#imagej

[wolframcarbide]

[filmvis]

Furiosa: A Mad Max Saga, George Miller, 2024

[sporadicali-ali]

When #automated analysis does not go to plan 😪 I had to look at if/how the Sox 11 protein effects brain development and one way to do that was to measure brain size, which I did my measuring the size of the layers in the brain. Manual analysis can take time so I tried to automate this using #imagej #fiji and let’s just say that I was less than successful 🫠 Slide 1: what I got measured Slide 2: what was supposed to be measured #neuroscience #neuro #neurodevelopment #grk #grk2162 (at Universitätsklinikum Erlangen Institut für Humangenetik) https://www.instagram.com/p/CmbZRN4t82w/?igshid=NGJjMDIxMWI=

[vividotg]

ImageJ 1.53 Java 7 Di Exagear Windows Emulator

[meticulousfragments]

I know there’s a joke somewhere about how every computer program used in paleontology seems like it’s a million years old but I’m too tired after fighting ImageJ to make it

[abysskeeper]

Today while working: Probably would horrify my artist friends with how I work with a tablet

[unopenablebox]

sweater WIP in question. this sleeve is way closer to done than i remember it being, thanks to my 2019 self for your many mitzvot

[fairlystitious]

being forced to analyze gods worst gel

[catinfroghat]

I finally got endnote to insert my references into my final document everyone cheered!!!! I for sure thought I was going to lose them all because I kept getting error messages and I was going to throw my laptop into a pond if I had to do them all over again

[tenfluenza]

no one was proud of me for getting this done and they're wrong what matters is IM proud of me for today

[wolframcarbide]

[filmvis]

Poor Things, Yorgos Lanthimos, 2023

[lixenn]

sorting out all those pictures is such a pain

I found pictures of dermis on my laptop but those are different ones than what i have on my presentation? i think my supervisor added the presentation ones and i don't have them saved.

well i saved them now and they are definitely better looking than the ones i had (because the qualtiy of those pictures... fucking horrible)

but i made lots of folders so hopefully i can sort this out and edit them a lil bit to make them look less god ugly

*stares at microscopy pictures on my new laptop*

HOly shit! I need to adjust them they look fucking horrible a few of them have this green undertone? the fuck?

Downloading ImageJ it is...

Fuck... how the hell do I open them in imagej when the pictures are on a power point

ummm

oh thank god i can save them from the powerpoint 🫡

[covid-safer-hotties]

Also preserved in our archive

By Dr. Sushama R. Chaphalkar, PhD.

In a recent research paper posted to the bioRxiv preprint* server, researchers in the United States investigated the potential effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on cholesterol metabolism, focusing on the role of the viral protein open reading frame 3a (ORF3a).

They found that SARS-CoV-2 causes cholesterol sequestration in lysosomes via the ORF3a protein, which disrupts protein trafficking and reduces the levels of bis(monoacylglycero)phosphate (BMP) in the cell, enhancing viral survival.

Background Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, disrupts lipid metabolism, particularly cholesterol homeostasis, which can persist during and after infection. This is linked to disease severity and long-term complications like dyslipidemia and cardiovascular diseases.

Cholesterol is crucial for cellular function and is primarily transported through lysosomes, where proteins like Niemann-Pick C1 and C2 (NPC1 and NPC2) facilitate its release. SARS-CoV-2 may exploit plasma membrane cholesterol to enhance infectivity.

Disruptions in the lysosomal cholesterol pathway can cause cholesterol buildup, impairing cellular functions, and viruses like Ebola are known to hijack this mechanism. Notably, BMP plays a dual role: it aids in cholesterol transport and contributes to viral infection by promoting viral fusion with lysosomal membranes.

In the present study, researchers investigated the potential impact of SARS-CoV-2 infection on cholesterol transport in cells, focusing on the role of the viral protein ORF3a.

About the Study A variety of experimental techniques were employed, including culturing A549, HeLa, and Vero E6 cells, followed by SARS-CoV-2 infection at different multiplicities of infection. SARS-CoV-2 ORF3a-VPS39 interaction was studied using mutations at key residues (notably W193 and Y184, which were identified as critical for this interaction). Immunofluorescence, filipin staining, and confocal microscopy were used to assess cholesterol localization and vesicular dynamics, while high-content imaging quantified cell-specific responses.

