![]() annotate ( 'local max', xy = ( 2, 1 ), xytext = ( 3, 1.5 ), arrowprops = dict ( facecolor = 'black', shrink = 0.05 )) ax. Import numpy as np import matplotlib.pyplot as plt fig, ax = plt. In an annotation, there are two points to consider: the location of the dataīeing annotated xy and the location of the annotation text xytext. Placing Artist at anchored Axes locations Placing text annotations relative to data Provide as much flexibility in positioning and styling as annotate. Text can also be used for simple text annotation, but does not Axes.annotate also provides an optional arrowįrom the text to the data and this arrow can be styled in various ways. Positioning data and annotations relative to each other and a variety of ![]() by thresholding, pixel classification, or by temporarily dipping into another tool, such as ImageJ.To download the full example code Annotations #Īnnotations are graphical elements, often pieces of text, that explain, addĬontext to, or otherwise highlight some portion of the visualized data.Īnnotate supports a number of coordinate systems for flexibly There are other, faster, fancier ways to create similar Annotation objects, i.e. The name can be shown or hidden in the viewer using View ‣ Show names, or the shortcut N. You can set these quickly for a selected annotation by pressing the Enter key. Setting properties Īnnotations can also have properties set.įor analysis purposes, the most important of these is usually the classification.īut for display, there are also name and color properties. You can access this by right-clicking on a selected annotation. To help reduce this risk, annotations can be locked or unlocked. Locking & unlocking įor that reason, losing or accidentally editing annotations can be rather upsetting. This is something of a special case, covered in Manual counting. See Separating stains for more information. Like the Brush tool, the Wand tool adapts according to magnification: zoom out to select large regions, zoom in to select smaller, more detailed regions.Īdditionally, the Wand tool is influenced by any color transforms that have been applied – so these can be used to adjust the image so the areas of interest have higher contrast. It can also work well in selecting dense areas of cells surrounding by more space.īut if the contrast is lower, the wand can appear to go out of control… and it’s best to revert back to the ‘standard’ Brush tool. This provides a very powerful way to annotate regions quickly and with a high level of accuracy… provided they are substantially darker or lighter than the surroundings. Not content with painting only a small circular region, it will spread out into a much larger circle - but only for so long as the pixels have intensities similar to the one that was clicked on. The Wand tool is like a more enthusiastic brush tool. You can change the absolute size of the brush in the settings, and also optionally turn off the size adaption according to zoom. This works either in additive (normal) or subtractive ( Alt pressed) mode - enabling ROIs to be cleaned up to be much more precise, and also to create holes within existing ROIs. The brush can refine ROIs drawn with other tools. Holding down the Alt key while using the brush causes it to ‘subtract’ regions… basically acting as an eraser (or painterly equivalent). In other words, if you zoom in then the brush effectively paints small regions - while zoomed out it can quickly mark in large areas. The size of the brush adapts according to magnification. This would have limited call for excitement, but the Brush tool within QuPath has a few particularly useful features: The idea is simple: it each click of the brush selects a small circle, but by dragging the mouse across the image then a region is ‘painted’ that way. The Brush tool is probably the drawing tool I use the most for annotating regions. ![]() Otherwise, the ROI is finished by double-clicking on the image at the location where the final point should be. If you start a polygon by clicking and dragging, then the polygon is complete when the mouse button is released. It’s possible to switch while drawing the same region. The latter if better if you have a steady hand and want to draw a more detailed region. The former is better if you might want to edit the polygon later, but dragging vertices to different places. The Polygon tool is a good standard for drawing around regions.Ĭlick and drag to draw a continuous line (which will be split into spaced vertices by QuPath) Lines can be drawn using the Line tool, by clicking once for the starting point, and double-clicking for the end point. Rather than drawing rectangles or ellipses, Objects ‣ Annotations… ‣ Specify annotation can be used to set coordinates exactly - and thereby give more control over the exact size and/or location.
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