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
Firstly, we looked at how #3DRCAN and other #DL based approaches behave when denoising iSIM images depicting a range of organelles, including: Actin, ER, Golgi, Lysosome, Microtubule, Mitochondria.

#microscopy #aimicroscopy #cellbio #deeplearning #superresolution

4/17
We were also interested in finding out the lowest level of illumination (and lowest SNR) for which #3DRCAN could still "work", i.e. create a good quality restoration. Imaging done on an iSIM.

#iSIM #microscopy #aimicroscopy #cellbio #deeplearning #bioimageanalysis #aivia

5/17
Now that we had nicely restored images (good performance in terms of SSIM and PSNR), we detected and analyzed mitochondria. This was nearly impossible when using the raw/input data.

#microscopy #aimicroscopy #cellbio #deeplearning #bioimageanalysis #aivia #3DRCAN

6/17
We then applied the trained #3DRCAN to live cell imaging data (4D). As a result we could study fusion and fission (as imaged by iSIM) events in mitochondria over long time lapses.

#microscopy #aimicroscopy #cellbio #deeplearning #bioimageanalysis

7/17
Secondly, we wanted to determine if #3DRCAN could be used for other types of super resolution microscopy - we used paired Confocal<->STED 3D data sets to train our models. Imaging done with a Leica SP8. @LeicaMicro

#STED #superresolution #aimicroscopy #microscopy

8/17
The trained #3DRCAN was applied to raw confocal data (incl. nuclear pores, microtubules and DNA), greatly improving (~2-fold) the spatial resolution. Imaging done with a Leica SP8. @LeicaMicro

#STED #superresolution #aimicroscopy #microscopy

9/17
Ultimately, we wanted to perform fast 4D confocal imaging and "convert" the raw data to STED-like images. So, we applied the trained #3DRCAN to live cell 3D (confocal) data sets. See 👇

#STED #superresolution #aimicroscopy #microscopy

10/17
Lastly, we tested whether it was possible to further increase the resolution of iSIM (itself a #superresolution microscopy modality). To do this, we used expansion microscopy to generate the GT we needed to train #3DRCAN for this task.

#iSIM #ExM #aimicroscopy #microscopy 11/17
#3DRCAN was shown to improve both the lateral and axial resolution of iSIM images. Moreover, the improvement in resolution was superior to deconvolving the raw images.

#iSIM #ExM #superresolution #aimicroscopy #Microscopy 12/17
As with the other key experiments, we successfully tested out the trained #3DRCAN on live cell 3D data sets. In this case we imaged mitochondria and microtubules using iSIM.

#iSIM #ExM #superresolution #aimicroscopy #Microscopy 13/17
Disclaimer: this being a twitter thread, a lot of the details are missing - you are most welcome to review the pre-print. Your suggestions and input are welcome.

15/17
You can train your own #3DRCAN models and/or test out the ones we have described here. See github.com/AiviaCommunity… There are also some test images there. Let us know if you have any questions and/or suggestions.

#python #opensource #openaccess #OpenScience #aimicroscopy

16/17
Note to Aivia users: in the very short term all the models described in the #3DRCAN preprint will be available in #Aivia, #AiviaWeb and #AiviaCloud.

17/17

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More from @lucianoaglucas

15 May
#ML powered image analysis is a great way to gain insight when all you have is RI variations - lable free. Quyen (linkedin.com/in/qatran/) and Luca (linkedin.com/in/luca-clario/) are doing a great job discussing the technology behind #Aivia and @NanoLiveLtd. Hosted by @MEDIASystemLab ImageImageImage
Now a live demo! Comparing "threshold based" segmentation methods vs #pixelclassifier (machine learning) based segmentation. There are pros and cons. For more details of the #pixelclassifier see: drvtechnologies.com/post/ascb-embo… Image
Read 5 tweets
15 Apr
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 Image
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 Image
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
25 Mar
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
21 Mar
The Seattle metro region and the whole #PNW are being severely affected by the #COVID19outbreak. In >1 month we went from "there is a small cluster of cases in a nursing home" to "we need to lock down the whole region to avoid worst case scenarios" (not happened yet) 1/13 ImageImageImageImage
The (social) media frenzy is impressive. Even Facebook and others are worried their servers / data centers may not be able to cope with demand for long (cnn.com/2020/03/18/tec…). We have used social media for good - checking in on friends and family all over the world. 2/13
While this is a challenging time, there are many positive things to be thankful for. Personally, I am enjoying having more time with my young boys (4 and 6 yo) and wife. the boys are curious and scared about the whole story - but 3/13
Read 14 tweets
6 Dec 19
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 Image
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 Image
Read 8 tweets
4 Jun 19
#ELMI2019 lightning talks... Go! Image
Image
Image
Read 19 tweets

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