open FAFB CATMAID in browser at a given XYZ location

+ + + + +

Summarising tracer contributions

+

+ + + + + +

summarise_contribution() suggest_authorship() write_authors() write_ack()

+ +

Summarise tracer contributions / suggest authorship for set of neurons

+ + + + +

Support functions

+

Functions intended primarily for developer use

+ + + + + +

tpsreg() xformpoints(<tpsreg>)

+ +

Thin plate spline registrations via nat::xform and friends

+ + + +

fafb_world_mapper()

+ +

Convert coordinates between different FAFB assemblies

+ + + + +

Data

+

Data objects

+ + + + + +

FAFB

+ +

templatebrain for assembled FAFB full adult female brain EM volume

+ + + +

FAFB.surf

+ +

FAFB brain and neuropil surface objects

+ + + +

elm.landmarks

+ +

ELM Landmarks created by Bock & Saalfeld groups at Janelia

+ + + +

dense_core_neurons

+ +

Sample EM tracings (homologous pair of neurons wrapping around lateral horn)

+ + +
+ + diff --git a/docs/reference/nblast_fafb.html b/docs/reference/nblast_fafb.html index 07ee0ac..d2fac23 100644 --- a/docs/reference/nblast_fafb.html +++ b/docs/reference/nblast_fafb.html @@ -25,6 +25,9 @@ + + + @@ -104,6 +107,7 @@ +
@@ -111,16 +115,19 @@ -
+

NBLAST EM tracing against FlyCircuit (or other databases of) neurons

- Source: R/nblast_fafb.R + Source: R/nblast_fafb.R +
+

NBLAST EM tracing against FlyCircuit (or other databases of) neurons

+ 
nblast_fafb(skids, db = NULL, conn = NULL, mirror = TRUE,
   normalised = TRUE, reverse = FALSE, reference = nat.flybrains::FCWB,
@@ -205,9 +212,9 @@ 
R
     
     
See also

 
-    
nblast,
+    
nblast,
   registerDoParallel for setting spreading load
-  across cores.

+  across cores.

     
 
     
Examples

@@ -263,6 +270,8 @@ 
Contents
+ + diff --git a/docs/reference/open_fafb.html b/docs/reference/open_fafb.html index 35b4a9a..c92026d 100644 --- a/docs/reference/open_fafb.html +++ b/docs/reference/open_fafb.html @@ -25,6 +25,9 @@ + + + @@ -104,6 +107,7 @@ +
@@ -111,16 +115,19 @@ -
+

Open FAFB CATMAID in browser at a given XYZ location

- Source: R/open_fafb.R + Source: R/open_fafb.R +
+

Open FAFB CATMAID in browser at a given XYZ location

+ 
open_fafb(x, s = rgl::select3d(), mirror = FALSE, sample = elmr::FAFB,
   zoom = 1, open = interactive(), active_skeleton_id = NULL,
@@ -177,7 +184,7 @@ 
Details
     
     
See also

 
-    
xform_brain

+    
xform_brain

     
 
     
Examples

@@ -217,6 +224,8 @@ 
Contents
+ + diff --git a/docs/reference/simplify_neuron-1.png b/docs/reference/simplify_neuron-1.png index 9d9c7ef..5ddee89 100644 Binary files a/docs/reference/simplify_neuron-1.png and b/docs/reference/simplify_neuron-1.png differ diff --git a/docs/reference/simplify_neuron.html b/docs/reference/simplify_neuron.html index 12b7ebd..a0dfee3 100644 --- a/docs/reference/simplify_neuron.html +++ b/docs/reference/simplify_neuron.html @@ -25,6 +25,9 @@ + + + @@ -104,6 +107,7 @@ +
@@ -111,16 +115,19 @@ -
+

Simplify a neuron to the longest tree with n branch points

- Source: R/simplify_neuron.R + Source: R/simplify_neuron.R +
+

Simplify a neuron to the longest tree with n branch points

+ 
simplify_neuron(x, n = 1, ...)
@@ -162,7 +169,7 @@

Details

See also

-

spine

+

spine

Examples

@@ -200,6 +207,8 @@

Contents

+ + diff --git a/docs/reference/stitch_neuron.html b/docs/reference/stitch_neuron.html index 2bcd38d..1d79dc6 100644 --- a/docs/reference/stitch_neuron.html +++ b/docs/reference/stitch_neuron.html @@ -25,6 +25,9 @@ + + + @@ -104,6 +107,7 @@ +
@@ -111,16 +115,19 @@ -
+

