Example usages

This page shows examples on how to use em-scalebartools.

Batch conversion: Crop info bar, add a scale bar and save as png.

This workflow is useful to send a folder of SEM/FIB images to colleagues with a removed info bar and a nice scale bar.

• For the following, you must first close any other images using File -> Close all before proceeding. Alternatively, open another Fiji instance. (This may be fixed in a future version...)
• Open a single SEM/FIB image from your folder, then run FEI Crop Scale Bar and change the scale bar appearance using the QuickScaleBar options menu until you are satisfied.
• Open Process -> Batch -> Macro..., set up the in-/output folder, set up the output format to png, and add the macro code runMacro('FEI_Crop_Scalebar.ijm');.
• Run a Test, and - if all worked out - Process the whole folder.

Batch conversion: Scale images and crop info bar.

This workflow is a pre-processing step (e.g. for segmentation tasks), whereby the (i) SEM images are scaled and (ii) the info bar at the bottom is cropped. In principle, you follow the batch processing steps above with the following options:

• For FEI Crop Scale Bar: Deselect Add scale bar, select Crop data bar, deselect rest. (Optional processing steps can be entered as a string under Run custom macro commands)
• In the Process -> Batch -> Macro... menu, make sure to set the output format to tiff to keep the original bit depth.