Category Archives: Research

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).

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.