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