ArticleFrontiers in neuroinformatics2014
Pydpiper: a flexible toolkit for constructing novel registration pipelines.
Article in Frontiers in neuroinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed.
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- Parental high-fat/high-sugar diets and their lasting impact on brain development in offspring: a longitudinal mouse MRI study.Translational psychiatry · 2025Article
- Neurodevelopmental Impacts of Ketamine and Alfaxalone Anesthesia Evaluated with Mouse MRI.Journal of the American Association for Laboratory Animal Science : JAALAS · 2025Article
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- Divergent outcomes of delta 9 - tetrahydrocannabinol (THC) in adolescence on mesocortical dopamine and cognitive development in male and female mice.Psychopharmacology · 2025Article
- A cross-species analysis of neuroanatomical covariance sex differences in humans and mice.Biology of sex differences · 2025Article
- Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 3-Ex vivo imaging: Data processing, comparisons with microscopy, and tractography.Magnetic resonance in medicine · 2025Review
- Altered adult brain morphology in a mouse model of late-onset fetal growth restriction.Imaging neuroscience (Cambridge, Mass.) · 2025Article
- Open-source platforms to investigate analytical flexibility in neuroimaging.Imaging neuroscience (Cambridge, Mass.) · 2025Article
- Sex chromosomes and hormones independently influence healthy brain development but act similarly after cranial radiation.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
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- TDP-43-M323K causes abnormal brain development and progressive cognitive and motor deficits associated with mislocalised and increased levels of TDP-43.Neurobiology of disease · 2024Article
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- Perinatal exposure to atazanavir-based antiretroviral regimens in a mouse model leads to differential long-term motor and cognitive deficits dependent on the NRTI backbone.Frontiers in molecular neuroscience · 2024Article
1 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Using neuroimaging technologies to elucidate the relationship between genotype and phenotype and brain and behavior will be a key contribution to biomedical research in the twenty-first century. Among the many methods for analyzing neuroimaging data, image registration deserves particular attention due to its wide range of applications. Finding strategies to register together many images and analyze the differences between them can be a challenge, particularly given that different experimental designs require different registration strategies. Moreover, writing software that can handle different types of image registration pipelines in a flexible, reusable and extensible way can be challenging. In response to this challenge, we have created Pydpiper, a neuroimaging registration toolkit written in Python. Pydpiper is an open-source, freely available software package that provides multiple modules for various image registration applications. Pydpiper offers five key innovations. Specifically: (1) a robust file handling class that allows access to outputs from all stages of registration at any point in the pipeline; (2) the ability of the framework to eliminate duplicate stages; (3) reusable, easy to subclass modules; (4) a development toolkit written for non-developers; (5) four complete applications that run complex image registration pipelines "out-of-the-box." In this paper, we will discuss both the general Pydpiper framework and the various ways in which component modules can be pieced together to easily create new registration pipelines. This will include a discussion of the core principles motivating code development and a comparison of Pydpiper with other available toolkits. We also provide a comprehensive, line-by-line example to orient users with limited programming knowledge and highlight some of the most useful features of Pydpiper. In addition, we will present the four current applications of the code.
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