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Nuclear_Morphology / methods / Filter a collection

Curating and filtering nuclei

The edge detection and segmentation to find nuclei does not always work perfectly, and so cells can be included in a dataset that have wonky outlines. This can throw off the angle profiling and make datasets look more variable than they truely are. To help avoid this, there are two ways to select only the cells you care about.

Filtering cells

Filtering is a quick way to exclude cells with poor edge detection, or simply to pull out a group of interest to you. Filtering can be performed from the Nuclear charts scatter tab.

Choose the parameters you want to filter on using the drop-down menus for the X and Y axes of the chart. The defaults are area and difference to the median profile; this usually shows outsized and oddly shaped nuclei quite clearly.

The nuclei can be filtered using the 'Filter visible' button. Zoom to a region on the chart so only a subset of the nuclei are visible, then click the 'Filter visible' button. A new child dataset will be created containing only the nuclei currently visible on the graph.

img/gifs/Filter_collection.gif

Curating cells

Manual curation allows you to accept or reject each cell in a dataset. Acceptable cells are copied to a new dataset and reanalysed. The old dataset is not affected. Select a dataset, then choose Dataset > Curate. A window will be displayed showing all the nuclei in the dataset oriented.

In the example below, the first four cells in the dataset (s100.tiff-35 to s100.tiff-38) have errors. One is two nuclei overlapping, and the other three have errors in the edge detection. We want to remove these cells from our curated dataset.

img/Curation_dialog.png

Select the nuclei to keep; the table background will turn green for selected nuclei. Use the 'Select all' option as a shortcut if you only need to skip a few nuclei, as in the right image above. You can also deselect the 'Rotate vertical' option to show the nuclei as they appear in their source image..

Once you are happy with your selection, click the Make new collection from selected button at the top of the window, and the chosen cells will be added to a new dataset.

For large datasets, it may take some time to load the image for all the nuclei. The loading progress is shown by a loading bar at the bottom of the window.

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