# Digital Twin to Model the Effect of Spaceflight on the Retina **URL:** \ **Category:** AIML AWG Open Projects\ **Tags:** aiml, digital-twin, retina\ **Created:** [May 24, 2024, 9:39pm UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417 "2024-05-24T21:39:43Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![jgong](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/jgong/32/1469_2.png) [@jgong](https://awg.osdr.space/u/jgong)\ **Post date:** [May 24, 2024, 9:39pm UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417/1 "2024-05-24T21:39:43Z")
We are investigating the effect of spaceflight on gene expression of retina through the RR9 dataset (combining other RR datasets), build data augmentation methods and digital twin models to make currently rather limited dataset more useful. This is a subgroup of AWG AIML. -=-=-=- EDIT BY LAUREN: For everyone new to this project, our subgroup lead Dr. Jian Gong gave a great talk on the goals of this project in the 2024 AWG Symposium: [https://youtu.be/psrO38DP454?si=jmuOL8y3iotErWMn&t=1964](https://youtu.be/psrO38DP454?si=jmuOL8y3iotErWMn&t=1964) Here is the Google Drive with the link to project materials and recordings: [Digital Twin - Google Drive](https://drive.google.com/drive/folders/1RuLxMuz6Ibr0SGrZJ7k3tCDkQrW22oIQ) Please take a look at the [Google Colab notebook](https://colab.research.google.com/drive/1r7-NYufjlQzdyXSZ5scFfWGqfj3voStW?usp=sharing) that I started, combining all the RR-9 retina/eye data and imputing missing values. Anyone can make a copy and move forward with this notebook. Next steps that someone can take would be: - Improve the imputation - Use this dataset to create a larger synthetic dataset - Use a CVAE or similar architecture to start training a digital twin! ---
**Author:** ![joel.steele](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/joel.steele/32/789_2.png) [@joel.steele](https://awg.osdr.space/u/joel.steele)\ **Post date:** [May 29, 2024, 10:50pm UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417/2 "2024-05-29T22:50:33Z")
In the same manner as those out of Mt Sinai i.e. Jen Van Eyk? @james.casaletto @jgong ? ---
**Author:** ![james.casaletto](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/james.casaletto/32/158_2.png) [@james.casaletto](https://awg.osdr.space/u/james.casaletto)\ **Post date:** [May 30, 2024, 1:08am UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417/3 "2024-05-30T01:08:35Z")
Hi @joel.steele I’m not very familiar with Jen’s research, but at first glance it looks like she does a lot with proteomics. At this point, with the data we have, we’re looking at transcriptomic data (along with phenotypic data). Is there something particular about Jen’s work that you’re thinking of here? ---
**Author:** ![dave](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/dave/32/123_2.png) [@dave](https://awg.osdr.space/u/dave)\ **Post date:** [May 30, 2024, 10:50pm UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417/4 "2024-05-30T22:50:07Z")
Hi @james.casaletto and @jgong , what type of phenotypic data do you have for retinas? My company can measure shapes very uniquely. Example: **Video [12 min]: Shape Analysis of PAP Smears by Shape Genie** [![](https://us1.discourse-cdn.com/flex001/uploads/osdr/original/1X/23c76f2d195b9d2f1941b85fa36b696aec3fce4f.jpeg "Shape Analysis of PAP Smears by Shape Genie") ](https://www.youtube.com/watch?v=yGkeejOFM94) Slides from video: > **[Shape analysis of Pap Smears by Shape Genie.pdf](https://drive.google.com/file/d/19L0eJoPt7tsB7H6MZQ7kWtR-I8eNPSmb/view?usp=sharing)** > > Google Drive file. Regards, Dave ---
**Author:** ![james.casaletto](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/james.casaletto/32/158_2.png) [@james.casaletto](https://awg.osdr.space/u/james.casaletto)\ **Post date:** [May 31, 2024, 6:58pm UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417/5 "2024-05-31T18:58:21Z")
Hi Dave Thank you for sharing your Shape Genie work – really awesome stuff!! The phenotypes we have for murine retina include: 1. depths (retina, choroid, sclera, pigment layer) and eye dimensions (ant-post, sup-inf) 2. photoreceptor layer immunostaining (HNE, PNA) 3. microscopy (ZO, TUNEL, PECAM) 4. tonometry And we have associated transcriptomic data for some of the same samples. cheers and happy Friday -james ---
**Author:** ![dave](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/dave/32/123_2.png) [@dave](https://awg.osdr.space/u/dave)\ **Post date:** [June 1, 2024, 5:05am UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417/6 "2024-06-01T05:05:25Z")
Hi @james.casaletto , If you send me some example pictures of control vs. experimental, I’d be happy to explain how Shape Genie can be used. Shape Genie offers free, long-term accounts and has tutorials. My email is [dave@brainscanology.com](mailto:dave@brainscanology.com) if you want to send the images privately. These other use-cases will give you a good idea of how we can measure the phenotypes you listed. Video [11 min]: LCPC Transform Measures Shape Distinctly From Area in 2D Cell Culture [![](https://us1.discourse-cdn.com/flex001/uploads/osdr/original/1X/82782191e3b87d13c646d1d240c2e835f255503a.jpeg "LCPC Transform Measures Cell Shape Distinctly From Area in 2D Cell Culture") ](https://www.youtube.com/watch?v=nlrx9sOPpFY) Video [14 min] Shape Genie Identifies Sub-Groups of Lung Alveoli [![](https://us1.discourse-cdn.com/flex001/uploads/osdr/original/1X/540aca54b6f506cf2df220386c6408d059f8d32a.jpeg "Shape Genie Identifies Sub-Groups of Lung Alveoli") ](https://www.youtube.com/watch?v=KH9LuHDuXZM) Best, Dave ---
