Discover and read the best of Twitter Threads about #Microscopy

Michael Lee

@MichaelLee04

Labeling bio images for AI just got 10x faster🏎. Today, we’re releasing Biodock Autolabel, and it’s kind of magical. We trained it on thousands of bio images so you can use it without training. (1/6)

@BiodockAI #microscopy #pathology #biology

Labeling objects is one of the most painful parts of training AI, especially in bio. Clicking 40 times or dragging the pen tool to define an ROI for hundreds of objects takes a very long time. And yet precise labels are so important for AI accuracy. (2/6)

Now, with Autolabel (powered by AI), this becomes two clicks (or one drag!). Our model takes your defined box and generates what it thinks is the precise object polygon label. For most biological objects, it just works, and it’s getting more and more accurate over time. (3/6)

Read 6 tweets

Cameron A. Schmidt, PhD 🇺🇲

@CAS_mitolab

Don't have access to a fancy Airyscan or STED?
Do have access to a good ole fashion confocal?
You can still do super resolution imaging!🧵#microscopy

All you need are good microscopy and digital imaging fundamentals. Everything you need to know can be found here: ibiology.org/online-biology… /2

Digital images are made up of spatially defined boxes called 'pixels'. Images are collections of pixels assigned color shades from a lookup table. /3

Read 13 tweets

Marine Laporte

@MarineLaporte8

“Cryo-ExM” or “how to see (almost) everything you ever dreamt of”
Want to know more ?!? Check our story out with @CentrioleLab @nikolai_klena in @naturemethods: nature.com/articles/s4159… which combines cryo-fixation/Freeze substitution with #expansion #microscopy (#UExM).

1/Cryo-fixation, as demonstrated in electron microscopy, outperformed chemical fixations on subcellular structure such as the endoplasmic reticulum

2/Cryo-fixation circumvent the artifact of chemical fixations such as loss of antigenicity as seen with the mitochondrial outer membrane marker TOMM20

Read 9 tweets

GAVNet

@GAValueNetwork

Daily Bookmarks to GAVNet 10/31/2021 greeneracresvaluenetwork.wordpress.com/2021/10/31/dai…

Adrienne LaFrance on Twitter and TreadReader

threadreaderapp.com/thread/1452591…

https://twitter.com/AdrienneLaF/status/1452591443172859906

#facebook #transparency #profit #MoralCompass #manipulation

SpaceX needs to tame toilet trouble before weekend launch

phys.org/news/2021-10-s…

#SpaceX #nasa #ToiletLeaks #repairs

Read 8 tweets

Bettina Weigelin

@BettinaWeigelin

It’s exciting to finally share and discuss our study on additive cytotoxicity, a crowd-based killing mechanism of cytotoxic T cells (CTL) to target cancer!
Highlights in the thread, free access @NatureComms here: nature.com/articles/s4146…
1/17
#immunology #microscopy

Initially, we aimed to study modulators of CTL serial killing capacity. But live-cell imaging of various mouse and human model systems, incl. OT1 CTL targeting OVA-expressing cancer cells surprisingly showed, that CTL are pretty bad killers and most contacts were non-lethal. 2/

We doubted our ability to culture cytotoxic T cells.... but in co-cultures with fibroblast-like cells, the same OT1 CTLs proved to be efficient serial killers. 3/

Read 17 tweets

Romain F. Laine

@LaineBioImaging

We are pleased to announce that our #ZeroCostDL4Mic work is now published!
nature.com/articles/s4146…
And our @github
github.com/HenriquesLab/Z…
#DeepLearning and #Microscopy for all!
For the occasion, I’ve put a small Tweetorial together to explain what this is all about!
Thread 0/7

Thread 1/7

You can implement Deep Learning for microscopy in several ways:
1- Using local resources (fast GPUs)
2- Using cloud-computing
3- Using pre-trained models

We think that (1) is uncommon, and that (3) can be unreliable. So we do (2)!

Thread 2/7

We built a platform using @GoogleColab and @ProjectJupyter notebooks that can perform training, quality control and prediction, all on the cloud and for free!

All of this dedicated to #microscopy !

