![]() ![]() T for Troy manager: shortcut to add ROI to the ROI Manager The image overlay: for ROIs that you only want to display The ROI Manager: for most ROIs that you want to be able to edit and use for measurements If you need control over multiple ROIs, there are two places in which you can store them. Normally, only a single ROI can be ‘active’ in ImageJ (i.e. This is especially true at very small scales (hundreds of nanometers or smaller), for resolution-related reasons that will be described in Blur & the PSF. This creates a new binary (black and white) image that differentiates between the pixels that are inside and outside the ROI.ĭon’t overestimate the accuracy of measurementsĪlthough ImageJ can measure very exactly whatever regions it is told to measure within an image, keep in mind that in light microscopy images any size measurements will not exactly correspond to sizes of structures in real life. One such command is Edit ‣ Selection ‣ Create Mask. This is why some extra commands to create or adjust ROIs appear under the Edit ‣ Selection submenu. Somewhat confusingly, ROIs are sometimes referred to as selections in ImageJ. ROIs in ImageJ are sometimes called selections – meaning the same thing When drawing a ROI, pressing Shift or Control before releasing the mouse button adds the ROI being drawn to any existing ROI already present. Right-clicking the tools often provides access to related tools, while double-clicking may give additional options. rectangles, circles, lines, points, polygons, freehand shapes) can be drawn using the commands in the tool bar ( Fig. The ROI in (B) was created by drawing one rectangular and two circular ROIs, holding down the Shift key between each so that the regions were combined. ![]() 14 ROI drawing tools are found on the left side of the ImageJ tool bar (A). tight_layout () glue_fig ( 'fig_rois_drawing', fig )įig. Only pixels within any ROI we draw will be included in the calculations when we run Analyze ‣ Measure.įig = create_figure ( figsize = ( 3, 3.5 )) show_image ( 'images/roi-toolbar.png', title = "Tool bar", pos = 211 ) show_image ( 'images/roi-glasses.png', title = "'Image + ROI", pos = 212 ) plt. Regions Of Interest (ROIs) can be used to define specific parts of an image that should be processed independently or measured. The two options that I think you should avoid can both result in something unexpected being measured if you don’t know (or have forgotten) that either was selected under Analyze ‣ Set Measurements….įortunately, they are not really needed if you master the art of generating, managing and transferring regions of interest between images. It sounds weird, but it’s intended for cases where you have two corresponding images one in which you can identify a region to measure, and one that contains the pixel values you should measure. Redirect to – measures a different image from the one that’s selected. Limit to threshold – restricts the region being measured according to any threshold that has been set don’t do this routinely, instead convert your threshold to a ROI and use that instead. Stack Position – includes the 2D plane that has been measured in an image with more dimensions. Some options within Analyze ‣ Set Measurements… are so universally useful that they should pretty much always be set.Ĭonversely, some options are manifestly confusing and dangerous and should be used rarely – or not at all.Īrea, Mean gray value, Standard deviation, Min & max gray value – basic summary values ![]() This also has an extra Results entry in its menu bar that other tables lack. Nevertheless, any new measurements you make with the Measure command will only be added to the original, official table. The ‘One True Results Table’ & its impostersĪ small idiosyncrasy to be aware of is that, as far as ImageJ is concerned, there is only ever one ‘official’ results table – the one with the title Results.ĭifferent, similar-looking tables can be created by different commands, or by duplicating an existing results table with File ‣ Duplicate…. ![]()
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