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)

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
yxyzt=β0+β1x1+β2x2+β3x3+...+βnxny_{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
yxyzt=β0+β1x1+β2x2+β3x3+...+βnxny_{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}}
yxyzt=β0+βcocainexcocainey_{xyzt} = \beta_0 + \beta_{\text{cocaine}}x_{\text{cocaine}}
+ \beta_{\text{pain}}x_{\text{pain}}
+βpainxpain + \beta_{\text{pain}}x_{\text{pain}}
+ \beta_{\text{attend}}x_{\text{attend}}
+βattendxattend + \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
yxyzt=β0+β1x1+β2x2+β3x3+...+βnxny_{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}}
yxyzt=β0+βcocainexcocainey_{xyzt} = \beta_0 + \beta_{\text{cocaine}}x_{\text{cocaine}}
+ \beta_{\text{pain}}x_{\text{pain}}
+βpainxpain + \beta_{\text{pain}}x_{\text{pain}}
+ \beta_{\text{attend}}x_{\text{attend}}
+βattendxattend + \beta_{\text{attend}}x_{\text{attend}}
+ \beta_{\text{cocaine}\times\text{attend}}x_{\text{cocaine}}x_{\text{attend}}
+βcocaine×attendxcocainexattend + \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}
AP×ML×DV216px×178px×178px\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 sections×20480px×12288px 100\text{ sections} \times 20480\text{px} \times 12288\text{px}

neurosynth.org

Vector graphics in neuroscience

?

Vector graphics in neuroscience

Bakker, Tiesinga, Kötter (2015) Neuroinformatics

Why does it matter?

Raster graphics:

Vector graphics:

Neuroanatomical Information Systems (NIS)

Neuroanatomical Information Systems (NIS)

Scale-invariant atlas

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
			c95.865,9.001,190.91,18.245,284.627,32.502c173.902,26.492,342.602,71.927,514.549,126.6l-1.422
                        ,4.347l-45.686,128.252c-235.213-55.725-470.736-95.438-693.863-133.773c-22.857-3.911-47.367-8.384-73.162-                      
                        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-         
                        410.305-c25.793,4.744,50.307,9.217,73.162,13.127c223.127,38.337,458.65,78.049,693.867,133.773l-151.455,424.957
			C6461.049,1392.584,6397.912,1382.523,6339.01,1370.213z"/>
	</g>
</g>
</svg>

Scale-invariant atlas

Scale-invariant atlas

Git

Anatomy as a social construction

Git

Anatomy as a

developmental process.

McKenna (2016) Science

lineage tracing by combinatorial and cumulative genome editing

Web based interface

Web based interface

Web based interface

Web based interface

Segmentation

Segmentation

Segmentation

Segmentation

Segmentation

Registration

Registration

Registration

Kazemi & Sullivan (2014); Bookstein (1989)

Registration

Kazemi & Sullivan (2014)

One Millisecond Face Alignment

Ensemble of Regression Trees

Dlib C++ library

Segmentation and registration

Connectivity tracing

Connectivity tracing

Pasteur (1885)

Connectivity tracing

SAD B19 (Rhabdoviridae)

(-)ssRNA 11-15 kb

Cytoplasmic replication

transcription gradient

Connectivity tracing

Schnell et al. (2010)

Connectivity tracing

Cell-type specific retrograde connectivity tracing

Connectivity tracing

Connectivity tracing

Connectivity tracing

Connectivity tracing

Decoding motor activity

Decoding motor activity

Decoding motor activity

Decoding motor activity

Decoding motor activity

Cell types

Cell types

mRNA

mRNA

mRNA

Scaling laws

Scaling laws

Scaling laws

Stevens (1999) Nature

Scaling laws

Scaling laws

Thank you for your attention

Histohub AB is hiring!

  • C++, GPU, OpenCV/VIPS
  • JavaScript, GoLang, MongoDB

Barcoding connections

Barcoding connections

What is needed?

A method that:

  • uniquely labels single postsynaptic neurons
  • uniquely labels their presynaptic partners
  • uniquely label axons and trace them

Barcoding connections

What is needed?

A method that:

  • uniquely labels single postsynaptic neurons
  • uniquely labels their presynaptic neurons
  • uniquely label axons and trace them

 

low MOI barcoded rabies virus
low MOI barcoded rabies virus

impossible with todays technology

Barcoding connections

mesoscale
connectivity

31'295 neurons

single neuronal projections
+target
+strength

MAPseq: barcoded sindbis virus
                  for projection mapping

Barcoding connections

Barcoding connections

Sindbis virus (Togaviridae)

(+)ssRNA 9.7-11.8 kb

Cytoplasmic replication

 

  • Non-structural polyprotein
    • processed by host and viral proteases
  • Structural polyprotein
    • expressed through a subgenomic mRNA

Barcoding connections

SAD B19 (Rhabdoviridae)

(-)ssRNA 11-15 kb

Cytoplasmic replication
located to Negri Bodies

G RABV

N RABV

Ménager et al. 2009; Lafon et al. 1985

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