Read 12 tweets

Ale (microbiobac)

@microbiale

Hola! my name is Ale (they/she) and I'm taking part in the #GlobalScienceShow
Today I'll be showing you some of my works about my exploration of the microbial world with drawings! 🦠
Check @GlobalSciShow to follow the whole show🤩

#scicomm #divulgarciencia #comunicacienciachile

I did my PhD in marine #microbiology and now I draw #scicomm comics/zines and cartoons (and a tiny bit of animations) in Spanish&English, to highlight the diversity of the microbial world 🦠and people in STEM✨,
including #queerinstem #bipocinstem
Here a bio-reel👇🏾

The big majority of planet is microscopic and they have a key role in the ecosystem, biogeochemical cycles and evolution of living organisms! 🦠
Our microbial world is huge and amazing!🤩

Read 13 tweets

Kirti Prakash🦉🐒

@kirtiprakash25

Hey #STED, #MINFLUX people,
To continue the public discussion, I list here some of the points I made during my talk.

Summary: MINFLUX is a promising technology but at an early stage of development esp for biological research.

Thread👇

cc @Stefan_W_Hell @BalzarottiFran

Disclaimer 1: I haven't seen or worked with #MINFLUX setup, my arguments mainly on application-side

Disclaimer 2: I asked these questions via email (Sept 2020) and requested raw data and codes but haven't received a reply yet

I hope @rita_strack @naturemethods can help!

You can learn more about #MINFLUX from this excellent talk by @Stefan_W_Hell

Also, some papers making an effort in this direction

Read 43 tweets

Luciano Lucas

@lucianoaglucas

Excited to introduce #3DRCAN for denoising, super resolution and expansion microscopy. Super proud of this colab with Hari Shroff, Jiji Chen et al.

@NIBIBgov @arpcomplex

Preprint: biorxiv.org/content/10.110…

Code: github.com/AiviaCommunity…

#microscopy #aimicroscopy #aivia

1/17

"Three-dimensional residual channel attention networks denoise and sharpen fluorescence microscopy image volumes"

J Chen, H Sasaki, H Lai, Y Su, J Liu, Y Wu, A Zhovmer, C Combs, I Rey-Suarez, H Chang, C Huang, X Li, M Guo, S Nizambad, A Upadhyaya, J Lee, L Lucas, H Shroff.
2/17

We are particularly interested in characterizing the limits of #deeplearning based approaches to image restoration. You will find several experiments comparing several best-in-class approaches: #3DRCAN, #CARE, #SRResNet and #ESRGAN.

#microscopy #aimicroscopy #iSIM

3/17

Read 17 tweets

Julia Bitencourt

@juliabtencourt_

Pra deixar o pessoal de laboratório feliz e as aulas EAD menos complicadas, segue em anexo:

🔬THREAD COM SIMULAÇÕES DE LABORATÓRIO VIRTUAL🔬

#BiomedTwitter #AcademicTwitter #science #biology

Nessa thread você vai encontrar simulações de laboratório de diagnóstico, #microscopy, #immunology, #molecularbiology, #cellbiology e tudo que eu encontrar. Dá uma olhada até o final pra ver se tem alguma simulação que te interessa! Vou atualizando aos poucos! :)

Antes de começar, gostaria de avisar que a maioria (talvez todas) das simulações são em inglês, infelizmente :(

🧬 Minha dica pra quem ainda não tem domínio da língua: ativa a tradução do google translate na página e vê se consegue entender o conteúdo da página. Talvez ajude!

Read 36 tweets

Mahmoud Bukar Maina PhD FRSA

@mahmoudbukar

#AfricanNeuroscience [Thread]

Ever wondered what #Neuroscience research looks like in #Africa? For 3 years, we have been working on profiling the neuroscience research landscape in the continent’s 54 countries. Very excited to share our latest work: biorxiv.org/content/10.110…

(1)

https://twitter.com/biorxivpreprint/status/1268676949209223170

Why is this important?
#Africa has real potential in #Neuroscience, but needs help to rise from its current position! To do this, we need accurate data that reflects the heterogeneity of research across the continent's 54 countries.

