Note: Usually if the scale is listed in the metadata, FIJI will scale the images automatically upon opening. Again, how it is listed may varry with file type. You will find the scale information listed here if it was in the image metadata. This is useful if you dont need bio-formats importer to open your image. So this gives us the scale of 0.454545 pixels per micron.Īs shown previously you can also find information from the metadata by going to Image -> Show Info (or shortcut Ctrl + I). In this example, if we scroll downt he metadata, we come to the units, listed as microns, and below that, the scale shown as X and Y resolutions of 0.454545. How it is listed will be dependent on the file type. The scale information can look different in the metadata of one file compared to another. To find the calibration in the metadata, ensure Display Metadata is selected in the bio-formats options as previously described. When opening a file using bio-formats importer you can also find the calibration in the metadata, although this can sometimes be hard to find within the long list of parameters. You do no need to make any changes here, select OK or close the window to exit. ![]() Under Set Scale the calibration (pixels/micron) is the inverse of that shown under image properties (microns/pixel). Here you will also find the dimensions correctly populated from the metadata if your image was already calibrated. You can also find the calibrated scale, this time in pixels/micron, by going to Analyze -> Set Scale. This will open a display window showing the dimensions of the image and the scale will be automatically populated at the correct size.įor this image we see the scale is automatically set at 2.2microns/pixel. ![]() In a calibrated image you can find the scale in microns/pixel by going to Image -> Properties (or use shortcut Ctrl+Shift+P). If the scale is already calibrated the dimensions shown on the image will be in microns instead of pixels. This is usually the case for images originally saved in the raw file format. In some circumstances FIJI will be able to calibrate your image automatically by reading the attached metadata. Finding Scale Information in the Image Properties This section uses the images Interstitium 2.tif and TrichromeIHC.tif for demonstration. We will also demonstrate how to add a scale bar and how to crop and resize images without altering the image data. In this section we will show you how to find calibration information from the image, and how to set the scale if the image is not calibrated. Calibration is also important when resizing your images. Calibrating an image is also important if you want to get meaningful size-related measurements out of the image in any later analysis. This allows the viewer to see the scale of the image being presented and make their own conclusions about the data. ![]() For proper presentation of images it is essential to include a scale bar.
0 Comments
Leave a Reply. |