Stitch two neurons together at their closest endpoints

- Source: R/stitch_neuron.R + Source: R/stitch_neuron.R +
+

Stitch two neurons together at their closest endpoints

+ 
stitch_neuron(a, b)
@@ -142,7 +149,7 @@

Details

See also

-

stitch_neurons

+

stitch_neurons

@@ -171,6 +178,8 @@

Contents

+ + diff --git a/docs/reference/stitch_neurons.html b/docs/reference/stitch_neurons.html index 045d0bc..cccf498 100644 --- a/docs/reference/stitch_neurons.html +++ b/docs/reference/stitch_neurons.html @@ -25,6 +25,9 @@ + + + @@ -104,6 +107,7 @@ +
@@ -111,16 +115,19 @@ -
+

Stitch multiple fragments into single neuron using nearest endpoints

- Source: R/stitch_neuron.R + Source: R/stitch_neuron.R +
+

Stitch multiple fragments into single neuron using nearest endpoints

+ 
stitch_neurons(x, prefer_soma = TRUE, sort = TRUE, warndist = 1000)
@@ -162,7 +169,7 @@

Details

See also

-

stitch_neuron

+

stitch_neuron

Examples

@@ -206,6 +213,8 @@

Contents

+ + diff --git a/docs/reference/summarise_contribution.html b/docs/reference/summarise_contribution.html index 9004867..198a6e3 100644 --- a/docs/reference/summarise_contribution.html +++ b/docs/reference/summarise_contribution.html @@ -25,6 +25,9 @@ + + + +

Summarise tracer contributions / suggest authorship for set of neurons

- Source: R/contributions.R + Source: R/contributions.R +
+

summarise_contribution produces a data.frame of contributions by user. suggest_authorship can use this to suggest @@ -133,6 +139,7 @@

Summarise tracer contributions / suggest authorship for set of neurons

write_authors produces a list of authors

write_ack produces an acknowledgements wording.

+ 
summarise_contribution(skids, type = c("nodes", "synapses", "pre", "post"),
   ...)
@@ -188,35 +195,35 @@ 
Value

