INCF

Neuroanatomical
Information
Systems

daniel.furth@ki.se
meletis lab, Histohub AB
karolinska institutet, SWEDEN

A web-based and open source stereotactic mouse brain atlas.
Ability to annotate and query.
>800'000 neurons in 21 brains.
Cell-type specific connectivity tracing in five different Cre-lines (D1, D2, ChAT, Camk2, Gad2).
Mapping out connectivity of ~160'000 neurons in the corticostriatal pathway (~0.23% of the entire mouse brain).
Simultaneous segmentation of cell bodies and fiber tracts.
Works with FP, IHC, ISH.
Reconstructing an entire brain in 20 min.
Compression of large TIFF files (>500 Mb) to ~20 Mb.
Sharing data and images easy over the web.

wholebrainsoftware.org/cms

openbrainmap.org

Geographical Information Systems (GIS)

Raster graphics in neuroscience

Freeman et al. (‎2014) Nature Methods

Raster graphics in neuroscience

8204 citations

Friston et al. (1994) Human Brain Mapping

Raster graphics in neuroscience

y_{xyzt} = \beta_0 + \beta_1x_1 + \beta_2x_2 + \beta_3x_3 + ... + \beta_nx_n

y_{xyzt} = \beta_0 + \beta_1x_1 + \beta_2x_2 + \beta_3x_3 + ... + \beta_nx_n

8204 citations

Friston et al. (1994) Human Brain Mapping

Raster graphics in neuroscience

y_{xyzt} = \beta_0 + \beta_1x_1 + \beta_2x_2 + \beta_3x_3 + ... + \beta_nx_n

y_{xyzt} = \beta_0 + \beta_1x_1 + \beta_2x_2 + \beta_3x_3 + ... + \beta_nx_n

y_{xyzt} = \beta_0 + \beta_{\text{cocaine}}x_{\text{cocaine}}

y_{xyzt} = \beta_0 + \beta_{\text{cocaine}}x_{\text{cocaine}}

+ \beta_{\text{pain}}x_{\text{pain}}

+ \beta_{\text{pain}}x_{\text{pain}}

+ \beta_{\text{attend}}x_{\text{attend}}

+ \beta_{\text{attend}}x_{\text{attend}}

Raster graphics in neuroscience

y_{xyzt} = \beta_0 + \beta_1x_1 + \beta_2x_2 + \beta_3x_3 + ... + \beta_nx_n

y_{xyzt} = \beta_0 + \beta_1x_1 + \beta_2x_2 + \beta_3x_3 + ... + \beta_nx_n

y_{xyzt} = \beta_0 + \beta_{\text{cocaine}}x_{\text{cocaine}}

y_{xyzt} = \beta_0 + \beta_{\text{cocaine}}x_{\text{cocaine}}

+ \beta_{\text{pain}}x_{\text{pain}}

+ \beta_{\text{pain}}x_{\text{pain}}

+ \beta_{\text{attend}}x_{\text{attend}}

+ \beta_{\text{attend}}x_{\text{attend}}

+ \beta_{\text{cocaine}\times\text{attend}}x_{\text{cocaine}}x_{\text{attend}}

+ \beta_{\text{cocaine}\times\text{attend}}x_{\text{cocaine}}x_{\text{attend}}

Raster graphics in neuroscience

food, weight, obese, eating, foods, obesity, reward, energy, hunger, calorie, intake, bmi, mass, body, satiety, normal, cues, responsivity, women, overweight, appetite, individuals, caloric, increases, lean, index, fat, pictures, gain, hungry, images, bed, palatable, craving, receipt, water, overeating, meal, kg, motivation

\text{AP}\times\text{ML}\times\text{DV} \quad 216\text{px} \times 178\text{px} \times 178\text{px}

\text{AP}\times\text{ML}\times\text{DV} \quad 216\text{px} \times 178\text{px} \times 178\text{px}

100\text{ sections} \times 20480\text{px} \times 12288\text{px}

100\text{ sections} \times 20480\text{px} \times 12288\text{px}

neurosynth.org

Vector graphics in neuroscience

Bakker, Tiesinga, Kötter (2015) Neuroinformatics

Why does it matter?

Raster graphics:

Vector graphics:

Neuroanatomical Information Systems (NIS)

Scale-invariant atlas

<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
	 width="9744.01px" height="6823.46px" viewBox="0 0 9744.01 6823.46" enable-background="new 0 0 9744.01 6823.46"
	 xml:space="preserve">
<g transform="scale(1.0)">
	<g id="_x31_82599275" transform=" scale(1.0, 1.0)">
		
		<path id="_x31_82599358" fill="none" stroke="#010101" stroke-width="64" d="M5921.469,690.055
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                        13.126L5921.469,690.055z"/>
		<path id="_x31_82599357" fill="none" stroke="#010101" stroke-width="64" d="M6339.01,1370.213
			c-115.707-24.292-298.684-59.227-409.08-100.604c-20.678-7.751-42.713-16.073-65.647-24.374l-0.001-0.075l42.232-         
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