Note: you can get away without doing the step above, but it makes finding errors much more difficult. Group your image files into folders where all have identical resolution and scale. Most of the time when you take photos on a microscope or on a tripod, the scale is the same among that group of photos.ġ. ImageJ is a useful tool for adding scale bars to images without much effort, but after extensive searching I was unable to find a script that would add scale bars to large groups of images. Part 1 – ImageJ batch adding scale bars to images: The program what will be used to batch caption and crop images. This program is used to manipulate filenames into usable captions (Use metamorphose 2 beta).
ImageJ: Is the photo editor we will use to generate scale bars.
Adding scale bar in imagej software#
The following tutorials will require the use of these software packages. In addition we can batch crop in this step.īEFORE YOU START THESE TUTORIALS MAKE BACKUPS OFF ALL OF YOUR PHOTO FOLDERS YOU PLAN TO USE. Batch adding captions or watermarks to photos based on file name. Using Metamorphose to manipulate files names into usable captions on photos. Using ImageJ to add scale bars to a large number of photos at once. I have broke it up by software packages so that you have points to jump in. You may want to know all the information that this tutorial provides or just a small portion. It does not store any personal data.Although this group of post is not valuable to many individuals, it may save a handful of people hundreds of hours. The cookie is set by the GDPR Cookie Consent plugin and is used to store whether or not user has consented to the use of cookies. The cookie is used to store the user consent for the cookies in the category "Performance". This cookie is set by GDPR Cookie Consent plugin. The cookie is used to store the user consent for the cookies in the category "Other. The cookies is used to store the user consent for the cookies in the category "Necessary". The cookie is set by GDPR cookie consent to record the user consent for the cookies in the category "Functional". The cookie is used to store the user consent for the cookies in the category "Analytics". These cookies ensure basic functionalities and security features of the website, anonymously. Necessary cookies are absolutely essential for the website to function properly. Right: Displaying also the scale bar of the screen shot, with a different color and size to make it more visible. Left: By default, only the original scale bar, imprinted in the screenshot, is visible.
Therefore, by default, screenshot viewers will automatically hide this extra scale bar (it can still be made visible by clicking on its “eye” icon in the layers panel). In theory, this new viewer containing the screenshot should also receive a scale bar of its own, which may be quite confusing for the user. Note regarding screenshots: Icy’s screenshot feature will imprint all layers (including the scale bar) onto a final image that is then displayed in a new viewer.To hide all scale bars and prevent scale bars from appearing automatically, the plugin can be deactivated from the “Preferences > Startup plugins” menu, by unticking “Enabled” and clicking on “Apply” or “Ok”.To hide the scale bar for a specific viewer, click on its “eye” icon on the “Layers” panel in the Inspector (see screenshot below).Here are two ways to adjust its behaviour: This plugin is a “startup” plugin, which means it runs in the background of Icy and will automatically add a scale bar on any opened sequence, as long as the plugin is “active”.Please make sure that the pixel size is correct, otherwise the scale bar will not be calibrated. This plugin calculates the size of the scale bar based on the pixel size stored in the image metadata.These options are accessible within the “Layers” section of the inspector (see screenshot below), and via the script editor: importClass(.Scale) Scale bar options Display size: untick to show the bar only.Auto-adjust size: if ticked, scale bar size will adjust to changes in the units used for the pixel size in metadata and scale according to the size of the image.