Noticed by Dana Galili on Windows 7 laptop

Error in git2r::clone(url, localdir, ...) : 
  Error in 'git2r_clone': Failed to make directory 'C:\Users\KADOWG~1\AppData\Local\rpkg-nat.templatebrains\rpkg-nat.templatebrains': The system cannot find the path specified.

• also has some holes

that would stretch by a factor of 1.47 in Z

It just has some physical calibration (the original had none).

We could use the new git repository features to download the registrations instead, but there's currently no support (as far as I am aware) for downloading surface data. Would it be best to add the latter instead?

For the time being brain2reg will isolate any path dependencies and so you can choose whatever approach you like and we will not need to change much. It might be a bit more modular if it relied on the object to have a function that returned appropriate paths. Bridging registrations are trickier though. Here we might eventually need another registry style approach (see nat::fileformats) i.e. an environment in nat that stores registrations it know about. Data packages would then use a nat function to tell it about the type location of registrations.

See natverse/nat#127

1. When I use "nat.flybrains::download_jefferislab_registrations()" function, there is an error. "Error in git2r::pull(repo):branch is NULL". I think maybe there is a loss of the file?
2. Here I get one bodyID in the neuprint and find and plot this neuron in natverse. I want to show it in the templatebrain. However, I can't use the two files: JRCFIB2018F and JRCFIB2018Fraw. It return "Error in get(paste0(as.character(x), ".surf")) : can't find the object 'JRCFIB2018Fraw.surf'". And also I can't use the xform_brain form JRCFIB2018Fraw to JFRC2.
   Could anyone answer these questions and give me some instructions to show this known neuron in hemibrain dataset in another template brain? Thanks a lot!

Although #25 tried to bring template brains up to date, we have no template object for the following:

> library(nat.flybrains)
> setdiff(igraph::V(bridging_graph())$name, ls(envir = as.environment('package:nat.flybrains')))
[1] "Dyak"       "Cell07"     "JFRC2014"   "JFRC2014DS" "V2"        

Currently, we have the following signatures:

xform:
  function(x, reg, ...)
xform.BrainTemplate:
  function(x, x2, data, transform, ...)

We cannot change xform() as this is part of nat, but we don't want reg as the whole point is to let the user avoid having to deal with registration files directly. This suggests that we should use a different function instead.

in the help sections (lines beginning #') of DATA.r

URLs are formatted like so:

\href{http://dx.doi.org/10.1038/nature06864}{doi:10.1038/nature06864}

Currently, mirror() looks in the BrainTemplate object to find where the mirroring registration is. This should be changed to infer the location in the same way that trans() does.

Hello,

Current available JRC2018U template has a resolution of 0.38x0.38x0.38um that have 456 stacks. It would be nice to have a template at the resolution of 0.519x0.519x1um that have 174 stacks (https://www.dropbox.com/s/cjcslfa2daxptu8/JRC2018_UNISEX_20x_HR.nrrd?dl=0) so that .nrrd neuron objects can be generated for driver line searching in MCFO Color depth MIP dataset.

Thanks!

So after our discussion, I think the simplest strategy looks like:

brain2reg(reference=, sample=, mirror=)
xform_brain(x, reference=, sample=, ...) xform(x, brain2reg(refererence,sample), ...)
mirror_brain(x, brain=, ...) xform_brain(x, brain2reg(brain=mirror,...)

I think there could be some reasonable discussion about whether a mirror_brain function was also necessary, but people might expect to find one given the existence of nat::mirror.

Would like either a function or simple examples showing how to calculate overlap with a label field.

Should we be including the VFB label field in e.g. JFRC2, FCWB, T1 and IS2 space?

i.e. those listed at

http://flybrain.mrc-lmb.cam.ac.uk/si/bridging/www/brains/

This is the approved name in Ito et al. 2014, Neuron

this could be achieved by providing an as.im3d method (which converts to an empty im3d object) and then using that.

