![]() Hold “Spacebar” and move the mouse to pan.Hold “Ctrl” and scroll mouse wheel to zoom in and out.Make sure the annotation layer is selected and highlighted.Draw the outline around nuclei in the nuclei layer.The background color will be blue (0,0,255).The foreground color will be red (255,0,0).It is useful to dedicate a layer to each class of object. Adjust the brightness and contrast to clearly show objects of interest. ![]() Check to see if the image mode is RGB.Download the annotation tutorial files.An outline image is exported from GIMP and then a CellProfiler pipeline converts this outline image into a label image. GIMP is used to draw outlines around objects of interest and to label background regions. This method is best for annotating or labeling objects to define their boundaries, exactly, as opposed to annotating an image with bounding boxes or centroids some tools that are adept at annotating with bounding boxes are labelme and labelbox.io. This blog post outlines a method for annotating image data using CellProfiler together with another open source software, GIMP. Annotated images are also essential for deep learning applications as training data, for example see the 2018 Data Science Bowl an in-depth discussion on how the Data Science Bowl images were annotated can be found on the Kaggle forum. The performance of the pipeline can be quantified by comparing the segmentation output to the ground truth and calculating a comparison metric, such as the Jaccard Index or F1 Score. When assessing the performance of a CellProfiler pipeline, for example a pipeline that segments nuclei, the annotated image data are used as the ground truth. You can use the same settings or try new settings.Annotated image data is valuable for assessing the performance of an image processing pipeline and as training data for machine learning methods such as deep learning. You can repeat the steps to add a separate border to the other images on the canvas. You have now added a border around the one image only. Next, press Shift + Control + A on Windows or Shift + Command + A on Mac to deselect the selection you created. Adjust the width to how thick you want your border. You can also play around with the other settings, but I suggest focusing on the Line Width. You can choose to use a solid color, your foreground color, or add a pattern to the frame. You can now adjust the settings as you want for your border. This tells GIMP only to apply the border around the selected layer since you created a selection around that layer. Once the color is set, go to Select > All or use the shortcut Control + A on Windows or Command + A on Mac. Set the foreground color by clicking on the foreground color swatch in the left-hand panel, then select your color from the Color Selection window. Your border automatically takes on the foreground color. Then, set the Foreground Color to what you want the border color. To add the border to the first image, select the image layer in the Layers Docker. This isn’t helpful if you want to add separate borders around each image. If you have more than one image on the canvas that you want to be placed against a background, adding the border using the first method will add the frame around the entire canvas. How to Add a Stroke Border to a Single Layer The frame is also added as a new layer in the Layers Docker, which you can turn on and off using the eye icon next to the layer. The border is added around the entire canvas, slightly increasing the size of the canvas.
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