BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes

doi:10.1007/s12021-023-09638-2

. 2023 Oct;21(4):637-639.

doi: 10.1007/s12021-023-09638-2. Epub 2023 Jul 3.

BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes

Thomas L Athey^{1

2}, Matthew A Wright³, Marija Pavlovic⁴, Vikram Chandrashekhar⁵, Karl Deisseroth^{4

6

7

8}, Michael I Miller^{5

9

10

11}, Joshua T Vogelstein^{5

9

10

11}

Affiliations

¹ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA. tathey1@jhu.edu.
² Institute of Computational Medicine, Johns Hopkins University, Baltimore, MD, USA. tathey1@jhu.edu.
³ Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA.
⁴ Department of Bioengineering, Stanford University, Stanford, CA, USA.
⁵ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
⁶ CNC Program, Stanford University, Stanford, CA, USA.
⁷ Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
⁸ Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
⁹ Institute of Computational Medicine, Johns Hopkins University, Baltimore, MD, USA.
¹⁰ Center for Imaging Science, Johns Hopkins University, Baltimore, MD, USA.
¹¹ Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA.

PMID: 37394568
PMCID: PMC10582119
DOI: 10.1007/s12021-023-09638-2

BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes

Thomas L Athey et al. Neuroinformatics. 2023 Oct.

. 2023 Oct;21(4):637-639.

doi: 10.1007/s12021-023-09638-2. Epub 2023 Jul 3.

Authors

Thomas L Athey^{1

2}, Matthew A Wright³, Marija Pavlovic⁴, Vikram Chandrashekhar⁵, Karl Deisseroth^{4

6

7

8}, Michael I Miller^{5

9

10

11}, Joshua T Vogelstein^{5

9

10

11}

Affiliations

¹ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA. tathey1@jhu.edu.
² Institute of Computational Medicine, Johns Hopkins University, Baltimore, MD, USA. tathey1@jhu.edu.
³ Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA.
⁴ Department of Bioengineering, Stanford University, Stanford, CA, USA.
⁵ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
⁶ CNC Program, Stanford University, Stanford, CA, USA.
⁷ Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
⁸ Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
⁹ Institute of Computational Medicine, Johns Hopkins University, Baltimore, MD, USA.
¹⁰ Center for Imaging Science, Johns Hopkins University, Baltimore, MD, USA.
¹¹ Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA.

PMID: 37394568
PMCID: PMC10582119
DOI: 10.1007/s12021-023-09638-2

No abstract available

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Conflict of interest statement

M.I.M. owns a significant share of Anatomy Works with the arrangement being managed by Johns Hopkins University in accordance with its conflict of interest policies. V.C. owns a significant share of Neurosimplicity, LLC, which is a medical device and technology company focusing on medical image processing. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Figures

**Fig. 1**
BrainLine allows for efficient processing of heterogeneous whole brain fluorescence volumes. a BrainLine combines CloudReg (Chandrashekhar et al., 2021), ilastik (Berg et al., 2019) and our package, brainlit, to produce results in both quantitative (**a.i**) and visual (**a.ii-a.iii**) formats. b Example images with fluorescently labeled axon projections and arrows pointing to regions with (green) and without (red) labeled axons. c Intensity histograms of 20x20x20 voxel subvolumes located at the arrows in b. d Comparison between axon segmentation performance after training on subvolumes from different samples (heterogeneous) or the same sample (homogeneous). e Example images with fluorescently labeled cell bodies and arrows pointing to regions with (green) and without (red) labeled cell bodies. f Intensity histograms of 20x20x20 voxel subvolumes located at the arrows in e. g Comparison between soma detection performance after training on subvolumes from different brain samples (heterogeneous) or a single brain sample (homogeneous)

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Update of

BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes.
Athey TL, Wright MA, Pavlovic M, Chandrashekhar V, Deisseroth K, Miller MI, Vogelstein JT. Athey TL, et al. bioRxiv [Preprint]. 2023 Mar 1:2023.02.28.530429. doi: 10.1101/2023.02.28.530429. bioRxiv. 2023. Update in: Neuroinformatics. 2023 Oct;21(4):637-639. doi: 10.1007/s12021-023-09638-2. PMID: 36909631 Free PMC article. Updated. Preprint.