     
Examples

     
pnsc=summarise_contribution("annotation:^PN$")
 suggest_authorship(pnsc)
#>     id      n              full_name        pct     cpct action
-#> 1  117 148540         Ruairi Roberts 15.4062206 15.40622   auth
-#> 2   12 110324          Jacob Ratliff 11.4425466 26.84877   auth
-#> 3   11  80447        bailey harrison  8.3437742 35.19254   auth
-#> 4   26  74615             Jawaid Ali  7.7388929 42.93143   auth
-#> 5   13  62988           Addy Adesina  6.5329677 49.46440   auth
-#> 6   94  49323       Philipp Schlegel  5.1156659 54.58007   auth
-#> 7   54  42978        Ben Koppenhaver  4.4575774 59.03765    ack
-#> 8   25  41756          Lucia Kmecova  4.3308344 63.36848    ack
-#> 9   53  39793      Najla Masoodpanah  4.1272367 67.49572    ack
-#> 10   4  34960           Corey Fisher  3.6259692 71.12169    ack
-#> 11  61  33676         Benjamin Gorko  3.4927958 74.61448    ack
-#> 12  17  30539              Adam John  3.1674335 77.78191    ack
-#> 13  22  23722     Michael Lingelbach  2.4603902 80.24231    ack
-#> 14 109  21048             Alex Bates  2.1830492 82.42535    ack
-#> 15  50  18728       Shahrozia Imtiaz  1.9424243 84.36778    ack
-#> 16 164  16921    Mahmoud Elbahnasawi  1.7550065 86.12279    ack
-#> 17 167  16316           Arian Jamasb  1.6922573 87.81504    ack
-#> 18  29  16126         Nadiya Sharifi  1.6725509 89.48759    ack
-#> 19  75  14783          Philipp Ranft  1.5332581 91.02085    ack
-#> 20 127  12081             Lisa Marin  1.2530130 92.27386    ack
-#> 21  55  10190          Greg Jefferis  1.0568829 93.33075    ack
-#> 22  27   7885             Sri Murthy  0.8178137 94.14856    ack
-#> 23 123   6612             Fiona Love  0.6857811 94.83434    ack
-#> 24 118   5064         Clement Hallou  0.5252262 95.35957    ack
-#> 25  44   4591             Ala Haddad  0.4761678 95.83574    ack
-#> 26 120   4582 Amelia Edmondson-Stait  0.4752343 96.31097    ack
-#> 27  28   3769           Bindu Gampah  0.3909118 96.70188    ack
-#> 28  76   3623           Steven Calle  0.3757691 97.07765    ack
-#> 29   2   3040              Davi Bock  0.3153017 97.39295    ack
write_authors(pnsc, auth=3.0)
#> Ruairi Roberts, Jacob Ratliff, bailey harrison, Jawaid Ali, Addy Adesina, Philipp Schlegel, Ben Koppenhaver, Lucia Kmecova, Najla Masoodpanah, Corey Fisher, Benjamin Gorko, Adam John
write_ack(pnsc)
#> We thank Ben Koppenhaver, Lucia Kmecova, Najla Masoodpanah, Corey Fisher, Benjamin Gorko, Adam John, Michael Lingelbach, Alex Bates, Shahrozia Imtiaz, Mahmoud Elbahnasawi, Arian Jamasb, Nadiya Sharifi, Philipp Ranft, Lisa Marin, Greg Jefferis, Sri Murthy, Fiona Love, Clement Hallou, Ala Haddad, Amelia Edmondson-Stait, Bindu Gampah, Steven Calle, Davi Bock for contributing 42.8 % of reconstructed arbour cable.

+#> 1  117 148781         Ruairi Roberts 15.4070071 15.40701   auth
+#> 2   12 110324          Jacob Ratliff 11.4245949 26.83160   auth
+#> 3   11  80447        bailey harrison  8.3306841 35.16229   auth
+#> 4   26  74626             Jawaid Ali  7.7278908 42.89018   auth
+#> 5   13  62988           Addy Adesina  6.5227184 49.41290   auth
+#> 6   94  50362       Philipp Schlegel  5.2152338 54.62813   auth
+#> 7   54  42978        Ben Koppenhaver  4.4505841 59.07871    ack
+#> 8   25  41756          Lucia Kmecova  4.3240400 63.40275    ack
+#> 9   53  39793      Najla Masoodpanah  4.1207616 67.52351    ack
+#> 10   4  34961           Corey Fisher  3.6203842 71.14390    ack
+#> 11  61  33676         Benjamin Gorko  3.4873161 74.63121    ack
+#> 12  17  30539              Adam John  3.1624642 77.79368    ack
+#> 13  22  23722     Michael Lingelbach  2.4565302 80.25021    ack
+#> 14 109  21051             Alex Bates  2.1799350 82.43014    ack
+#> 15  50  18728       Shahrozia Imtiaz  1.9393769 84.36952    ack
+#> 16 164  16921    Mahmoud Elbahnasawi  1.7522531 86.12177    ack
+#> 17 167  16316           Arian Jamasb  1.6896024 87.81138    ack
+#> 18  29  16126         Nadiya Sharifi  1.6699269 89.48130    ack
+#> 19  75  14783          Philipp Ranft  1.5308526 91.01216    ack
+#> 20 127  12084             Lisa Marin  1.2513579 92.26351    ack
+#> 21  55  10190          Greg Jefferis  1.0552248 93.31874    ack
+#> 22  27   7885             Sri Murthy  0.8165307 94.13527    ack
+#> 23 123   6613             Fiona Love  0.6848088 94.82008    ack
+#> 24 118   5064         Clement Hallou  0.5244022 95.34448    ack
+#> 25  44   4591             Ala Haddad  0.4754207 95.81990    ack
+#> 26 120   4582 Amelia Edmondson-Stait  0.4744887 96.29439    ack
+#> 27  28   3769           Bindu Gampah  0.3902986 96.68469    ack
+#> 28  76   3624           Steven Calle  0.3752831 97.05997    ack
+#> 29   2   3040              Davi Bock  0.3148070 97.37478    ack
write_authors(pnsc, auth=3.0)
#> Ruairi Roberts, Jacob Ratliff, bailey harrison, Jawaid Ali, Addy Adesina, Philipp Schlegel, Ben Koppenhaver, Lucia Kmecova, Najla Masoodpanah, Corey Fisher, Benjamin Gorko, Adam John
write_ack(pnsc)
#> We thank Ben Koppenhaver, Lucia Kmecova, Najla Masoodpanah, Corey Fisher, Benjamin Gorko, Adam John, Michael Lingelbach, Alex Bates, Shahrozia Imtiaz, Mahmoud Elbahnasawi, Arian Jamasb, Nadiya Sharifi, Philipp Ranft, Lisa Marin, Greg Jefferis, Sri Murthy, Fiona Love, Clement Hallou, Ala Haddad, Amelia Edmondson-Stait, Bindu Gampah, Steven Calle, Davi Bock for contributing 42.7 % of reconstructed arbour cable.

