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Example usages

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Lukas Grünewald edited this page Dec 15, 2021 · 10 revisions

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

Basic usage of FEI Crop Scale Bar

Basic usage with cropping of a TFS/FEI databar, addition of a scale bar (and changing the appearance in the options menu), moving and removing of the scale bar:

Example

Using the Auto re-scale images option

The next GIF shows the application of Auto re-scale images to upscale a small (in terms of pixels) inset of an image.
This is useful for software like, e.g., Microsoft PowerPoint which automatically smooth/interpolate such images by default.

Example

Using the hotkey c to quickly copy images to other programs

The following GIF shows an example workflow when working with presentations (here Microsoft PowerPoint).
For a horizontal alignment of images (here an SEM and an HAADF-STEM image) with the same desired image height, the scale bar reference is switched to Height in the options. Note the automatic handling of unit-switching and re-scaling as in the previous examples. The image is then copied via the hotkey c to the system clipboard and pasted into PowerPoint.

Example

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. Close the image.
  • 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.
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