Cholesterol levels were measured using gas chromatography-mass spectrometry (GC-MS), and lipid species were analyzed through shotgun lipidomics. For further protein analysis, western blotting was performed to detect secreted NPC2 and cathepsin D, along with cell lysates. Data were analyzed using ImageJ and Prism 9, and statistical significance was determined by t-tests or analysis of variance.

Results and Discussion SARS-CoV-2 infection was found to increase filipin-positive puncta in lysosomes of A549-hACE2 and Vero E6 cells, indicating altered cholesterol distribution, especially in lysosomes, without affecting total cholesterol levels. Among the 28 viral proteins tested, ORF3a showed the strongest increase in filipin puncta, suggesting significant lysosomal cholesterol sequestration.

Notably, SARS-CoV-2 ORF3a localized to lysosomes and caused them to swell, whereas SARS-CoV ORF3a did not induce such effects, highlighting a distinct pathogenic strategy unique to SARS-CoV-2.

ORF3a was found to interact with VPS39, a key component of the HOPS complex involved in cholesterol egress from lysosomes. Key residues W193 and Y184 were shown to form a hydrophobic binding interface critical for this interaction, distinguishing SARS-CoV-2 ORF3a from its SARS-CoV counterpart. Mutations at W193 and Y184 disrupted this interaction, while S171 and H182 had no significant effect.

SARS-CoV-2 ORF3a expression was shown to cause cholesterol accumulation in lysosomes, which was reduced by the W193A mutation. It also led to the mislocalization of NPC2 and increased its secretion, indicating disrupted NPC2 trafficking, likely due to interference with TGN-to-endosome transport. Additionally, BMP levels were significantly reduced in infected cells, which likely exacerbates lysosomal cholesterol sequestration.

In SARS-CoV-2-infected Vero E6 cells, BMP levels were found to decrease at 12 hours post-infection, coinciding with increased cholesterol at 18 hours. In HeLa-Flp-In cells, SARS-CoV-2 ORF3a was found to reduce BMP levels by 20%, with partial rescue in the W193A mutant. Lipidomics confirmed this reduction, correlating BMP loss with cholesterol accumulation and suggesting BMP reduction may contribute to cholesterol sequestration.

SARS-CoV-2 may reduce plasma membrane cholesterol to limit secondary infections, as shown by decreased SARS-CoV-2 infection in NPC1 inhibitor-treated cells. This supports the hypothesis that the virus manipulates cholesterol distribution to optimize replication conditions. Interestingly, the virus also appears to reduce its own infectivity within a single cell, suggesting a self-regulating mechanism to prevent viral overload and ensure broader host-level spread.

Conclusion In conclusion, a novel mechanism by which SARS-CoV-2 disrupts host cell lipid metabolism, specifically through cholesterol sequestration in lysosomes, has been elucidated. By uncovering the specific interaction between the viral protein ORF3a and host protein VPS39, the study highlights a critical role of lysosomal cholesterol trafficking disruption in SARS-CoV-2 pathogenesis.

This discovery opens potential therapeutic avenues to target lipid dysregulation in COVID-19, which could help mitigate both the disease's immediate and long-term metabolic consequences, including dyslipidemia and cardiovascular complications.

Journal reference: Preliminary scientific report. Manipulation of Host Cholesterol by SARS-CoV-2. Aliza Doyle et al., bioRxiv, 2024.11.13.623299 (2024), DOI: 10.1101/2024.11.13.623299,

Study Link: www.biorxiv.org/content/10.1101/2024.11.13.623299v1

[nyaagolor]

Finding SV Character Heights Part 1

Procrastination leads to wonderful places, and for me that's "hey what if I could get rough estimates for canon heights using the ingame models?" So I did! Unfortunately, this post got long so I only included the heights of a few major characters for now. Teachers, Gym Leaders + League, and Team Star will be in separate posts!

Protagonist: 5'0" Nemona: 5'8" Penny: 5'1" Arven: 5'7" Clavell: 5'7" Sada: 5'9" Turo: 6'1"

I used imageJ / Fiji for analysis and some screenshots from MunchingOrange's playthrough of the game on youtube. I explain the process and attached all the screenshots under the cut so you can judge the legitimacy of my "math" yourself!