It would be nice to be able to use just one function for all transformations such that bridging and mirroring could be done with just one command, with the function working out what should be done based on the number of templates it is given.

We should explain how to use external bridging/mirroring registrations. It may be that we should also include a mechanism for downloading them.

@istvantaisz would you be able to add this based on previous examples? You could add this amira surface JRC2018_VNC_UNISEX_4iso_8bit3-30k.surf.zip
to data-raw and use this

$ unu head /GD/projects/WeiLee/vnctemplates/JRC2018_VNC_UNISEX_4iso_8bit.nrrd 

to make a .nhdr file as I have done elsewhere

NRRD0004
# Created by Nrrd_Writer at Thu Nov 21 20:04:23 GMT 2019
type: uint8
encoding: gzip
endian: big
dimension: 3
sizes: 660 1290 382
space dimension: 3
space directions: (0.4,0,0) (0,0.4,0) (0,0,0.4)
space units: "microns" "microns" "microns"

Let me know if you have any trouble! This will help us get high quality support for VNC transforms properly integrated.

Error:

xform_brain("/Volumes/teraraid/flybrain/Shahar/SplitRegistration/IS2/reformatted/IS2_JK733SF457-1_02_warp_m0g80c8e1e-1x26r4.nrrd", ref=JFRC2, sample=IS2, outfile=path.expand("~/projects/Shahar/Screen/AdditionalOutputs/JFRC2_IS2_JK733SF457-1_02_warp_m0g80c8e1e-1x26r4.nrrd"))

Error in basename(as.character(f)) :
argument "target" is missing, with no default

OK:

xform_brain("/Volumes/teraraid/flybrain/Shahar/SplitRegistration/IS2/reformatted/IS2_JK733SF457-1_02_warp_m0g80c8e1e-1x26r4.nrrd", ref=JFRC2, sample=IS2, target=JFRC2, outfile=path.expand("~/projects/Shahar/Screen/AdditionalOutputs/JFRC2_IS2_JK733SF457-1_02_warp_m0g80c8e1e-1x26r4.nrrd"))
Reading transformation from studylist /Library/Frameworks/R.framework/Versions/3.2/Resources/library/nat.flybrains/extdata/bridgingregistrations/JFRC2_IS2.list
WARNING: image does not have valid orientation meta information; cannot reorient.
cmd:
'/usr/local/lib/cmtk/bin/reformatx' --verbose --outfile '/Volumes/teraraid/flybrain/Shahar/SplitRegistration/IS2/reformatted/JFRC2_IS2_JK733SF457-1_02_warp_m0g80c8e1e-1x26r4.nrrd' --floating '/Volumes/teraraid/flybrain/Shahar/SplitRegistration/IS2/reformatted/IS2_JK733SF457-1_02_warp_m0g80c8e1e-1x26r4.nrrd' --interpolation linear --outfile '/Volumes/teraraid/flybrain/Shahar/SplitRegistration/IS2/reformatted/JFRC2_IS2_JK733SF457-1_02_warp_m0g80c8e1e-1x26r4.nrrd' --target-grid 1024,512,218:0.622088,0.622088,0.622088:0.000000,0.000000,0.000000 '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/nat.flybrains/extdata/bridgingregistrations/JFRC2_IS2.list'

(moved from)

It would be nice if the JRC2018U (unisex) template brain could be included. I added a bridging registration to the BridingRegistration package, but need a templatebrain object to use it with some nat functionality (e.g. writing NRRD files) in order to have meta-information like the voxdims available.

I tried to add this templatebrain object following the existing JRC2018F example, but couldn't get R to make this object available and use it when the bridging registration is used. Therefore I add this as an issue here including the information I collected so far.

