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Options to measure and export tracks.
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Options to measure and export tracks.
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Some measurement options are/will be proposed here, as well as options to export the segmentation to use in other image analysis softwares as Fiji.
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Some measurement options are/will be proposed here, as well as options to export the segmentation/measurements to use in other image analysis softwares as Fiji.
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# Options
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* [Apply on: define current selection](#define-current-selection)
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* [Export to extern plugins](#other-plugins)
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## Selection
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* [Export segmentations](#save-segmentations)
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* [Measure cell features](#measure-cell-features)
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You can choose which cells to analyse/export with the first option in the interface:
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* [Measure track features](#measure-track-features)
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* `Only selected cell` will measure/export only the currently selected label/cell. Its value can be seen and modified in the left panel under `label`. You can select `show selected` option in that panel to see only this cell.
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* `Only checked cells` will measure/export all the checked cells. To see which cells are checked, you can select the option `see checked cells` in the `Edit` panel of Epicure.
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* `All cells` will measure/export all the cells in the `Segmentation` layer.
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## Define current selection
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## ROI export
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You can choose which cells to analyse/export with the `Apply on` option in the interface:
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* `Only selected cell` will measure/export only the currently selected label/cell. Its value can be seen and modified in the left panel under `label`. You can select `show selected` option in that panel to see only this cell.
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The button `Save ROI(s)` allows to export the segmentation as Fiji ROIs. It will export only the selected set of cells (the selected cell, the checked cells or all the cells). In all cases, it creates **a ROI file for each cell**, containing the contour of the cell at all time frames where it is present. The file(s) are saved in the output folder, named `*imagename*_cell_*celllabel*.zip`, for each cell.
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* _`GroupName`_ will measure/export all the cells in the corresponding Group (that have beend defined with the `Edit>Group` options. To see which cells are in the group, you can select the option `see group cells` in the `Edit>Group` panel of Epicure.
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* `All cells` will measure/export all the cells in the `Segmentation` layer.
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## Save segmentation
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---
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The button `Save segmentation(s)` allows to save the label image of the segmented cell(s) depending on the selection (only the selected cell, the checked cells or all the cells).
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# Save segmentations
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# Features table
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The curated segmented and tracked file can be exported in several formats to be used directly in other softwares/pipelines.
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The feature table contains measurement of cell properties based on the segmentation. The table will be created/updated when clicking on the `Create features table` button.
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Click on the check box on top of the `export segmentation` panel to remove it when you don't need it anymore.
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If you click on one value in the table, it will show the corresponding cell at the corresponding time frame.
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The table can be sorted by a given column by clicking on the column name. |
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## ROI export
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The button `Save ROI(s)` allows to export the segmentation as Fiji ROIs. It will export only the selected set of cells (the selected cell, the checked cells or all the cells). In all cases, it creates **a ROI file for each cell**, containing the contour of the cell at all time frames where it is present. The file(s) are saved in the output folder, named `*imagename*_cell_*celllabel*.zip`, for each cell.
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## Save segmentation
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The button `Save segmentation(s)` allows to save the label image of the segmented cell(s) depending on the selection (only the selected cell, cells in a given group or all the cells).
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## Save skeleton
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Allows to save the skeleton: the binary of the junctions, of the current selection (only selected cells, cells of a given group, or all cells). The file will be saved in the output folder.
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The skeleton can also be displayed by pressing <kbd>k>/kdb> when the segmentation layer is active.
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---
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# Measure cell features
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## Features table
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The feature table contains measurement of cell properties based on the segmentation. The table will be created/updated when clicking on the `Create features table` button.
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If you click on one value in the table, it will show the corresponding cell at the corresponding time frame.
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The table can be sorted by a given column by clicking on the column name.
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## Feature map
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Each measured feature (in the table) can also be displayed as a colored map, where each cell is colored by the value of this feature.
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For this, select the feature to map in the `Draw feature map` interface, and a new layer will be added in the list of layers on the left panel of Napari. You can change the colormap colors in the top-left panel of Napari by selecting this layer, and then use the `colormap` option.
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