{"id":750,"date":"2009-11-24T21:46:46","date_gmt":"2009-11-24T21:46:46","guid":{"rendered":"http:\/\/occamstypewriter.org\/mindthegap\/2009\/11\/24\/in_which_i_pimp_my_data\/"},"modified":"2009-11-24T21:46:46","modified_gmt":"2009-11-24T21:46:46","slug":"in_which_i_pimp_my_data","status":"publish","type":"post","link":"https:\/\/occamstypewriter.org\/mindthegap\/2009\/11\/24\/in_which_i_pimp_my_data\/","title":{"rendered":"In which I pimp my data"},"content":{"rendered":"

I sat down the other day to prepare a figure for a paper I’m co-authoring<\/a>, confident I’d have it dispatched in a matter of minutes. <\/p>\n

\nYou can see where this is going already, can’t you?<\/p>\n

\nIt was a relatively clean Western blot result \u2013 a black band on a grey background, and no other offending pixels. The sort of biochemical result that is so unambiguous and clean that you don’t bother getting more than two or three exposures when you’re in the darkroom \u2013 especially when you’ve been busy flirting with that mysterious stranger with the New Zealand accent<\/a>. After I scanned the X-ray film into a tif file, I could see that it certainly wasn’t perfect \u2013 the film we’ve been using tends to come out quite dark, so I knew I’d have to fiddle with some settings in Photoshop to make it publication quality. But I didn’t really expect it to be a problem.<\/p>\n

\n\"\"
\nPure, unadulterated biochemical genius<\/em>*<\/p>\n

\nA few hours later, I was stumped. To make a long story short, what looked beautiful on screen looked like a dog’s breakfast when printed out; and what looked decent on a printout looked awful on my computer. I tried Levels, I tried Curves, I tried Desaturation; I tried sacrificing a vial of virgin Drosophila to the Photoshop gods. Despite the unambiguity of the result, making the band stand out cosmetically in both formats seemed impossible. And I think it’s important for a figure to look good both ways; after all, a referee might look at your images on screen, or print them out. There is really no way to tell how your data might be consumed. And superficial appearances, unfortunately, are often more important than substance.<\/p>\n

\n\"\"
\nPhotoshop is evil<\/em><\/p>\n

\nThis wasn’t the first time I’d hit a wall in image presentation. A few days previously, I’d had a similar problem trying to print out a rough result for my lab notebook. This had been a three-color confocal montage from the Leica SP5, processed through ImageJ, adjusted in Photoshop and mocked up in Illustrator. Heart-stoppingly beautiful images on-screen \u2013 but they were almost invisible on the printout, as if my cells were being viewed through a thick smog. Various postdocs gave me various bits of advice \u2013 adjust the Levels; convert to CYMK; pull the legs off of virgin Drosophila while reciting the alphabet backwards. I was told various bits of conflicting lore: for example, using Levels and Curves isn’t formally cheating, but adjusting the Brightness\/Contrast is. And vice versa. After an entire day of this, I gave up, and the murky, uninformative printout in my notebook contains a scribbled caption that says, rather defensively, “this looks a lot better in the electronic version, but it seems that actin is decreased on over-expression of the gene”. No future archivist will ever believe it, though: the rare case of a thousand words being worth a picture.<\/p>\n

\nAt that point, I started to try to remember the last time I’d mocked up a data figure for publication. Why didn’t I seem to know any of the Photoshop tricks? It was only then I realized that I’d actually never done it before. When I was publishing in Leiden, I had a team of people working for me, and they did all the image processing for our papers. And before that, as a post-doc in London, none of my figures required this sort of manipulation, being mostly graphs and regular photographic images of cell cultures under phase contrast. Even more previously, as a graduate student, you took your blots and gels, mocked up with glued labels, down to the friendly guys in the Photography department and casually suggested that they might consider downplaying this or that particular background band when they were committing your data to old-fashioned 8×10 glossies.<\/p>\n

\nIt was at that point, with sinking heart, that I realized I might actually have to take a Photoshop course. <\/p>\n

\nOh dear God, no.<\/p>\n","protected":false},"excerpt":{"rendered":"

I sat down the other day to prepare a figure for a paper I’m co-authoring, confident I’d have it dispatched in a matter of minutes. You can see where this is going already, can’t you? It was a relatively clean … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":6,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-750","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/posts\/750","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/comments?post=750"}],"version-history":[{"count":0,"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/posts\/750\/revisions"}],"wp:attachment":[{"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/media?parent=750"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/categories?post=750"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/tags?post=750"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}