(2)

Such data is lacking, as previous estimates about research outputs from #Africa are mostly inaccurate, partly because it is difficult to tell whether the research was, in fact, conducted within Africa or outside the continent in collaboration with #Africanscientists

(3)

Read 20 tweets

Amy Proal, PhD

@microbeminded2

Good news! This new human #tumor microbiome study is excellent. They used hundreds of negative controls for contamination + an extensive combo of methods to identify #bacteria in 7 #cancer types (lung, ovary, pancreas, melanoma, bone, brain): science.sciencemag.org/content/368/64…

2/ Bacterial LPS + 16SrRNA were frequently detected in all tumor types, w/ #breast cancer harboring a particularly rich and diverse #microbiome. The image below shows LPS/16SrRNA in breast cancer cells. Bacteria were also found in normal breast samples from healthy subjects

3/ In one experiment the team grew live #bacteria from three main phyla (Proteobacteria, Firmicutes, Actinobacteria) from fresh breast #tumor samples collected from women undergoing breast surgery

Read 5 tweets

Caleb Dawson

@calebadawson

We found unique breast immune cells in the duct walls – ductal macrophages. They remove dying cells, help remodelling + are key players in cancer.

How did we get from this first sighting to finding their identity and function? Follow this thread!
bit.ly/35o2XSj
1/n

The breast contains mammary ducts surrounded by fat, blood vessels, immune + other cells.

We use 3D imaging to investigate the complex relationships b/w these cells to better understand disease.
#microscopy #mammarygland
2/n

The ducts form a tree that branches through the breast and blooms and recedes in pregnancy and weaning. These are precancerous mouse ducts, alveoli in lactation and a summary of development in mice.
3/n

Read 43 tweets

Luciano Lucas

@lucianoaglucas

@3dtrevor @Mariposa_Rising @MascalchiP and the wider team are running another well attended hands on online #bioimageanalysis workshop. Today about 3d segmentation and tracking! See more: drvtechnologies.com/aivia-online-w… #aivia #aimicroscopy #Microscopy

Uses the freely available #aiviaweb.

Setting ROIs to get quick previews.

Read 3 tweets

Luciano Lucas

@lucianoaglucas

The #OSABiophotonics20 (20-23 of April) congress has been moved to an 100% online format due to #covid19. This event is packed with great (microscopy and image analysis) presentations and is FREE to attend! Register here: osa.org/en-us/meetings… 1/3
#aimicroscopy #biophotonics

My talk "AI for Microscopy Applications|The Era of Implementation", highlights 2+ years of R&D (colab w/ Hari Shroff et al.), and is influenced by @kaifulee @EricTopol @loicaroyer @martweig @florianjug @TheGeneMyers @uschmidt83 @PavelTomancak @HenriquesLab #OSABiophotonics20 2/3

KUDOS to @OpticalSociety @OSAPublishing and organizers for quickly moving the event to "online" and for making it free to participate. Also, I thank the organizers for the invite to present our work - MUCH appreciated. 3/3
#communityimpact #OpenScience #aimicroscopy #microscopy

Read 4 tweets

Luciano Lucas

@lucianoaglucas

My talk on #AIMicroscopy as presented at the "NIH AI Imaging Workshops".

Intro/history of AI, apps in #microscopy, intro to #deeplearning, and some of our recent research results into image restoration (in colab with Hari Shroff et al).

Organized by: @NCIDataSci @NIH @NIBIBgov

Slides: dropbox.com/sh/wi2rez5xocs…

Video: cbiit.webex.com/cbiit/lsr.php?…

#AImicroscopy

The video of my part starts from 1:00:45.

Before that is a talk from Dr. Matt Guay from NIBIB (I recommend it too!). "An Introduction to Content-Aware Computation for Optical Microscopy" #CARE @loicaroyer @florianjug @uschmidt83 @martweig

Read 3 tweets

Luciano Lucas

@lucianoaglucas

We will start to roll out #AiviaWeb at no cost to use, tomorrow. All #aivia functionality accessible via a web browser. This is part of our #covid19 mitigation plan - more actions soon so you can continue to be productive while #wfh. #bioimageanalyis #aiviacommunity #microscopy

To get early access to #AiviaWeb please sign in/up. See drvtechnologies.com

Once you are signed up we will reach out to you with all the details including usage and booking guidelines. A webpage dedicated to our covid19 / wfh mitigation plan will be up very soon too. Many more resources are in the pipeline.