This is the information I get when loading the reference brain NRRD file with as.tenplatebrain():

=== Template Brain ===                
Name: JRC2018_UNISEX_20x_HR           
Short Name: JRC2018_UNISEX_20x_HR     
Type:                                 
Sex:                                  
Dimensions:1210 x 566 x 174 voxels    
Voxel size:                           
  x = 0.518916129032258 microns       
  y = 0.51891610619469 microns        
  z = 1 microns                       
Bounding box (microns):               
  x = 0, y = 0, z = 0,                
  x = 627.3696, y = 293.1876, z = 173.
Description:                          

I also extraced the NRRD header of the original JRC2018U reference NRRD file (data-raw/RC2018_UNISEX_20x_HR.nrrd):

NRRD0004
# Created by Nrrd_Writer at Thu Nov 29 15:08:01 EST 2018
type: uint16
encoding: gzip
endian: big
dimension: 3
sizes: 1210 566 174
space dimension: 3
space directions: (0.5189161,0,0) (0,0.5189161,0) (0,0,1.0)
space units: "microns" "microns" "microns"

This is the templatebrain object I added to data-raw/jrc2018.R, based on JRC2018F:

JRC2018U <-
  as.templatebrain('data-raw/JRC2018_UNISEX_20x_HR.nrrd',
    regName = 'JRC2018U',
    type = 'Average template brain',
    sex = 'U',
    doi = 'https://doi.org/10.1101/376384',
    description="Average template brain constructed from JRC2018F and JRC2018M."
  )
use_data(JRC2018U, overwrite = T

This didn't work though, the JRC2018U templatebrain wasn't available after installing a new version of this package. I likely forgot to add something, but figured this might be easier solvable here. Also, I am not sure the meta information above is correct, I merely guessed what it could be.

Seems to me that we should really have something like

nat.refbrain

for the generic functionality and then another package for the fly stuff since we could have e.g. fish brains as well.

This is now of particular interest as it is being used as the endpoint of a bridging registration to the FAFB whole adult brain EM volume. It is also widely used for light data at Janelia.

grDevices is a base package so we can't mask that function

Being told that the process may take some time after it has finished is not particularly useful...

Hi, I am a newer in R. I ran it in Windows. When I follow the instructions to install natverse, I can't install some packages(elmr,flycircuit,nat.jrcbrains) because of nat.flybrains is not installed.
The error is as follows:

Error in as.templatebrain.character("data-raw/JRC2018_MALE_38um_iso_16bit.nrrd",  : 
  x does not specify a valid path!
Error: unable to load R code in package 'nat.flybrains'
Execution halted
ERROR: lazy loading failed for package 'nat.flybrains'

As a result, there is no 'natverse' package, I can't use 'library(natverse)'
Could anyone help me? I would appreciate it.

It would be useful to be able to do, for example,

xform_brain(object, template1, template2, template3)

to bridge object from template1 to template3 via template2, rather than

xform_brain(xform_brain(object, template1, template2),  template2, template3)

https://github.com/jefferislab/nat.flybrains/blob/f293ff05823bd14f5b6a5cd5bc3bf2096cda31c2/R/DATA-Drosophilids.r#L35

Looks like it should be http://dx.doi.org/10.5281/zenodo.10594

Rather than have an S4 method that works out whether a bridging or mirroring registration should be performed, with the associated documentation issues, have two methods, xform_brain() and mirror_brain() that are completely decoupled from xform() (for method signature purposes) and that are as clear as possible with regard to which brain is the template, which is the reference, etc.

These would normally be registrations that would be relevant to the sample space.

e.g. you might want to do

xform_brain("unregistered.nrrd", sample=IS2, ref=JFRC2, samplereg="IS2_unregistered_warp.list")

m=as.mesh3d(subset(IS2NP.surf,'MB_ML_R'))

has a small extra volume that causes a problem with pointsinside inappropriately reporting that points in the LH_L are inside that area.

maybe could check if any points that are a little bit outside this volume are inside other volumes as a quality control.

see https://github.com/VirtualFlyBrain/DrosAdultVNSdomains/blob/master/template/Neuropil_LPS.nrrd. This in theory is the current "best" VNC template at Janelia and has been used for a bunch of registrations. Reference is https://www.biorxiv.org/content/early/2017/04/26/122952