Bi-channel Image Registration and Deep-learning Segmentation (BIRDS) for efficient, versatile 3D mapping of mouse brain
Abstract
We have developed an open-source software called BIRDS (bi-channel image registration and deep-learning segmentation) for the mapping and analysis of 3D microscopy data and applied this to the mouse brain. The BIRDS pipeline includes image pre-processing, bi-channel registration, automatic annotation, creation of a 3D digital frame, high-resolution visualization, and expandable quantitative analysis. This new bi-channel registration algorithm is adaptive to various types of whole-brain data from different microscopy platforms and shows dramatically improved registration accuracy. Additionally, as this platform combines registration with neural networks, its improved function relative to other platforms lies in the fact that the registration procedure can readily provide training data for network construction, while the trained neural network can efficiently segment incomplete/defective brain data that is otherwise difficult to register. Our software is thus optimized to enable either minute-timescale registration-based segmentation of cross-modality, whole-brain datasets or real-time inference-based image segmentation of various brain regions of interest. Jobs can be easily submitted and implemented via a Fiji plugin that can be adapted to most computing environments.
Data availability
The Allen CCF is open access and available with related tools at https://atlas.brain-map.org/The datasets (Brain1~5) have been deposited in Dryad at https://datadryad.org/stash/share/4fesXcJif0L2DnSj7YmjREe37yPm1bEnUiK49ELtALgThe code and plugin can be found at the following link:https://github.com/bleach1by1/BIRDS_pluginhttps://github.com/bleach1by1/birds_reghttps://github.com/bleach1by1/birds_dl.githttps://github.com/bleach1by1/BIRDS_demoAll data generated or analysed during this study are included in the manuscript. Source data files have been provided for Figures 1, 2, 3, 4, 5 and Figure 2-figure supplement 3,4; Figure 5-figure supplement 2,3
-
Brain 1 and 2Dryad Digital Repository.
-
Brain 5Dryad Digital Repository.
-
Brain 3 and 4Dryad Digital Repository.
Article and author information
Author details
Funding
National Key R&D program of China (2017YFA0700501)
- Peng Fei
National Natural Science Foundation of China (21874052)
- Peng Fei
National Natural Science Foundation of China (31871089)
- Yunyun Han
Innovation Fund of WNLO
- Peng Fei
Junior Thousand Talents Program of China
- Peng Fei
Junior Thousand Talents Program of China
- Yunyun Han
The FRFCU (HUST:2172019kfyXKJC077)
- Yunyun Han
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2021, Wang et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 6,177
- views
-
- 683
- downloads
-
- 18
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Further reading
-
- Computational and Systems Biology
Organ function declines with age, and large-scale transcriptomic analyses have highlighted differential aging trajectories across tissues. The mechanism underlying shared and organ-selective functional changes across the lifespan, however, still remains poorly understood. Given the central role of mitochondria in powering cellular processes needed to maintain tissue health, we therefore undertook a systematic assessment of respiratory activity across 33 different tissues in young (2.5 months) and old (20 months) mice of both sexes. Our high-resolution mitochondrial respiration atlas reveals: (1) within any group of mice, mitochondrial activity varies widely across tissues, with the highest values consistently seen in heart, brown fat, and kidney; (2) biological sex is a significant but minor contributor to mitochondrial respiration, and its contributions are tissue-specific, with major differences seen in the pancreas, stomach, and white adipose tissue; (3) age is a dominant factor affecting mitochondrial activity, especially across most brain regions, different fat depots, skeletal muscle groups, eyes, and different regions of the gastrointestinal tract; (4) age effects can be sex- and tissue-specific, with some of the largest effects seen in pancreas, heart, adipose tissue, and skeletal muscle; and (5) while aging alters the functional trajectories of mitochondria in a majority of tissues, some are remarkably resilient to age-induced changes. Altogether, our data provide the most comprehensive compendium of mitochondrial respiration and illuminate functional signatures of aging across diverse tissues and organ systems.