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. 2014 Oct;11(10):982-4.
doi: 10.1038/nmeth.3125.

Neuronal morphometry directly from bitmap images

Tiago A Ferreira  1 , Arne V Blackman  2 , Julia Oyrer  2 , Sriram Jayabal  3 , Andrew J Chung  1 , Alanna J Watt  4 , P Jesper Sjöström  5 , Donald J van Meyel  6
Affiliations

Neuronal morphometry directly from bitmap images

Tiago A Ferreira et al. Nat Methods. 2014 Oct.
No abstract available

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Conflict of interest statement

The authors declare no competing financial interests.

Figures

Figure 1
Figure 1
Sholl Analysis provides metrics of complex arbors in Brainbow-expressing mice and classifies cortical interneurons, without tracing or reconstruction. (a) Maximum-intensity projections of tiled image stacks from cerebellar cortex. Reconstructions depict the range of morphologies among the seven Brainbow-labeled Purkinje neurons (i–vii) that were quantified. (b) Maximum-intensity projection of the cell highlighted in a. Original stacks were preprocessed (b) to reduce background and eliminate signal from adjacent cells. (c) Linear Sholl plots comparing results for bitmap images to those from manual reconstructions for the seven Purkinje neurons. Dots show the mean, shading the s.e.m., and solid lines the best-fit polynomials (9th order). (d) Metrics (mean ± s.e.m.) calculated for bitmap images versus manual reconstructions for the seven Purkinje neurons. P values obtained by Student’s t-test using Holm-Šídák correction. (e,f) Maximum-intensity projections of dye-loaded PV interneurons of type 1 (e) or type 2 (f). Original stacks were preprocessed to reduce background and eliminate the signal from the recording pipette (*). (g) Dendrogram of Ward’s hierarchical clustering of PV interneurons based on Sholl Analysis metrics (see supplementary Fig. 4). Dotted line marks the 25% linkage best cut, and circles note correct PV subtype identities based on manual reconstructions and analysis of axonal projections. (h) Linear Sholl plots for type 1 (n = 5) versus type 2 (n = 7) PV interneurons, showing the mean (solid lines) and s.e.m. (shaded regions). Dashed lines show best-fit polynomials (type 1, 8th degree; type 2, 6th degree). Scale bars: a,b, 40 μm; e,f, 100 μm. bitmap images is an efficient method for quantification of neuronal arbors and classification of cells.
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