Merge branch 'main' of https://github.com/flyconnectome/bancr

R/data.R

@@ -4,7 +4,7 @@
 #' @docType data
 #' @description `banc.surf` is unsymmetrical and not a normalised version of the mesh.
 #' It is the outline of the dataset in nanometers.`banc_neuropil.surf` represents the synaptic neuropil.
-#' Built from the BANC synapse coud, but not optimised to inlude 100% of bone fide presynapses.
+#' Built from the BANC synapse cloud, but not optimised to include 100% of bona fide presynapses.
 #' `banc_neuropils.surf` contains the standard Ito et al., 2014 brain neuropil volumes transformed into BANC space.
 #' `banc_al.surf` contains the standard Bates and Schlegel et al, 2021 right antennal lobe glomeruli brain neuropil volumes transformed into BANC space.
 #'
@@ -49,7 +49,7 @@
 # banc.surf$Vertices[,"Z"] <- banc.surf$Vertices[,"Z"]*0.9462 # scaling Jasper worked out
 # usethis::use_data(banc.surf, overwrite = TRUE)
 
-#' Thin-Plate Spline Registration from BANC to JRC2018F templatebrain
+#' Thin-Plate Spline Registration from BANC to JRC2018F template brain
 #'
 #' @description
 #' A thin-plate spline (TPS) registration object that transforms 3D points

R/synapses.R

@@ -6,7 +6,7 @@
 #'
 #' @param path The google storage path to the desired synapses file. Read using \code{readr::read_csv}.
 #' @param overwrite Logical, whether or not to overwrite an extant \code{banc_data.sqlite} file.
-#' @param n_max Numeric, the maximum number of rows ot read from \code{path} if you just want to see
+#' @param n_max Numeric, the maximum number of rows to read from \code{path} if you just want to see
 #' a taster of the file.
 #' @param details Logical Whether or not to read all data columns in the target synapse \code{.csv}. Defaults to
 #' \code{FALSE} in order to read only the essential presynapse position data.

R/xform.R

@@ -448,7 +448,7 @@ banc_to_JRC2018F <- function(x,
 #'   If NULL, uses default files.
 #' @param method Character string specifying the transformation method.
 #'   Must be either "elastix" or "tpsreg". Default is "elastix".
-#' @param ... Additional arguments passed to nat.templatebrains::mirror_brain.
+#' @param ... Additional arguments passed to \code{nat.templatebrains::\link{mirror_brain}}.
 #'
 #' @return The input object with mirrored 3D points.
 #'

README.md

@@ -450,15 +450,14 @@ citation(package = "bancr")
 Acknowledgements
 ----------------
 
-The BANC data set was collected at Harvard Medical School in he laboratory of Wei-Chung Allen Lee, by Minsu Kim and Jasper Phelps.
+The BANC data set was collected at Harvard Medical School in the laboratory of Wei-Chung Allen Lee, by Minsu Kim and Jasper Phelps.
 The segmentation and synapse prediction was built by [Zetta.ai](https://zetta.ai/). 
-The neuron reconstruction effort has been hosted and support by [FlyWire](https://flywire.ai/).
-This R package was built from principles developed
-by Greg Jefferis at the Laboratory of Molecular Biology.
+The neuron reconstruction effort has been hosted and supported by [FlyWire](https://flywire.ai/).
+This R package was initialised using the [fancr](https://github.com/flyconnectome/fancr) package developed by Greg Jefferis at the MRC Laboratory of Molecular Biology, Cambridge.
 Alex Bates worked on this R package while in the laboratory of Rachel Wilson
 at Harvard Medical School.
 
 References
 ----------
 
-**Bates, Alexander Shakeel, James D. Manton, Sridhar R. Jagannathan, Marta Costa, Philipp Schlegel, Torsten Rohlfing, and Gregory SWE Jefferis**. 2020. *The Natverse, a Versatile Toolbox for Combining and Analysing Neuroanatomical Data.* eLife 9 (April). https://doi.org/10.7554/eLife.53350.
+**Bates, Alexander Shakeel, James D. Manton, Sridhar R. Jagannathan, Marta Costa, Philipp Schlegel, Torsten Rohlfing, and Gregory SXE Jefferis**. 2020. *The Natverse, a Versatile Toolbox for Combining and Analysing Neuroanatomical Data.* eLife 9 (April). https://doi.org/10.7554/eLife.53350.

inst/WORDLIST

@@ -1,11 +1,11 @@
+Antennal
 Buhmann
 CATMAID
 CAVEclient
 CMD
 CloudVolume
+Connectome
 FAFB
-banc
-banc's
 FlyWire
 Itanna
 MANC
@@ -19,10 +19,14 @@ Tuthill
 URIs
 Wei
 Zetta
+antennal
 autapses
 autoseg
 autosegmentation
+banc
+banc's
 cloudvolume
+connectome
 dotprops
 erroring
 etc