#imagej stuff

[halfslashmoon]

kind of more limited ability to upload videos (fair) so im breaking off into a separate post but this is a more active ijm script from last year that lets you watch a virtual slime fight for its life and eventually deplete its resources, toxify its environment and die so hard that future molds struggle to survive on top of its remains. Hooray!!!!

[lixenn]

Now that I'm waiting for my introdcution to be proofread, I should probably start working on the result part. (Since my supervisor should also add some Method and Material stuff and I don't want to mess with it until I get feedback).

Which means I need to get my results on my new laptop and I forgot to transfer them on my USB so... need to open up the broken laptop again. I hate extra steps.

Then I will need to figure out what to show, which I think I can just use what I have in the result presentation but idk if I should tweak with the image lighting of my microscopy pictures a bit. They are kinda dark. That would mean downloading ImageJ again. Ugh...

[time-sponges]

So none of you were gonna tell me that science was 15% doing stuff with cells and 85% hating imageJ?

[bressa]

Productivity vs Anxiety

Good day to you (: 

I wasn’t going to post anything today because I didn’t do anything aesthetic that would look pretty here. I’ve got some foliar area to measure and I use ImageJ for that. And there are thousands of pictures still to go. It is the boring part of working with plants, but I like everything else, so that measures up. I also decided to give you a short list for things I do when I can’t study because of my anxiety. For me, it is difficult when I sit in front of my computer to get stuff done and I just can’t do it, and the more I try the more it gets worst. I suffer from this for a long time now, and I came to realise what I need to do to couple with what I’m feeling at that moment. It doesn’t make the anxiety go away, it doesn’t make the physical symptoms to shut off at once, but with some time, I can come back to work feeling good. Well, this is what I do: 

–   First I struggle. Even going through this for many years, I still try to force myself working for some days before realising what I really have to do. By forcing myself to a certain state, it gets worse. If you’re not feeling ok to do something, even though you love it, don’t feel ashamed. Don’t make less of yourself because of that. It is natural, it is ok. There is only so much our body can take – or make – at once, and the same goes for our brains, our minds. If you need a rest, step away a bit. 

–   By realising that going on with what I should be doing is making me more ill, I stop doing it. At first, not really, as I keep blaming myself for not doing it, but then that feeling goes away. I accept better my situation; I try to do what I like doing but within some boundaries. For example, I love reading. But as I know myself better and better with time, I know that by reading a story that I love today will probably make me to not want to read that paper tomorrow (when I’m in this state only). So, I don’t read. Hence, you have to listen your body and your inner self, get to know you and answer accordingly. Remember: you don’t have to accomplish it all at once. Living is enough. 

–   The next thing is turning off my mobile. Even when you’re feeling well again, let it off for a couple more of days. I can’t explain how much that helps. But don’t just turn it off and keep thinking about what messages may there be, or what is happening on Instagram. Let it go. Shake it off your system for the time being. 

–   Things don’t have a right order here, but for my “mentally resting time” I really just let myself be. I’m an introvert that in some occasions behaves like an extrovert, and I do love building friendships. So, if you feel like it, hang out with your friends, go explore some place new – in the wild or not – run, exercise, yell, or simply do some gardening, play with your pet, hug whoever you love, read that book, meditate, sleep even. Just find what works out for you to let all that tension go away and leave space for new feelings, memories, accomplishments. I personally like playing with my cats, I find that alongside with meditation and gardening the most powerful tools. But that is for me. You should experiment. 

–   So, I rested a couple of days, probably didn’t talk to anyone but my parents and pets, and I feel better. It may take you a few more days to get to that point or not, but know it will happen – but, of course, you have to want to. Then I take another day “off”, but not exactly. I just try to let myself realise that I am rested, I am well, everything is ok inside-out and that the next day is a work day. I don’t rush anything, I don’t plan anything (making plans get me so so so exhausted and anxious every time) I just do some calming stuff as the past days, but start doing something that is actually work. Something easier or that I simply don’t mind if I do it all wrong and have to redo the next day. That is the point: allow yourself doing something without caring about perfection. I postponed the very existence of this tumblr for years because I wanted it to be perfect, and it never seem to be right time for me to doing so. And now, I’m finishing my masters! How much could I have done?! Don’t try to be perfect! You’re awesome and what you do is awesome. 

–   The next day, is a work day. I wake up earlier than I would for planning that day only. Take small steps. If you feel ok by planning, then go ahead and plan your whole week. If I do that, I guess my brain wants to do it all in 5 minutes. It doesn’t work well. So I don’t do that anymore, unless I really have to. I specifically don’t do that when I’m anxious. When I’m in this state I just think about that day or the next day. I’m trying to work on my self-discipline for that all ~ planning the whole week hour by hour ~ and actually doing it, so if you have any tips, please let it in the comments. I appreciate that very much. Anyways, I woke up earlier, had a nice cup of coffee, and planned my day. Then I actually start my day, by doing what have to be done, but in that more positive mindset. At the end of the day, I plan the next day. And so on. 

It takes me 6 days more or less to get back to normal. And even after that, I try to keep myself in that mindset of acceptance, that I don’t have to hurry things and all. But, honestly, it doesn’t last long. Or not as long as I wish it would. But I actually don’t feel bad for a pretty good time, months even. Things just get back to normal, but eventually I have to stop and do it all again. Remember that I’m human. That I can do whatever I want, but it doesn’t have to be all at once, or in a specific amount of time, or in a specific way. I’m allowed to make mistakes, and I shouldn’t care about being judged, because even if I just try, I’m worthy and precious only for doing so. 

I hope this helps anybody that needs it. I don’t have professional tips. I’m not saying these are the right thing to do, but it is something that have helped. It is fine, only natural, to not feel bright and be productive all the time. No matter what, you’re worthy, you’re precious.

[cancerbiophd]

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

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!

How to Create Publication-Quality Figures: A step-by-step guide (using free software!)

What is the best software for making and editing scientific images for publication quality figures? (ResearchGate Forum)

Ten Simple Rules for Better Figures (from PLOS)

Making figures for scientific papers

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! 

[halfslashmoon]

it took me more than an hour to get a clip of this because to really demonstrate it requires Good Circumstances or a Lot of Time because it just is inherently a very slow burn thing. but heres my latest ijm script. i wrote a really rudimentary 3D renderer and went to fucking town.

[halfslashmoon]

2020 era ImageJ Macro script that attempted to make some places. Sometimes it works. Sometimes it really doesn't. Sometimes Lizard

im not sure about risky horsewater

[halfslashmoon]

im not sure about risky horsewater

[halfslashmoon]

Cute script plays mad libs with a big text file and then draws planets. Had a bot that posted them on Twitter back when that was fun and not upsetting.

im not sure about risky horsewater

[halfslashmoon]

Isomapper. the 3d is fake. had to really sift through this one because the string manipulation was way more cursed than I remembered

im not sure about risky horsewater