A quick overview of how I did this: there's a (free to use) software called Fiji made for processing images (google Fiji ImageJ and it'll be the first link). It's used in a lot of data analysis, which is mostly what I use it for, but it has some fun features to play around with too. (if people want a tutorial lmk I'd be happy to write one up). The most important part for our purposes is the measure function-- if you draw a line on an image, it will tell you how long that line is in pixels. This line can be straight, curved, angled in any direction, or even multi-segmented, making it pretty good for comparing things. Then all I had to do was get images of characters standing next to each other-- from there I could transitive property my way to the height of every character in the game!

First step was getting a good basis for comparison-- I can easily get ratios of character heights but without at least one confirmed height I can't translate it into real world metrics. Since the characters themselves don't have canon heights, it had to be a pokemon. This introduced another problem, which is that in SV, pokemon are varying sizes within a species, so I can't count on the overworld models to work. Plus, some of them aren't even accurate!

However, there was one pokemon I could compare to the protagonist pretty easily whose height was a little less skeptical: the main legendary (koraidon in my case). A few cursory comparisons led me to guess that Koraidon's 8'2" "height" is measured from head to toe while standing in apex form. Anything else gives heights of characters that make zero real world sense so this is what I went with in the end. Thus we get the screenshot that starts it all!

Koraidon's head is bowed, but this was the closest I could get so I guesstimated that the top of the blue ridges was about where Koraidon's head would be. Knowing that Koraidon is 8'2", we get the following heights:

Koraidon: 536 pixels - 98 inches - 8'2" Protagonist: 328 pixels - 60 inches - 5'0" Nemona: 372 pixels - 68 inches - 5'8"

Thus far it looks like we're on the right track! Assuming the protagonist is 14 and Nemona is 16/17, these heights seem pretty normal. Knowing the protagonist's height gives us the ability to find out most other characters, so we're off to a good start!

(side note: the calculation I used to turn pixels into inches was pixels1 / inch1 = pixels2 / inch2. The pixels we can get from the lines on the images, and the inches we know from Koraidon's pokedex entry, so we just solve for inch2)

Next up is Clavell (mostly because he showed up first). Something interesting is that he's actually slightly shorter than Nemona, you can see it in the first cutscene in front of Nemona's house (i can add a screenshot in the reblogs / replies but didn't want to clog the post with another image). From this image, we can find:

Protagonist: 685 pixels - 60 inches - 5'0" Clavell: 769 pixels - 67 inches - 5'7"

You heard it here first, the director is a short king

Next up is Arven!

Protagonist: 782 pixels - 60 inches - 5'0" Arven: 880 pixels - 67 inches - 5'7"

(The math actually says Arven is 5'7.5", but I'm not bothering with decimals. This makes him sliiiiiiightly taller than Clavell)

Penny is seen angled from the protagonist in her intro scenes, so I skipped all the way to her boss battle to find a good screenshot. To my surprise, she's actually slightly taller than the protagonist!

Protagonist: 368 pixels - 60 inches - 5'0" Penny: 376 pixels - 61 inches - 5'1"

(Side note 2: Characters are measured from their heels to the crown of their head-- if they have really big hair it doesn't count as part of their height)

Last one in this round is the professor (Sada in my case, as I'm using a Scarlet playthrough for screenshots). I'm gonna assume that the AI and Professor are the same height for this

Protagonist: 507 pixels - 60 inches - 5'0" Sada: 584 pixels - 69 inches (nice) - 5'9"

Turo forced me to use a different playthrough to grab a screenshot, which used a female protagonist. I'm fairly positive that the male and female protagonist models are the exact same height (if not the exact same model) so I don't think there's any snags with this, but if anyone knows otherwise lmk. Btw, I used the playthrough by Rubhen925 for this screenshot!

Protagonist: 501 pixels - 60 inches - 5'0" Turo: 611 pixels - 73 inches - 6'1"

Turo is pretty damn tall :0 !

This post is getting absurdly long, so I'm going to make separate posts for the League / Gym Leaders, Team Star, and the teachers! Hope you've enjoyed, and if there's any specific trainer class or other character you wanna know the height of just lmk :) I also plan on making a post of some more silly measurements (like the exact dimensions of Penny's backpack, the proportion of Geeta's height that's just her legs, the size of Arven's camping bag and whether or not his friends could reasonably curl up inside, etc)

[knuckleduster]

thought i was so genius for editing the txt file for the macro i want to run in imagej but turns out it didnt actually change anything