Hey /sci/, I'm trying to analyse the number of tau accumulations

>>8986974
Sorry, I should clarify that I imaged the medulla not just individual neurons

>>8986974
I dont get why they dont want you to use imageJ? it's fantastic.

I would do it manually, then using imageJ, correlate the results and prove to your teacher there is nothing wrong with it. assuming you take very clear images, it works extremely well for it's purpose.

Alternatively you could design your own program to do such, but that's way above what i know. But ive seen similar methods employed to count ecDNA, with very very accurate results (especially when using very conservative identification parameters)

>>8986979
are you able to post a sample image? may help

>>8986989
I use imageJ for everything (measuring microtubule length/MT disorganisation/axonal mitochondria/counting presynaptic densitites). I think she's just more skeptical about me repurposing a different plugin.

>>8986990
Unfortunately not, I'm not allowed to take my hard drive out of the lab

>>8986994
what's wrong with re purposing a different plugin...?
i would just manual count them. it's a bitch, but that's probably what she wants. It's like having to count cells on a hemocytometer when you have a flow cytometer, it's more about learning the concept/ultimate ways to do something than relying on current hardware. which i don't think makes much sense

>>8987003
I'm not too sure to be honest with you. Like we both said I think I'll do both, see if there's much of a discrepancy between the two and take it from there.

Luckily we have someone from one of our affiliates writing a script to do it so it's only a matter of time until we can do it (the biggest issue we have is that when the neurons bend they also look kind of like but not exactly like accumulations so we need something that can distinguish the two). Unluckily for me my lab rotation finishes on Friday. Although I am doing a PhD in the lab so at least we should have it up and running by the time I come back

>>8987017
Very nice, i am starting a program in the fall, and extremely excited. If you have any advice i would love to hear it.

That's great collaboration, a guy i met during our admit trip was a coder who was capable of doing shit like that, and it amazed me. He is one of the only other 2 biochem admits who are starting next fall so feel he's already a great resource.
For the script, maybe have it distinguish the bend angle as a count, if it's unique to it and not in the accumulations. or find another distinct feature of the accumulation so it can identify and discount it.

what year are you?

>>8986974
Whoh! Look at the brains on this human person. That is impressive. Bravo, I'm too stupid to help you. I use a filter mesh to grade rocks and sand at a cement plant. Can you do something like that?

>>8987025
Just finishing a masters in the UK mate, so this is my fourth year at uni.

In regards to working in a lab. Say yes to everything, take every opportunity and don't look back. I did and I got an unconditional PhD offer that allows me to go to one of the best institutes on the planet in Japan for two of the years.

Also accept you're going to make mistakes, they're the most important part of the process. I've worked with a girl that was obsessed with doing everything perfectly and she ended up with hardly any results at the end because she ended up fucking things up a lot more than me because she was sweating about every stage of the protocols.

And I guess finally (and something I need to start adhering to) don't just invest all your time into lab work.You MUST strike a life/work balance.

>>8987033
Haha not in the slightest, the only brains that matter belong to my flies!

>>8987037
very good advice, thank you. The good thing is i know i will make mistakes, ive failed out of uni before and other shit so i've gotten over the proud stage. Also really fucked up a cancer research project when i forgot to add SDS to a lysis buffer. luckily i kept the cell pellet residue due to my slight hoarding tendencies and it saved my ass, but that experience was really humbling.
Do you know what your future research will be in? I am currently interested in either advanced imaging techniques or possibly bioengineering GFP molecules for use in a biosensor.

>>8987033
we are not that smart, we are just smart in certain subjects which are conducive to biology research. Ask me if i have any fucking idea what those math kids are talking about

>>8987060
Do you have any fucking idea what those math kids are talking about?

>>8987070
rarely, and i've taken up to calc 2.

>>8987057
My focus is Alzheimer's disease but obviously after my PhD the pathway I go down is anyone's guess

>>8987060
Someone said

0.999 = 1
Thats fucking stupid

>>8987073
do you think Alzheimer's is caused by an infections prion-like rogue Amyloid Beta particle with a 30-40 year incubation period? We had an interesting presentation where that was the conclusion.

>>8987077
But then why does LOAD almost always onset after late 60s and very rarely earlier?

>>8987077
Sorry, I'm british so I ended up going to bed before I saw this, hope you see this before the thread disappears.

I'm most likely biased to my case but I'm more convinced it's oxidative stress that causes it. After oxidative stress it's anyone's guess but I think it's something like this:
Increased ROS production -> A Beta plaque formation/increased JNK activity/tau detachment and aggregation/breakdown of microtubules and subsequent prevention of axonal transport of mitochondria and synaptic vesicles.
ABeta, JNK and Tau all seem to have positive feedback on each other and all possibly increase ROS production so making a timeline or pathway of events is always gonna be hard but my PhD intends to make a bit of a pathway out of the events so maybe we'll find out in four years time

>>8987465
basically the enormous incubation time. a single infectious particle enters the body and it just takes a shitload of time for it to 1.find it's way to the brain 2. find more amyloid beta fibers to convert, but slowly as it gets bigger more and more are, then it breaks apart, process repeats itself, just takes a long time to cause the senile plaque formations.
>>8988104
the beauty of /sci/, long lasting threads.

really what was interesting about that presentation was the experiment designed. mice were injected with human alzheimer's brain lysate, and over time the mice developed senile plaques. The same mice did not develop alzheimer's when their blood was put through dialysis with an Abeta antibody on a bead, when their blood was ran through the machine every month, 2 months, 3 months, up to 6 months. The mice who received dialysis every 6 months did begin to show signs of alzheimer's but even then it was very minor, especially compared to the 0 seen in the 5 month and more frequent. and this was only doing 60% of their total blood volume!

it was pretty interesting stuff, but im simplifying the fuck out of it, id have to look for my notes over it

>>8988154
Yeah, I can see that now haha. I'm a /fit/izen so used to very short threads. I personally think that loss of axonal transport is going to become much more important as more discoveries are made. About 60% of ATP metabolised in a neuron is metabolised at the synaptic terminal for example so a good microtubule network is absolutely essential and I have data that shows microtubules becoming more than 4 times more disorganised under oxidative stress and closer to 10 times in the loss of tau and ox stress

>>8986994
post a similar image from somewhere else so we can see what the fuck you're talking about

>>8988161
well i appreciate the talk, you've gotten me even more excited about starting in the Fall, i cannot wait.

i think you're right in that i need to be wary of losing my life to labwork, as im mostly introverted, and tend to get obsessive about a problem when one arises.