# DNA Damage Microscopy Image Classification Project **URL:** \ **Category:** AIML AWG Open Projects\ **Tags:** aiml, radiation\ **Created:** [May 29, 2024, 1:23am UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429 "2024-05-29T01:23:14Z")\ **Posts on this page:** 20\ **Page:** 3
**Author:** ![evartsb](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/evartsb/32/250_2.png) [@evartsb](https://awg.osdr.space/u/evartsb)\ **Post date:** [August 21, 2024, 7:17pm UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429/43 "2024-08-21T19:17:37Z")
@rtscott2001 - great idea! Once the team settles on a meeting time, I’ll post the meeting invite on the calendar on the forum. ---
**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:** [August 21, 2024, 8:18pm UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429/44 "2024-08-21T20:18:17Z")
Excellent, of not when you create a calendar invite New Topic → AI/ML AWG Calendar ![image](https://us1.discourse-cdn.com/flex001/uploads/osdr/original/1X/099816c84b7ff46906ca131b3ba70fa4ab327a45.png) Then Gear Wheel → Create Event ![image](https://us1.discourse-cdn.com/flex001/uploads/osdr/original/1X/b57d9b894b382002399cd7d21e568d2c35e08f65.png) Then date/title/url for mtg/ PRIVATE / and make sure to tag AIML AWG ![image](https://us1.discourse-cdn.com/flex001/uploads/osdr/original/1X/ed86615f6f8627874e18447459c52d5cd666b872.png) ---
**Author:** ![evartsb](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/evartsb/32/250_2.png) [@evartsb](https://awg.osdr.space/u/evartsb)\ **Post date:** [August 23, 2024, 12:45am UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429/45 "2024-08-23T00:45:49Z")
Interesting paper on this topic. @rtscott2001 @svcostes Can we create a topic that is not strictly focused on the AI/ML aspects of this project and have a place for related papers and discussion? Interesting paper - " DdrC, a unique DNA repair factor from _D. radiodurans_ , senses and stabilizes DNA breaks through a novel lesion-recognition mechanism" > **[DdrC, a unique DNA repair factor from D. radiodurans, senses and stabilizes...](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae635/7717837?login=false)** > > Abstract. The bacterium Deinococcus radiodurans is known to survive high doses of DNA damaging agents. This resistance is the result of robust antioxidant ---
**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:** [August 23, 2024, 1:49am UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429/46 "2024-08-23T01:49:23Z")
Absolutely. Here is how to make a post as a general “discussion” in the generic AWG Discussion category ![IMG_5397](https://us1.discourse-cdn.com/flex001/uploads/osdr/original/1X/a43c3bac94808046981a4ec9918a5f8c1e30163e.jpeg) ---
**Author:** ![anuiris](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/anuiris/32/1358_2.png) [@anuiris](https://awg.osdr.space/u/anuiris)\ **Post date:** [August 26, 2024, 8:36am UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429/47 "2024-08-26T08:36:48Z")
Hi, do we have a new time and date set for the next meeting? Thanks! ---
**Author:** ![lauren.sanders](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/lauren.sanders/32/186_2.png) [@lauren.sanders](https://awg.osdr.space/u/lauren.sanders)\ **Post date:** [November 20, 2024, 4:48pm UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429/48 "2024-11-20T16:48:24Z")
Reminder that this subgroup is meeting in ~10 minutes. Message me privately if you are part of this subgroup and don’t have the Zoom info. **Agenda:** Since there are several efforts ongoing within this subgroup, we would like to invite everyone who has an ongoing effort to present their status at this next meeting. Please come prepared to address the following items: - What is the problem you are trying to solve? (radiation type classification, foci detection/segmentation, etc) - What is your approach to solving that problem? - What is your status? (model performance/accuracy, xAI status) - How close are you to being happy with your completed code and research product? What are your next steps? We would like to start moving toward one or several manuscripts, so please keep that in mind while preparing for this next meeting. ---
**Author:** ![mboerrigter](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/mboerrigter/32/92_2.png) [@mboerrigter](https://awg.osdr.space/u/mboerrigter)\ **Post date:** [December 13, 2024, 2:24pm UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429/49 "2024-12-13T14:24:07Z")
I had a couple of questions before I start with developing a classifier (for X-ray dose). 1. Are we (still) using only images with a maximum intensity of 4,000? 2. Are we scaling the images, i.e. they all have values between 0-255, prior to feeding them into a classifier or deriving meta features from them? 3. (for @walt ) Could you list the meta features you used once more. I downloaded the 2011 article you mentioned but wanted to make sure. Thank you! ---
**Author:** ![lauren.sanders](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/lauren.sanders/32/186_2.png) [@lauren.sanders](https://awg.osdr.space/u/lauren.sanders)\ **Post date:** [December 16, 2024, 7:02pm UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429/50 "2024-12-16T19:02:52Z")
Hi @mboerrigter , 1. Yes 2. Scale between vmin=400, vmax=4000 3. - Mean Phase Congruency (MPC) - