If you wanted to get that information, you’d have to go back to the original file and open it with Bio-Formats. Just open each image stack separately, then run Image > Stack > Merge Channels., assigning each image stack to the desired channel. If you just want to create a simple collage with different transparencies, you can use an online tool to do so without having to. Saving your files as plain TIFFs will store some of the meta data, like calibration but not something like excitation wavelength. This way, you can later re-open that file and take a look at which excitation wavelength the third channel was acquired.Ĭheck the Display OME-XML metadata box to see the information in the standardized form: So opening a vendor file with Bio-Formats and saving it to OME-TIFF will store information, like excitation wavelengths, objectives used during acquisition, temporal information, etc., in a standardized form in the file. So whenever you use Bio-Formats to open a file that has been generated on a microscope with a vendor software, they are translating information that the vendor puts in its file formats to a standardized form. Use the Image>Overlay>To ROI Manager command to move the selections in a overlay to the ROI Manager. Use the Image>Overlay>List Elements command to list the selections in an overlay. Where are overlays saved in an ImageJ file As mentioned in 3: Image Types: Lossy Compression and Metadata, overlays are saved in the header of tif images, and do not need to be saved externally when using TIFF, the default file format of ImageJ. The way around this is to use the Image Overlay Flatten command. Activate a selection in an overlay by long pressing on it. Size, color and background of text labels can be adjusted in the Image Overlay Labels prompt. An overlay in ImageJ is a list of selections that are displayed on the image. You can also store overlays in the header part of TIFF file (and it works… hopefully).īio-Formats is “The solution for reading proprietary microscopy image data and metadata”. Show This drop-down menu specifies which image (or overlay) should ImageJ display after the analysis (see Display options of ParticleAnalyzer). Once the code installed as explained above, open the demo image by the Plugins -> Macros -> Open Sample Image 2 menu. TIFF is a flexible image format that can not only contain pixels/intensities, but also additional information like scale information (X microns/px) or calibration. If you have the red and green channels as separate images, you can overlay them using the Image > Color > Merge Channels command. Sorry can you please explain a bit more what you mean by this?
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