Scalable Brain Composer

Questions

Is it safe to view private data with SBA composer?

How to find brain regions by point-and-click?

How to find brain regions by name?

How to 3D print structures from SBA composer?

Application Program Interface (API) related

How to generate a link to SBA composer showing particular brain regions?

How to generate a link to SBA composer showing quantitative data mapped to brain region colors?

How to generate a link to SBA composer showing my own 2d or 3d image?

How to generate a link to SBA composer showing my own 3d graphics object?

Answers

Is it safe to view private/confidential data with SBA composer?

Yes this is safe, as long as the data is imported via the button 'Import file from my computer'. These files are processed on your own computer/browser, there is no data-exchange with the SBA server at all.

If you share data with colleagues via the API using any of the methods that involve data-URLs, then it is technically unavoidable that data passes through the SBA server. Beyond the default caching and logging behaviour of our web server, the data is not processed, analyzed or stored by us in any way. The page also runs a google-analytics script to count visitors. This script has as a side effect that visited URLs get sent to Google to collect statistics.

How to find brain regions by point-and-click?

To find brain regions by point and click, you first need to load 'something' into the viewer. For example, load one of the 'atlas imaging modalities', activate 'saggital view' and click on a point of interest. You see a message about the coordinate that you clicked and the corresponding brain region, which you can subsequently display as a 3d model. Note: this feature only works on non-transparent objects. To find brain regions at the whole brain surface, make the 'whole brain'-region visible and set its opacity to 1.

How to find brain regions by name?

Enter the first characters of the brain region full name or abbreviation in the search field on top of the list of brain regions in the navigation panel. A popup menu shows a list of matching brain regions with the typed characters in bold. On select, the navigation tree unfolds and highlights the selected brain region.

How to 3D print structures from SBA composer?

There is no built-in functionality yet, but you can use the open source software "Meshlab".
Load a single brain structure into SBA composer, then Export to X3D.
In Meshlab, use "Import Mesh" from the file menu to load the X3D. Then use "Export Mesh" to export to STL.
STL is a format that nearly all 3D printers can process.

API: How to generate a link to SBA composer showing particular brain regions?

Use the following URL template:
https://scalablebrainatlas.incf.org/composer?template=A&scene={"regions":{ "R1":["rgb1",a1], "R2":["rgb2",a2], etc. },"background":"BG"}
where

A is the atlas template-id, like ABA_v3 for Allen Brain Atlas version 3.
R1 is region 1 to display.
rgb1 is the color of R1, in 6-character hex Red-Green-Blue format, like FFFF00 for yellow.
a1 is the alpha (opacity) of R1, where 1 is opaque and 0 is fully transparent.
BG is the background color, in 6-character hex Red-Green-Blue format, like 000055 for dark blue.

Example: https://scalablebrainatlas.incf.org/composer/?template=ABA_v3&scene={regions:{"root":["BBBBBB",0.3],"MO":["1F9C59",1]},background:"000055"}

API: How to generate a link to SBA composer showing quantitative data mapped to brain region colors?

Use the following URL template:
https://scalablebrainatlas.incf.org/composer?template=A&scene={"regions":{ "R1":y1, "R2":y2, etc. },"background":"BG","colormap":[["rgb1",s1], ["rgb2",s2], etc.]}
where

A is the atlas template-id, like ABA_v3 for Allen Brain Atlas version 3.
R1 is region 1 to display.
y1 is the quantitative value used in conjunction with the colormap to paint region R1.
BG is the background color, in 6-character hex Red-Green-Blue format, like 000066 for dark blue.
rgb1 is the color at the first stop s1 of the colormap, rgb2 is the color at value s2, etc. In between the stops, the colormap is linearly interpolated. So a simple colormap from black to red is: [["000000",0.0],["FF0000",1.0]]

Example: https://scalablebrainatlas.incf.org/composer/?template=ABA_v3&scene={regions:{"root":["BBBBBB",0.3],"MO":0.2,"SS":0.8},background:"000055",colormap:[["000000",0.0],["FF0000",1.0]]}

API: How to generate a link to SBA composer showing my own 2d or 3d image?

Currenty, only gzipped nifti volume files are supported for this feature. Use the following URL template:
https://scalablebrainatlas.incf.org/composer?template=A&scene={"imports":{"name1":"url1", "name2":"url2", etc.}}
where

A is the atlas template-id, like ABA_v3 for Allen Brain Atlas version 3.
name1 is the name of the first imported file.
url1 is the URL of the first imported file. The URL can be a weblink or a data-URL. If it is a weblink, than the server that hosts the data must be configured for cross-origin resource sharing. If the data file is small (below 8k), it can be passed as a data-URL. Here is the code to generate such a data-URL from file 'mydata.nii.gz' in python:
```
def gznii2dataurl(filename):
  prefix = 'data:image/gznii;base64,'
  with open(filename,'rb') as fp:
    contents = fp.read()
  import base64
  return prefix + base64.b64encode(contents)
```

API: How to generate a link to SBA composer showing my own 3d graphics object?

This feature is part of a future release.