 pnsc=summarise_contribution("annotation:^PN$", type='synapses')
+ + diff --git a/docs/reference/tpsreg-1.png b/docs/reference/tpsreg-1.png index f9b14e0..c3a4013 100644 Binary files a/docs/reference/tpsreg-1.png and b/docs/reference/tpsreg-1.png differ diff --git a/docs/reference/tpsreg.html b/docs/reference/tpsreg.html index 3f775b9..d1aaf33 100644 --- a/docs/reference/tpsreg.html +++ b/docs/reference/tpsreg.html @@ -25,6 +25,9 @@ + + + +

Thin plate spline registrations via nat::xform and friends

- Source: R/xform_tps.R + Source: R/xform_tps.R +
+

tpsreg creates an object encapsulating a thin plate spine transform mapping a paired landmark set.

@@ -131,6 +137,7 @@

Thin plate spline registrations via nat::xform and friends

vertices) using a thin plate spline mapping stored in a tpsreg object.

+ 
tpsreg(sample, reference, ...)
 
@@ -176,7 +183,7 @@ 
Details
     
     
See also

 
-    
reglist, read.landmarks

+    
reglist, read.landmarks

     
 
     
Examples

@@ -191,9 +198,7 @@ 
Examp
 emlandmarks[,'shortname']=str_match(emlandmarks[,'name'], "(.*)([LR]) Landmark.*")[,2]
 emlandmarks[,'shortname']=sub("[_ ]+$", "", emlandmarks[,'shortname'])
 library(dplyr)
#> -#> Attaching package: ‘dplyr’
#> The following object is masked from ‘package:testthat’: -#> -#> matches
#> The following objects are masked from ‘package:nat’: +#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:nat’: #> #> intersect, setdiff, union
#> The following objects are masked from ‘package:stats’: #> @@ -244,6 +249,8 @@

Contents

+ + diff --git a/docs/reference/unspike-1.png b/docs/reference/unspike-1.png index 40753e1..a946a8b 100644 Binary files a/docs/reference/unspike-1.png and b/docs/reference/unspike-1.png differ diff --git a/docs/reference/unspike.html b/docs/reference/unspike.html index 25e2da0..2d370c7 100644 --- a/docs/reference/unspike.html +++ b/docs/reference/unspike.html @@ -25,6 +25,9 @@ + + + @@ -104,6 +107,7 @@ +
@@ -111,16 +115,19 @@ -
+

Remove artefactual spikes in neuron tracing due to registration errors

- Source: R/unspike.R + Source: R/unspike.R +
+

Remove artefactual spikes in neuron tracing due to registration errors

+ 
unspike(x, threshold, ...)
 
@@ -173,7 +180,7 @@ 
See also

 
-    
smooth_neuron

+    
smooth_neuron

     
 
     
Examples

@@ -212,6 +219,8 @@ 
Contents
+ +