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Click on Image in the main menu and select 'Calibration...' to open the Spatial Calibration dialogue box. Click the unobtrusive little arrow icon on the right of the box (ringed in red in the adjacent image) to expand a list of saved calibrations. These have been measured by light microscopy facility staff members so they may only include the most popular lens and camera binning combinations. If you want to use a different magnification factor (e.g. 4x binning, 2.5x optovar lens, etc.) then please email a request to the light microscopy facility. Select a saved calibration and click Calibrate. All images in the document will now be calibrated.

IMPORTANT: All the images in the document will have the same calibration so if you have changed magnification or binning while capturing to the same document at least some of your calibrations will be wrong. The best thing to do is to make sure all images in a document are captured at the same magnification and to open a new document if you want to change magnification.

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Saving data in Openlab

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I would recommend saving data in Openlab's native LIFF format initially so all image metadata (including calibrations) is retained. Openlab LIFF files (not to be confused with Leica's LIF confocal file format) are compatible with the Bioformats Importer so you should be able to open them in Fiji provided all the images in the file are at the same depth. You can also save in other formats like TIFF but the image metadata will not be retained so you will have to make a note of the image calibration. TIFF for Publication is a spacial special format that saves the data at a depth of RGB colour regardless of what it was captured at. This is so images captured at unusual depths like 12-bit render correctly in basic image viewers like Mac Preview and Windows Photo Viewer as well as in PowerPoint. TIFF for Publication images are for presentation only and should not be used for quantitationfor quantification.

Save As Multiple... saves layers separately rather than as a single layered file. You might find this useful if you want to save images as TIFFs to further process in photo editing software because Photoshop and GIMP don't support layers in the way as scientific processing software. You have to select the layers you want to save and you have to define a Naming scheme for the images (e.g. by sequentially numbering them).

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