Cited by

Preserving Derivative Information while Transforming Neuronal Curves.
Athey TL, Tward DJ, Mueller U, Younes L, Vogelstein JT, Miller MI. Athey TL, et al. Neuroinformatics. 2024 Jan;22(1):63-74. doi: 10.1007/s12021-023-09648-0. Epub 2023 Nov 30. Neuroinformatics. 2024. PMID: 38036915 Free PMC article.

References

1. Berg, S., Kutra, D., Kroeger, T. et al. (2019). Ilastik: interactive machine learning for (bio)image analysis. Nature methods, 16(12):1226–1232. - PubMed
1. Chandrashekhar, V., Tward, D. J., Crowley, D. et al. (2021). Cloudreg: automatic terabyte-scale cross-modal brain volume registration. Nature methods, 18(8):845–846. - PMC - PubMed
1. Claudi, F., Tyson, A. L., Petrucco, L., et al. (2021). Visualizing anatomically registered data with brainrender. eLife, 10:e65751. - PMC - PubMed
1. Friedmann, D., Pun, A., Adams, E. L., et al. (2020). Mapping mesoscale axonal projections in the mouse brain using a 3d convolutional network. Proceedings of the National Academy of Sciences, 117(20):11068–11075. - PMC - PubMed
1. Geisa, A., Mehta, R., Helm, H. S., et al. (2021). Towards a theory of out-of-distribution learning. arXiv preprint arXiv:2109.14501

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[1] Berg, S., Kutra, D., Kroeger, T. et al. (2019). Ilastik: interactive machine learning for (bio)image analysis. Nature methods, 16(12):1226–1232. - PubMed

[2] Berg, S., Kutra, D., Kroeger, T. et al. (2019). Ilastik: interactive machine learning for (bio)image analysis. Nature methods, 16(12):1226–1232. - PubMed

[3] Chandrashekhar, V., Tward, D. J., Crowley, D. et al. (2021). Cloudreg: automatic terabyte-scale cross-modal brain volume registration. Nature methods, 18(8):845–846. - PMC - PubMed

[4] Chandrashekhar, V., Tward, D. J., Crowley, D. et al. (2021). Cloudreg: automatic terabyte-scale cross-modal brain volume registration. Nature methods, 18(8):845–846. - PMC - PubMed

[5] Claudi, F., Tyson, A. L., Petrucco, L., et al. (2021). Visualizing anatomically registered data with brainrender. eLife, 10:e65751. - PMC - PubMed

[6] Claudi, F., Tyson, A. L., Petrucco, L., et al. (2021). Visualizing anatomically registered data with brainrender. eLife, 10:e65751. - PMC - PubMed

[7] Friedmann, D., Pun, A., Adams, E. L., et al. (2020). Mapping mesoscale axonal projections in the mouse brain using a 3d convolutional network. Proceedings of the National Academy of Sciences, 117(20):11068–11075. - PMC - PubMed

[8] Friedmann, D., Pun, A., Adams, E. L., et al. (2020). Mapping mesoscale axonal projections in the mouse brain using a 3d convolutional network. Proceedings of the National Academy of Sciences, 117(20):11068–11075. - PMC - PubMed

[9] Geisa, A., Mehta, R., Helm, H. S., et al. (2021). Towards a theory of out-of-distribution learning. arXiv preprint arXiv:2109.14501

[10] Geisa, A., Mehta, R., Helm, H. S., et al. (2021). Towards a theory of out-of-distribution learning. arXiv preprint arXiv:2109.14501

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BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes

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BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes

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