AnalyzER v1
The AnalyzER program provides quantitative analysis of the morphology and dynamics of the Endoplasmic Reticulum (ER) from confocal time-series. The tubular network and cisternae are automatically segmented and converted to graph representation with nodes at junctions connected by edges along the tub...
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| Format: | Dataset |
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University of Oxford
2018
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| _version_ | 1797094956010045440 |
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| author | Fricker, M |
| author2 | Fricker, M |
| author_facet | Fricker, M Fricker, M |
| author_sort | Fricker, M |
| collection | OXFORD |
| description | The AnalyzER program provides quantitative analysis of the morphology and dynamics of the Endoplasmic Reticulum (ER) from confocal time-series. The tubular network and cisternae are automatically segmented and converted to graph representation with nodes at junctions connected by edges along the tubules. The program measures:
(i) The length, width, morphology and protein distribution along the ER tubules;
(ii) The degree and branch angles at junctions (nodes) in the tubular network;
(iii) The size, shape, and protein distribution in cisternal sheets and around the perimeter of the cisternae;
(iv) The topological organisation of the tubular and cisternal network determined using graph-theoretic metrics;
(v) The distribution of immobile nodes, tubules and cisternae using persistency mapping;
(vi) The local speed and direction of movement of tubules and cisternae using optical flow;
(vii) The size and shape of the polygonal regions enclosed by the network.
The AnalyzER package is implemented in MatLab (2017a) and can be downloaded as a MatLab app, or as a standalone *.exe package for Windows 10.
A full manual, tutorial and test data sets can also be downloaded.
All aspects of the analyses are handled through a single graphical user interface (GUI) to provide an integrated platform. An additional GUI is provided to facilitate statistical analysis by concatenating results from multiple experiments. The endoplasmic reticulum (ER) is a highly dynamic polygonal membrane network composed of interconnected tubules and sheets (cisternae) that forms the first compartment in the secretory pathway involved in protein translocation, folding, glycosylation, quality control, lipid synthesis, calcium signalling, and metabolon formation. Despite its central role in this plethora of biosynthetic, metabolic and physiological processes, there is little quantitative information on ER structure, morphology or dynamics. Here we describe a software package (AnalyzER) to automatically extract ER tubules and cisternae from multi-dimensional fluorescence images of plant ER. The structure, topology, protein-localisation patterns, and dynamics are automatically quantified using spatial, intensity and graph-theoretic metrics. We validate the method against manually-traced ground-truth networks, and calibrate the sub-resolution width estimates against ER profiles identified in serial block-face SEM images. We apply the approach to quantify the effects on ER morphology of drug treatments, abiotic stress and over-expression of ER tubule-shaping and cisternal-modifying proteins. |
| first_indexed | 2024-03-07T04:21:06Z |
| format | Dataset |
| id | oxford-uuid:cb0e2845-2a9c-495a-84f0-4dd2c5164463 |
| institution | University of Oxford |
| last_indexed | 2024-03-07T04:21:06Z |
| publishDate | 2018 |
| publisher | University of Oxford |
| record_format | dspace |
| spelling | oxford-uuid:cb0e2845-2a9c-495a-84f0-4dd2c51644632022-03-27T07:12:07ZAnalyzER v1Datasethttp://purl.org/coar/resource_type/c_ddb1uuid:cb0e2845-2a9c-495a-84f0-4dd2c5164463Quantitative image analysisConfocal MicroscopyCell BiologyORA DepositUniversity of Oxford2018Fricker, MFricker, MPain, CHawes, CKriechbaumer, VThe AnalyzER program provides quantitative analysis of the morphology and dynamics of the Endoplasmic Reticulum (ER) from confocal time-series. The tubular network and cisternae are automatically segmented and converted to graph representation with nodes at junctions connected by edges along the tubules. The program measures: (i) The length, width, morphology and protein distribution along the ER tubules; (ii) The degree and branch angles at junctions (nodes) in the tubular network; (iii) The size, shape, and protein distribution in cisternal sheets and around the perimeter of the cisternae; (iv) The topological organisation of the tubular and cisternal network determined using graph-theoretic metrics; (v) The distribution of immobile nodes, tubules and cisternae using persistency mapping; (vi) The local speed and direction of movement of tubules and cisternae using optical flow; (vii) The size and shape of the polygonal regions enclosed by the network. The AnalyzER package is implemented in MatLab (2017a) and can be downloaded as a MatLab app, or as a standalone *.exe package for Windows 10. A full manual, tutorial and test data sets can also be downloaded. All aspects of the analyses are handled through a single graphical user interface (GUI) to provide an integrated platform. An additional GUI is provided to facilitate statistical analysis by concatenating results from multiple experiments. The endoplasmic reticulum (ER) is a highly dynamic polygonal membrane network composed of interconnected tubules and sheets (cisternae) that forms the first compartment in the secretory pathway involved in protein translocation, folding, glycosylation, quality control, lipid synthesis, calcium signalling, and metabolon formation. Despite its central role in this plethora of biosynthetic, metabolic and physiological processes, there is little quantitative information on ER structure, morphology or dynamics. Here we describe a software package (AnalyzER) to automatically extract ER tubules and cisternae from multi-dimensional fluorescence images of plant ER. The structure, topology, protein-localisation patterns, and dynamics are automatically quantified using spatial, intensity and graph-theoretic metrics. We validate the method against manually-traced ground-truth networks, and calibrate the sub-resolution width estimates against ER profiles identified in serial block-face SEM images. We apply the approach to quantify the effects on ER morphology of drug treatments, abiotic stress and over-expression of ER tubule-shaping and cisternal-modifying proteins. |
| spellingShingle | Quantitative image analysis Confocal Microscopy Cell Biology Fricker, M AnalyzER v1 |
| title | AnalyzER v1 |
| title_full | AnalyzER v1 |
| title_fullStr | AnalyzER v1 |
| title_full_unstemmed | AnalyzER v1 |
| title_short | AnalyzER v1 |
| title_sort | analyzer v1 |
| topic | Quantitative image analysis Confocal Microscopy Cell Biology |
| work_keys_str_mv | AT frickerm analyzerv1 |