RNA Detection

incorporates information from all genes mitigates against this

limitation.

8.Scoring the mismatches between scRNAseq and spatial ref-

erence: symmetric vs asymmetric penalization scheme:For

the correspondence score calculation, the user can choose

between two penalization schemes: symmetric and asymmetric.

The asymmetric scheme only penalizes mismatches when the

gene is expressed in the RNA-seq data and not in the reference

atlas, while the symmetric scheme also penalizes similarly mis-

matches that arise when a gene is not expressed in the RNA-seq

but expressed in the reference atlas.

For symmetrical penalization, specificity scores need to be

computed on the whole reference dataset. This can be done in

the same way as described for the single cell data. Since the

reference dataset is binarized, the resulting specificity score for

each gene will fall in the interval [0,1] thus suppressing the

need to transform these data. In this context the scoring system

becomes:

sc,ref¼

XM

m¼ 1

frc,m ec,m;eref,m



with

frc,m ec,m;eref,m



¼

trc,m



, ec,m¼eref,m¼ 1

trc,m



, ec,m¼1, eref,m¼ 0

r^0 ref,m, ec,m¼0, eref,m¼ 1

0, Otherwise

8

>>

<

>>

:

and

trc,m



¼

rc,m

1 þrc,m

and

r^0 ref,m¼

D^0 ref,m

1

N

PN

a¼ 1 D

0

a,m

With ||Ref|| xMread count matrix,D^0 , whereD^0 ref,mis the

binary expression in voxel ref for genem.Nis the number of

voxels in the reference atlas.

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   P, Cardona A (2012) Fiji: an open-source

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Methods 9(7):676–682. doi:10.1038/nmeth.

2019

2. Yoo TS, Ackerman MJ, Lorensen WE, Schroe-
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