Category Archives: Academic

How to get more pixels when you export Powerpoint slides to graphic files

Microsoft, in their wisdom, cripple PowerPoint’s abilities to export slides to high resolution graphic files, and by default they compress images imported to a mere 220 pixels per inch or less. Here are a couple of tricks to improve things.

1. Tell PowerPoint not to automatically compress imported images.

Open PowerPoint.On the File menu choose Options. In the options dialog choose Advanced. In the right panel under Image Size and Quality select Do not compress images in file.

This setting will stay with the file, but you will need to reapply it for new files where you want the highest resolution in your images. There is probably a way to make this the default… stay tuned.

2. Change the export resolution for PowerPoint slides

This step involves editing the registry. The registry is a database maintained by the system of all the relevant settings that allow programs to work. If you muck up the registry, things might not work afterwards. If you are unsure, get expert assistance. That said, it isn’t difficult if you follow the instructions here: https://support.microsoft.com/en-us/help/827745/how-to-change-the-export-resolution-of-a-powerpoint-slide 

Since this change is done in the registry, it will be in operation whenever you use PowerPoint from then on. Note that if you upgrade to a new powerpoint, the registry change may not be copied to the new version so you may need to repeat the process after each version upgrade.

Note that no matter how high you set the resolution in the registry PowerPoint will not export slides as image files with sides greater than 3072 pixels – that is usually enough, but may not be for some applications. The next section has an approach that gets around this limitation.

3. Alternative — export by printing to a PDF file

This is less convenient but does not need changes in the registry. Print the slide (or slides) using a PDF writer. WIth Adobe’s PDF writer you can set a high resolution (the default is to compress large images to 150 ppi). In the print dialog with Adobe PDF selected choose Properties

In the Document properties dialog, choose a setting with high dpi settings such as Press quality:

Or you can edit one of the other settings and change the images compression properties to whatever resolution you want.

If you don’t have adobe PDF writer, there are lots of alternative free programs such as Foxit PDF, or CutePDF Writer which can give high quality output.

Once you have the slide(s) saved as a PDF file containing embedded high resolution images you can save them as image files from Acrobat (paid version) or open them using programs such as (expensive) Adobe photoshop or Adobe Illustrator, or (free, open source programs) GIMP (sim to photoshop) or Inkscape (sim to Illustrator), from where you can export to whatever graphic file format you require.

 

Prettier graphs using Excel

Excel is commonly used for processing data, but the default graphs lack a little something when it comes to scientific presentation (I guess perceptual accuracy and aesthetics are not a key criterion for business graphs, so we get stuck with ugly graphs).

I made these notes a few years ago using Office 2007, but the process is similar with the more recent versions.

Plotting graphs using Excel / Office 2007

First get your data: here is some I prepared earlier… we want to plot the data in the column under “y” with the sem under SEM

In this example I will do a column chart so I have put in a set of labels for the groups I am potting – this makes it easier to get the labels on the x-axis quickly. I have selected the labels and y data

Change to the “insert” Tab and select the graph type – here I will select a column plot

… and choose a simple plot type suitable for the data.

The graph is created with labels but no error bars:

 

 

 

 

 

I have made the plot narrower by dragging the right border to the left.

I have selected the data by clicking on one of the columns

 

 

Under the “Layout” tab choose “analysis and select “error Bars” and under this choose “more error bars”

Use the menu under “Error amount” to pick “custom”, and select the error data for both the plus error bar and the minus error bar. Your graph now should have error bars showing the SEM.

Now you can tidy up the graph (Layout tab), add axis labels (Layout::Axis titles) and graph title (Layout::Chart Title), remove or adjust the legend (Layout::Legend), format the axis numbering (Layout::Axis), add lines of best fit (Layout::Trendline), format/remove gridlines, etc etc.

With a bit of fiddling you can make the graph look reasonably good

 

 

 

 

 

You can even add adornments like markers to indicate statistical significances etc… (Insert::Shapes gives you lines, boxes etc – the usual suite of office drawing tools)

Alternatively you can paste the graph into PowerPoint  — if you use Paste::Special::Enhanced Metafile, then ungroup (twice) you convert the image of the graph into Microsoft office drawing objects which you can edit using the normal PowerPoint tools. I often find this approach makes it easier to set line thicknesses, colours, text fonts etc etc than doing the equivalent in Excel graph mode. It also allows you to lay out multiple graphs or other images onto a page, with easy resizing etc to make things fit together aesthetically. Of course doing it that way loses the ability for automatic recalculation of the graph in the presentation by changing the data etc that you get if you paste the graph in as an excel object (the default paste mode). Have a play and you can choose which ever approach is most appropriate for your needs.

Once you have a graph format in excel you can re-use it with different data too. Just copy and paste into a new location to get a duplicate, then under the Design tab choose Select data to feed in the new numbers. The formats, colours, fonts etc that you so laboriously chose will stay with the graph, so once you have changed the data used by the graph you should have a nice graph of your other data (you will probably need to change the graph axis ranges if you set these manually; you may need to redraw any adornments you added – P values, text, lines etc, and perhaps move the legend to a new location).