Read 6 tweets

Mascalchi Patrice

@MascalchiP

*** 1/9 ***
Today is HIS-TO-RI-CAL about Aivia!!!

We are releasing a free to use software called Aivia Community
It’s meant to be a collaborative tool, allowing you to…
(see next tweets)

#Microscopy #ImageAnalysis #bioimageanalysis #3Drendering

*** 2/9 ***
Open and interactively explore 2-to-5D microscopy data sets
(tested up to 3 TB files)

*** 3/9 ***
Create attractive visual outputs (such as snapshots, video animation) from:
•raw microscopy images
•OR data sets previously analyzed with Aivia (with 3D surfaces, traced neurons for instance)

#3Drendering #Animations #VideoExport #Snapshots #3Dsurfaces

Read 10 tweets

Paulo Navarro-Costa

@germcells

1/n - Did you know developing #sperm cells are interconnected by cytoplasmic bridges until released from the testis? Just check out this awesome electron #microscopy 🔬image (by the late Don Fawcett) of two neighboring sperm cells. Note the arrow connecting them 🧐

2/n- An intriguing property of these bridges is that the proteins that form them are also involved in the regulation of meiotic chromsomes 🤔 Topoisomerase 2 is a recently identified example 👇academic.oup.com/biolreprod/art…

3/3 - This suggests there's something more to these bridges than just being channels between neighboring cells... If you are curious about these intriguing structures stay tuned 📻 for future developments 🤓

Read 3 tweets

Luciano Lucas

@lucianoaglucas

1/ At #ASCBEMBO19 we will present five posters and a tech talk on #aimicroscopy and #CLEM. Details here: drvtechnologies.com/ascbembo2019

Many thanks to our collaborators Hari Shroff, Jiji Chen, @huzhao4, Rachel Wong, Chris Combs, @3i_inc.

#microscopy #imageanalysis #Aivia #ASCBEMBO2019

2/ P35/B36 Universal EM Connectomic analyses by Deep Learning Powered App‐matching Image Conversion

drvtechnologies.com/post/ascb-embo…

With Prof. Rachel Wong and @Sallywing

#ASCBEMBO19 #AImicroscopy #Aivia #AiviaCloud #imageanalysis #microscopy #CellBiology #machinelearning #drawacell

3/ P57/B58 GPU‐accelerated Machine Learning‐powered 3d Image Segmentation at Scale

Details: drvtechnologies.com/post/ascb-embo…

#ASCBEMBO19 #AImicroscopy #Aivia #AiviaCloud #imageanalysis #microscopy #CellBiology #machinelearning #drawacell #pixelclassifier #imagesegmentation

Read 8 tweets

Beck Laboratory

@Beck_Laboratory

How do you make nuclear pores away from the nucleus?
Our paper online today bit.ly/AL-NPC
@embl @a_schw @SchwabYannick @CellCellPress #development #Nuclearpores #microscopy
https://t.co/f4Xq1Vsk31
1/11 [a thread]

Background: Mothers stockpile nuclear pores (NPCs) in the cytoplasm of their eggs to enable embryonic cell cycles that are too fast for conventional NPC assembly (bit.ly/ALembryo). These are arranged in stacked ER sheets called Annulate Lamellae (AL, see 4/11).
2/11

These are Drosophila egg chambers; where the growing oocyte is transcriptionally silent, while so-called nurse cells produce the material for its development and transport it to the front. We wanted to see if this includes AL and whether they accumulate over time.
3/11

Read 11 tweets

Discover and read the best of Twitter Threads about #Microscopy

Most recents (24)

Related hashtags

Discover and read the best of Twitter Threads about #Microscopy

Most recents (24)

Related hashtags

Did Thread Reader help you today?