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Synaptograms

This docker image uses neurodata's BOSS to download regions
for plotting in synaptograms. You will need a boss
configuration file named neurodata.conf that looks like this

[Default]
protocol = https
host = api.boss.neurodata.io
token = your_token_here

Your token can be obtained here.

You will also need a file named config.conf structured as follows with
your specific information filled in. Below is an example using the
collman14 dataset.

#### For getting synapse cubes

## Boolean for running get cube code
getCube=true

## collection id
COLL='collman'

## experiment id
EXP='collman14v2'

## coordinate frame id
FM='collman_collman14v2'

## buffer size in x y z
BUFF='108 108 5'      

## file of locations in x,y,z without header
LOC='xyzTesting.csv' 

## output filename 
OUT='testing.csv'

## boss configuration filename with token
CON='neurodata.conf'


#### For plotting synaptograms

## Boolean for running synaptogram code after cubes have downloaded
genSynaptograms=true

## cubes file
SYIN='testing.csv.h5'

## output file prefix
SYOUT='synTest'

## parameters file
PARAM='params.csv'

params.csv

The parameters file should be in csv format with a header that matches
the feature names.
The means and standard deviations are used to scale each feature F0
value before plotting.

"names" bIIItubulin ... VGluT1 EM10K
"colors" "blue" ... "green" "white"
"means" 2120026.746139 ... 1396392.87548263 0
"sds" 848444.631131951 ... 524801.872574875 NA

Usage

docker run -v <working directory with config files>:/home/ -t neurodata/synaptograms

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neurodata