Colourblindness and graphics

About one in ten males (including myself) have some degree of red-green colour blindness (and 0.5% of females), so you should bear that in mind when you are making graphics to display to others. Red-green colour blindness comes in varying degrees – it isn’t necessarily that red and green cannot be distinguished, but that are clearly different to people with normal colour vision may be hard (or impossible) to discriminate for others. Here are some hints.

colour-blind-examples-01Thin lines are difficult. Thin lines don’t activate many colour sensors (cones) in the retina, so it may be difficult to discriminate the colours of thin lines. On the graph to the right I am hard pressed to tell which line is which colour. In fact, I am not certain these lines are coloured – they could be grey.

 

colour-blind-examples-02Making the lines thicker aids clarity and makes the colour MUCH easier to discriminate. In this version of the graph I can work out which line is red and which is green without too much effort, at least at the size this shows on screen in this page. If one is sitting at the back of a theatre looking at a tiny version on a screen … then we are back to the too few cones activated problem.

colour-blind-examples-03Using solid symbols adds extra colour area to activate more cones. This helps. But for those on the weaker end of the colour blindness spectrum it still makes for difficulties.

 

 

colour-blind-examples-04Here we have a secondary means of discriminating the lines – hollow vs solid symbol and dashed vs continuous line. Now the lines are clearly distinct, even for those who are totally colour blind.

 

 

colour-blind-examples-05Alternatively, to accommodate red-green colour-blindness, use a colour palette which is friendly. The blue line is clearly distinct from the red ??? or is it green or grey??? Whatever, the two lines are distinctly different because I can see blue well.

 

colour-blind-examples-06Another approach is to use different degrees of brightness, as well as different colours, for the lines and symbols. One can see differences in shade clearly on this version even if you cannot discriminate any colours.

 

 

Loading sets of images into powerpoint slides

Sometimes one may want to generate a PowerPoint slide with a set of images – for example a set of micrograph images to discuss with your colleagues (or a lovely set of your holiday photos to make your friends jealous). You can do this by manually adding each image, one by one, then resizing, repositioning, formatting …. , but there is a much quicker way. Here is a guide to automating the process. Continue reading

Fluorescence Images: Merging and optimising

If you are using fluorescence microscopy you may need to merge images taken with different filter sets – for example DAPI to pick out nuclei together with fluorescent staining with or or more specific antibodies. Commonly you will want to merge these images into a composite. Image optimisation and merging can be achieved easily using the free Fiji package with ImageJ. Continue reading

Uterine flushing proteome of the tammar wallaby

Uterine flushing proteome of the tammar wallaby after reactivatiCynthia Martin’s manuscript “Uterine flushing proteome of the tammar wallaby after reactivation from diapause.” was just accepted by the international journal Reproduction. The pre-press manuscript is available at http://www.reproduction-online.org/content/early/2016/08/01/REP-16-0154. The work is a collaboration between Cynthia, Chin Seng Ang, a proteomics specialist at Bio21, and her supervisors Geoff, David and Marilyn. This is the first study to investigate changes in uterine secretion profiles using extremely sensitive, cutting-edge LC-MS/MS approaches, and highlights some of the factors that may be involved in the regulation of embryonic diapause.

Pubmed Record: http://www.ncbi.nlm.nih.gov/pubmed/27486272

New Publication: Uterine morphology …

Laird-2016-Uterine morphology during diapause and early pregnancy in the tammar wallaby-JAnat_Page_01-600Recently published is the result of a collaboration between our laboratory, our past PhD student Cyrma Hearn and Melanie Laird at the University of Sydney,  These findings demonstrate that diapause, like pregnancy, is under unilateral endocrine control in the tammar, and that preparation for and maintenance of diapause requires substantial changes to uterine endometrial cell ultrastructure and activity.

http://www.ncbi.nlm.nih.gov/pubmed/27168485

Laird-2016-Uterine morphology during diapause and early pregnancy in the tammar wallaby-JAnat-fig2-600

NEW PAPER: Rewinding the process of mammalian extinction.

ZooBiol2016Marilyn Renfree among a group of concerned scientists convened a multidisciplinary meeting under the name “Conservation by Cellular Technologies.” The outcome of this meeting was a proposed road map that, if successfully implemented, would ultimately lead to a self-sustaining population of an extremely endangered species are outlined here. This new paper provides an overview of these ideas.

Continue reading

Effects of nutritional manipulation on body composition in the developing marsupial, Macropus eugenii

Hot off the press:  http://dx.doi.org/10.1016/j.mce.2016.03.030hetz16

When 60-day-old tammar wallaby pouch young (Macropus eugenii) are fostered to mothers at 120 days of lactation, their growth, developmental rate and maturation of their GH/IGF axes are markedly accelerated. To determine the effect of fostering on energy intake, body composition and fat accretion, we first measured total body fat and lean mass in these young. Next, we mimicked the triglyceride oleic and palmitic acid composition of 120-day milk by supplementing 60 day young with these fatty acids and comparing their growth with that of growth accelerated young. There was no difference in the weight or growth axis maturation of supplemented young but there was significantly more body fat in these and in the growth-accelerated fostered young than in controls. We conclude that the accelerated growth and GH/IGF axis maturation observed previously in fostered young is most likely due to increased milk consumption and earlier access to specific nutrients.