generate dps files for Gal4 images

[Michael Kunst]

Hi Greg,

I have a large set of Gal4 expression pattern for larval zebrafish and I would like to convert them to dotprops so I can search for lines that have a specific neuron type using NBLAST. I already thresholded the image, skeletonized it and saved it as nrrd. How do I now convert the .nnrd file into a dotprop object?

Best,

Michael

[Greg Jefferis]

Dear Michael,

I have a large set of Gal4 expression pattern for larval zebrafish and I would like to convert them to dotprops so I can search for lines that have a specific neuron type using NBLAST. I already thresholded the image, skeletonized it and saved it as nrrd. How do I now convert the .nnrd file into a dotprop object?

That’s great. I’ll be very interested to hear how the search works. You’ve done the difficult part. Here is some sample code:

ff = dir(pattern = "nrrd$")

# it's a good id to set this to some kind of ifentifier for each line

names(ff) <- tools::file_path_sans_ext(basename(ff))

# choice of k may depend somewhat on spatial scale of branches etc in

# your expression patterns

gal4s=nlapply(ff[1:3], dotprops, k=5)

# you can add additional metadata to the neuronlist object like so

gal4s[,'id']=names(gal4s)

gal4s[,]=merge(gal4s[,], metadata_table)

To find out more about neuronlist objects (the wrapper for multiple neurons or expression patterns), see http://jefferis.github.io/nat/articles/neurons-intro.html.

Best wishes,

Greg.

[Michael Kunst]

Dear Greg,

Thanks a lot, it works. I will convert a test set of Gal4 lines to dotprops and keep you posted about the success. 

Best,

Michael