m a r i e l ♥

Third year graduate student in Biochemistry and Molecular Biophysics.
Feel free to talk to me about anything. Don't forget to follow, and enjoy my blog!
-my personal is @mashedpotatoes, which I use to follow!

thewaythroughthewoods sent:
Hi, do you have any advice/tutorials/links on how to make figures? I have a whole pile of scanned western blots and coomasssie stained gels to make into decent figures and have basically no idea where to start. I know how to lay it all out just from seeing them in papers, but I'm not really clear on whether stuff like improving the brightness/contrast is ok. Tbh I'm not even sure I've scanned them with the right settings etc. Any advice would be much appreciated! Thanks x
  • cancerbiophd replied:

    I use ImageJ (free download here, also what I use to analyze densitometry for western blot bands) and Prism (for graphs), and then I put together everything in powerpoint (like cropping, labeling, etc) for general presentation of data like for lab meetings (and the print out for my lab notebook). I also save it as a PDF file when it’s time to submit (journals don’t like powerpoints, but they’re ok with PDF’s). But basically I just follow whatever my PI (and the journal requirements) want. 

    If your lab has ever presented data/published papers in the past with figures, they already have programs/protocols they use. So firstly, check with your PI/mentor about how to make figures/what’s ok to change/etc. Every lab likes to do things a certain way, so my advice may all be unnecessary. The journal you want to submit to in the future will also probably have guidelines/suggestions regarding figures, so check that too. 

    Here are some resources I found via google. I personally have not used any of these sites because again, I just do as my PI says, so I can’t speak to the validity of anything, but feel free to have a look-see!

    And here’s what PLOS ONE has to say about blots and gels. I know there are some features that can be manipulated on an image (like certain wavelengths), but I personally never do*, because a) getting caught is not worth it, even if I did not mean to be presenting false data and b) if my western band is not clear enough already, then do I even trust my data to begin with?

    (*with the exception of cropping the gel/straightening it so that only the kDA of interest is shown, but I always have the original saved just in case anyone asks. This cropping/straightening can be done either on ImageJ or powerpoint)

    Hope that helped! Let me know if you need anything else, and good luck with everything!

    #gradblr and #sciblr: if you have any suggestions to add, please do! 

    • 51 notes
    1. cassinotes said: if you have a ton of Image J images to analyze that are all similar, use their macro tool!
    2. molecular-scholar reblogged this from cancerbiophd
    3. mina81ngstudyblr reblogged this from biopsychs
    4. biopsychs reblogged this from cancerbiophd
    5. marielstudies reblogged this from cancerbiophd
    6. marouflet reblogged this from cancerbiophd
    7. cancerbiophd posted this
    @