CelltrackR: An R package for fast and flexible analysis of immune cell migration data
Visualization of cell migration via time-lapse microscopy has greatly advanced our understanding of the immune system. However, subtle differences in migration dynamics are easily obscured by biases and imaging artifacts. While several analysis methods have been suggested to address these issues, an...
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| Format: | Article |
| Language: | English |
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Elsevier
2021-10-01
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| Series: | ImmunoInformatics |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2667119021000033 |
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| author | Inge M.N. Wortel Annie Y. Liu Katharina Dannenberg Jeffrey C. Berry Mark J. Miller Johannes Textor |
| author_facet | Inge M.N. Wortel Annie Y. Liu Katharina Dannenberg Jeffrey C. Berry Mark J. Miller Johannes Textor |
| author_sort | Inge M.N. Wortel |
| collection | DOAJ |
| description | Visualization of cell migration via time-lapse microscopy has greatly advanced our understanding of the immune system. However, subtle differences in migration dynamics are easily obscured by biases and imaging artifacts. While several analysis methods have been suggested to address these issues, an integrated tool implementing them is currently lacking. Here, we present celltrackR, an R package containing a diverse set of state-of-the-art analysis methods for (immune) cell tracks. CelltrackR supports the complete pipeline for track analysis by providing methods for data management, quality control, extracting and visualizing migration statistics, clustering tracks, and simulating cell migration. CelltrackR supports the analysis of both 2D and 3D cell tracks. CelltrackR is an open-source package released under the GPL-2 license, and is freely available on both GitHub and CRAN. Although the package was designed specifically for immune cell migration data, many of its methods will also be of use in other research areas dealing with moving objects. |
| format | Article |
| id | doaj-art-7a27101ba9bd4ea28a45232b473f4ba8 |
| institution | Kabale University |
| issn | 2667-1190 |
| language | English |
| publishDate | 2021-10-01 |
| publisher | Elsevier |
| record_format | Article |
| series | ImmunoInformatics |
| spelling | doaj-art-7a27101ba9bd4ea28a45232b473f4ba82025-01-10T04:38:17ZengElsevierImmunoInformatics2667-11902021-10-011100003CelltrackR: An R package for fast and flexible analysis of immune cell migration dataInge M.N. Wortel0Annie Y. Liu1Katharina Dannenberg2Jeffrey C. Berry3Mark J. Miller4Johannes Textor5Corresponding author.; Department of Tumor Immunology, Radboud Institute of Molecular Life Sciences, Geert Grooteplein 26-28, Nijmegen, the NetherlandsDivision of Infectious Diseases, Washington University School of Medicine, 4523 Clayton Avenue, St. Louis, USAInstitute for Theoretical Computer Science, Universität zu Lübeck, Ratzeburger Allee 160, Lübeck, GermanyDivision of Infectious Diseases, Washington University School of Medicine, 4523 Clayton Avenue, St. Louis, USADivision of Infectious Diseases, Washington University School of Medicine, 4523 Clayton Avenue, St. Louis, USADepartment of Tumor Immunology, Radboud Institute of Molecular Life Sciences, Geert Grooteplein 26-28, Nijmegen, the NetherlandsVisualization of cell migration via time-lapse microscopy has greatly advanced our understanding of the immune system. However, subtle differences in migration dynamics are easily obscured by biases and imaging artifacts. While several analysis methods have been suggested to address these issues, an integrated tool implementing them is currently lacking. Here, we present celltrackR, an R package containing a diverse set of state-of-the-art analysis methods for (immune) cell tracks. CelltrackR supports the complete pipeline for track analysis by providing methods for data management, quality control, extracting and visualizing migration statistics, clustering tracks, and simulating cell migration. CelltrackR supports the analysis of both 2D and 3D cell tracks. CelltrackR is an open-source package released under the GPL-2 license, and is freely available on both GitHub and CRAN. Although the package was designed specifically for immune cell migration data, many of its methods will also be of use in other research areas dealing with moving objects.http://www.sciencedirect.com/science/article/pii/S2667119021000033Immune cell migrationCell track analysisTwo-photon imagingModelingMotion statistics |
| spellingShingle | Inge M.N. Wortel Annie Y. Liu Katharina Dannenberg Jeffrey C. Berry Mark J. Miller Johannes Textor CelltrackR: An R package for fast and flexible analysis of immune cell migration data ImmunoInformatics Immune cell migration Cell track analysis Two-photon imaging Modeling Motion statistics |
| title | CelltrackR: An R package for fast and flexible analysis of immune cell migration data |
| title_full | CelltrackR: An R package for fast and flexible analysis of immune cell migration data |
| title_fullStr | CelltrackR: An R package for fast and flexible analysis of immune cell migration data |
| title_full_unstemmed | CelltrackR: An R package for fast and flexible analysis of immune cell migration data |
| title_short | CelltrackR: An R package for fast and flexible analysis of immune cell migration data |
| title_sort | celltrackr an r package for fast and flexible analysis of immune cell migration data |
| topic | Immune cell migration Cell track analysis Two-photon imaging Modeling Motion statistics |
| url | http://www.sciencedirect.com/science/article/pii/S2667119021000033 |
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