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hamid13r.bsky.social @hamid13r.bsky.social · 8h

Thank you so much, Alister! I turned this into my first stand-alone github and added a readme file:

GitHub - hamid13r/warp_remove_skipped_views: Removing etomo skipped views from Warp xml files to improve the tomogram reconstruction.

Removing etomo skipped views from Warp xml files to improve the tomogram reconstruction. - GitHub - hamid13r/warp_remove_skipped_views: Removing etomo skipped views from Warp xml files to improve ...

github.com

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hamid13r.bsky.social @hamid13r.bsky.social · 14h

Also I forgot to thank @alisterburt.bsky.social for answering all my Warp questions so promptly and clearly!

hamid13r.bsky.social @hamid13r.bsky.social · 14h

I used this opportunity (and github copilot!) to turn this into my first github repository with README and examples, etc. This was a lot of fun! Hopefully, I didn't completely mess it up!

github.com/hamid13r/war...

GitHub - hamid13r/warp_remove_skipped_views: Removing etomo skipped views from Warp xml files to improve the tomogram reconstruction.

Removing etomo skipped views from Warp xml files to improve the tomogram reconstruction. - GitHub - hamid13r/warp_remove_skipped_views: Removing etomo skipped views from Warp xml files to improve ...

github.com

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hamid13r.bsky.social @hamid13r.bsky.social · 1d

Afaik * lol

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hamid13r.bsky.social @hamid13r.bsky.social · 1d

Well, asaik there are "vectors" somewhere in there!

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hamid13r.bsky.social @hamid13r.bsky.social · 2d

Yes. The problem is especially there when views are skipped at fine alignment and not from the beginning. This helped me a bunch for high-res in vitro project I am working on.

Let me know if you need help running it, I am not a very good and clear coder haha

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hamid13r.bsky.social @hamid13r.bsky.social · 2d

Working on #WarpTools I have the old problem of removing "bad tilts". These are views that I skipped in #etomo to get a better model...

I wrote a python code to turn the UseTilt to False in the XML files for those views and improve the tomo reconstruction.
#teamtomo
github.com/hamid13r/war...

warp_lamella_adapters/remove_bad_views.py at main · hamid13r/warp_lamella_adapters

A short optimized pipeline to get lamella tomography (with pretilt and with some tilts obscured or mistracked) to work well with Warp - hamid13r/warp_lamella_adapters

github.com

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Reposted by hamid13r.bsky.social

Alister Burt @alisterburt.bsky.social · 15d

The SerialEM Python interface has been a huge driver of innovation at the hardware-software boundary in cryo-EM: suddenly the scientist with some programming chops can readily implement their ideas 🥰

This looks like a fantastic meeting!

Guenter Resch @nexperion.net · 16d

Happy to announce "Technical Innovations Using #SerialEM: A Community Meeting", a new format of hybrid meeting David Mastronarde and I are organizing in April 2026. For more info, a preliminary list of speakers, pre-registration etc. visit
www.nexperion.net/semcm2026

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Reposted by hamid13r.bsky.social

Dovile Januliene @djanuliene.bsky.social · 22d

We all love colours, especially, when they can be generated automatically! Fantastic talk by Danielle Grotjahn @nanigrotjahn.bsky.social linking method development, structural biology and cell biology! #WEHeraeusSeminar #cryoEM #StructuralBiology #Microscopy @arnemoeller.bsky.social

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Reposted by hamid13r.bsky.social

Jan Philipp Kreysing @jpkreysing.bsky.social · Aug 23

More great cryo-ET benchmarking work from my colleagues Maarten Tuijtel, Tomáš Majtner, Beata Turoňová, & @becklab.bsky.social: Systematic study of how tilt increment choice affects downstream TM & STA. Preprint has the optimally balanced tilt increment. #TeamTomo www.biorxiv.org/content/10.1...

Optimal tilt-increment for cryo-ET

Cryo-electron tomography (cryo-ET) enables high-resolution, three-dimensional imaging of cellular structures in their native, frozen state. However, image quality is limited by a trade-off between ang...

www.biorxiv.org

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hamid13r.bsky.social @hamid13r.bsky.social · Jul 9

Ran out of github copilot prompts while programming and realized I was already depending on in too much :(

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hamid13r.bsky.social @hamid13r.bsky.social · Jun 25

thank you.

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hamid13r.bsky.social @hamid13r.bsky.social · Jun 25

Yes. And what they disliked about the believers was that new muslims wanted to pretty much change the whole system of that society! So they werent like "oh you dont believe in my god" their beliefs were dangerous to the normal order of things asaik

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hamid13r.bsky.social @hamid13r.bsky.social · Jun 24

Like, why not just "politicians lie"!

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hamid13r.bsky.social @hamid13r.bsky.social · Jun 24

the persecution mentioned in the Quran is actually the Arab pagans torturing or killing the first believers of the prophet, notably they did NOT live under Christian, or Jewish (wtf?) governments!

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hamid13r.bsky.social @hamid13r.bsky.social · Jun 24

Reading Ferdowsi by Amir Khadem is top notch work.
He is a expert and very good at explaining... I am not sure how good it is for learning persian though...
readingferdowsi.com

فردوسی‌خوانی

readingferdowsi.com

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hamid13r.bsky.social @hamid13r.bsky.social · Jun 24

What audiobook was it? Poetic farsi breaks from grammar often... But out of all poetry books, shahnameh is a good one!

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hamid13r.bsky.social @hamid13r.bsky.social · Jun 24

You are lucky this is not twitter!!

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hamid13r.bsky.social @hamid13r.bsky.social · Jun 23

I knew some iranian user on instagram who made a video as a joke that if you flip and copy the open AI logo it looks like star of david. Now his satirical video if everywhere on social media!!!

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hamid13r.bsky.social @hamid13r.bsky.social · Jun 23

Huh, they javent even put the moon in the sickle yet? I wouldbut i am afriad the chatGPT debacle will repeat! (Please tell me you saw that?!)

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hamid13r.bsky.social @hamid13r.bsky.social · Jun 23

No, the antisemitism was quite obvious.

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hamid13r.bsky.social @hamid13r.bsky.social · Jun 23

Lol advocacy

hamid13r.bsky.social @hamid13r.bsky.social · Jun 23

I dont see any Palestinian adcovacy in this account?

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hamid13r.bsky.social @hamid13r.bsky.social · Jun 22

Miga is one letter away from "i will fuck you" in persian!

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hamid13r.bsky.social @hamid13r.bsky.social · Jun 21

I am not a neuroscientist (i have just looked at neuronal mitochondria under TEM), but sometimes clarifying the question itself is more enlightening than the answer. I *think* everything in the brain comes on top of a baseline neuronal activity, so some maybe some sense of thinking is intrinsic?

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