**Author:** ![alavia](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/alavia/32/2000_2.png) [@alavia](https://awg.osdr.space/u/alavia)\ **Post date:** [August 16, 2024, 10:55am UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417/7 "2024-08-16T10:55:33Z")
Hello @jgong & @james.casaletto ! I would like to contribute to this project of yours. Do you have any space left in the group? ---
**Author:** ![james.casaletto](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/james.casaletto/32/158_2.png) [@james.casaletto](https://awg.osdr.space/u/james.casaletto)\ **Post date:** [August 16, 2024, 3:37pm UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417/8 "2024-08-16T15:37:56Z")
Hi Alavia Absolutely we have space. Jian please add Alavia to our email list. We look forward to meeting you at our next meeting. cheers -james ---
**Author:** ![alavia](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/alavia/32/2000_2.png) [@alavia](https://awg.osdr.space/u/alavia)\ **Post date:** [August 16, 2024, 3:39pm UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417/9 "2024-08-16T15:39:45Z")
Thank you so much! Looking forward to the meeting. ---
**Author:** ![jgong](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/jgong/32/1469_2.png) [@jgong](https://awg.osdr.space/u/jgong)\ **Post date:** [August 16, 2024, 3:57pm UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417/10 "2024-08-16T15:57:12Z")
I’ve added you to our email list, Alavia, thank you for the interest! We will meet again very soon! Jian. ---
**Author:** ![PatS](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/pats/32/652_2.png) [@PatS](https://awg.osdr.space/u/PatS)\ **Post date:** [August 23, 2024, 3:52am UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417/11 "2024-08-23T03:52:41Z")
Hi Jian, Would you be able to add me to the mailing list too, I’m also interested in the project. Satyam ---
**Author:** ![jgong](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/jgong/32/1469_2.png) [@jgong](https://awg.osdr.space/u/jgong)\ **Post date:** [August 23, 2024, 4:10am UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417/12 "2024-08-23T04:10:48Z")
Thank you Satyam. Will add you and keep you informed! Jian. ---
**Author:** ![ongjo](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/ongjo/32/898_2.png) [@ongjo](https://awg.osdr.space/u/ongjo)\ **Post date:** [September 19, 2024, 3:47am UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417/13 "2024-09-19T03:47:44Z")
Hi @jgong, I hope you are doing well! Ethan Waisberg ([ethan.waisberg@gmail.com](mailto:ethan.waisberg@gmail.com)) and I (ongjo@med.umich.edu) would be very interested in joining this project if there are spots available. Thank you! Best, Joshua ---
**Author:** ![rtscott2001](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/rtscott2001/32/5_2.png) [@rtscott2001](https://awg.osdr.space/u/rtscott2001)\ **Post date:** [September 19, 2024, 10:33pm UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417/14 "2024-09-19T22:33:57Z")
Thanks so much @ongjo & Ethan 🎉 ---
**Author:** ![eunice](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/eunice/32/914_2.png) [@eunice](https://awg.osdr.space/u/eunice)\ **Post date:** [September 25, 2024, 8:59pm UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417/15 "2024-09-25T20:59:45Z")
Hello @jgong, I just joint AWG recently and I find this project interesting! I would love to learn more about it and contribute, so I am very interested in joining this project if there are spots available! Thank you very much! Best, Eunice ([eunicecwyan@gmail.com](mailto:eunicecwyan@gmail.com)) ---
**Author:** ![npelonis](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/npelonis/32/139_2.png) [@npelonis](https://awg.osdr.space/u/npelonis)\ **Post date:** [September 27, 2024, 12:50am UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417/16 "2024-09-27T00:50:44Z")
Hello! Are you guys accepting people to help contribute to the model from undergraduates? ---
**Author:** ![jgong](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/jgong/32/1469_2.png) [@jgong](https://awg.osdr.space/u/jgong)\ **Post date:** [September 27, 2024, 1:43am UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417/17 "2024-09-27T01:43:23Z")
Yes we do. Please send them (their emails) my way! Jian. ---
**Author:** ![npelonis](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/npelonis/32/139_2.png) [@npelonis](https://awg.osdr.space/u/npelonis)\ **Post date:** [September 27, 2024, 2:00am UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417/18 "2024-09-27T02:00:11Z")
I sent you a message! ---
**Author:** ![rtscott2001](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/rtscott2001/32/5_2.png) [@rtscott2001](https://awg.osdr.space/u/rtscott2001)\ **Post date:** [September 28, 2024, 10:41pm UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417/19 "2024-09-28T22:41:41Z")
@jgong @james.casaletto when you get the subgroup set, need help setting up the calendar for the regular subgroup mtg? ---
**Author:** ![jgong](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/jgong/32/1469_2.png) [@jgong](https://awg.osdr.space/u/jgong)\ **Post date:** [September 30, 2024, 10:05pm UTC](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417/20 "2024-09-30T22:05:50Z")
Hi Ryan, Thanks so much for posting the tutorial on setting up the calendar for sub-group meetings! Very useful!! [Next page](https://awg.osdr.space/t/digital-twin-to-model-the-effect-of-spaceflight-on-the-retina/417.md?page=2)