Go Figure, Part 2

In Part 1, we learned the basics of Desktop Publishing with Inkscape. In this, the second part, we’ll take what we’ve already created and use it as a template for adding in some imaging data.

If you want to skip part 1 you can download the file from here (right click and Save Link As).

Going From Source

For any type of publication, it’s important to get the best quality images you can and that means going back to the original data for your paper. Unlike JPEG or PNG files which Inkscape can handle natively, most likely you will not be able to drag your raw data (czi, lif, nd2 &c.) straight into Inkscape. Thankfully Fiji will be able to open anything you throw at it, so go ahead and open Fiji then open your images.

Using Fiji is a great idea for a second reason and that’s to make sure that your images are being displayed at Full Range. Unless you’re comfortable with your very good reason to start adjusting the brightness and contrast, display everything at full range and state as much in the figure legend.

OK, so open your images in Fiji, make sure that you’re displaying full range by opening the [ Image > Adjust > Brightness and Contrast ] dialog, hit set then select the appropriate bit depth. Also select to propagate to other channels of the same image. Hit OK.

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We want to display 3 channels in greyscale and a merge, so using the Channels tool ( [ Image > Color > Channels Tool ] ) select Grayscale mode.

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All you need to do now is to make sure your windows is active (click in the title bar) then use [ Edit > Copy to System ].

Meanwhile … back in Inkscape

Back in Inkscape, open the Layers dialog, select the Masks layer and adjust the whole layer opacity to 20% (either drag the bar at the bottom or type in a number).

Add a new layer called Data and put it at the bottom of the stack of layers. You can do this either by selecting the bottom later (we called it ‘Masks’) and after hitting the + button, selecting “Below current”. Alternatively just make a new layer then drag the order around.

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Now, with the Data layer selected, paste (Ctrl+v or [ Edit > Paste ] ) your image into the layer. You should notice that the image is pasted under the masks. If this doesn’t happen, make sure your layers are ordered correctly and that you had the data layer selected when you pasted.

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Pro-Tip; You can always move selected objects between layers by hitting Shift+PgUp or Shift+PgDn. Furthermore, the layer of the currently selected object is given in the Statusbar.

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You could scale the image down to size manually but it’s quicker and cleaner to use the boxes in the Toolbar as we did with the original mask boxes. Select the image and scale it to 200×200 pixels (px). You can now use the align tool to overlay the scaled image with the top left mask. To do this:

  • Select the blue mask box in the top left (panel A)
  • Holding down Shift, select the now rescaled image (so you have both selected)
  • Make sure the align tools are set to Align to the “First Selected”
  • Align with the left and then align with the top (the order doesn’t matter)

You should now have something that looks like this:

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Bingo! Go ahead and repeat for the other two channels of your original image (remembering to re-select the Data layer every time), then finally, in Fiji, put the colour mode back into composite (to get the Merge), and repeat the same process to import. Once you get the hang of it, this should take you all of about 2 minutes.

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Two last things to do: Firstly, make the Mask layer invisible by clicking on the eye next to the layer name. Secondly, you will want to select the labels and change their fill colour to white. You may find this is easier to do if you turn off the data layer (as we did the masks) so you can only select the text. When you’ve done this, turn the data layer back on. All done!

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I’ve already covered adding scale bars, but the other thing I would HIGHLY recommend is to make notes on your data layer, outside the borders of the page. This can include the location and filename of your original data, any processing or scaling that you’ve applied and if you’ve messed with it, the display range. This makes coming back to your figures really easy for you or someone else later if they need to track down the original data. Also if you export by page as we did in Part 1, you don’t have to worry about this being included in your final figure.

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Multiplying Figures

The obvious option for making multiple figures is to copy your original file (or “save as”), then edit it and keep as many files as you have figures for your paper. This is a great idea, but who needs more files?

If you create a new Layer and call it “Figure 1” for example, you can drag existing layers into the layer to create sub layers.

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This then allows you to control visibility and edit locking for a set of layers (independent of the visibility state of layers themselves). Now of course you can copy the layer group “Figure 1” (right click and select Duplicate) rename it to “Figure 2”, delete the data layer and start all over again.

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I admit that this can get a bit awkward at times if you have more than one “Figure” visible, but it’s really handy if you can (and want to) wrap your brain around it.

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One thought on “Go Figure, Part 2

  1. Pingback: Go Figure, Part 1 | Post-Acquisition

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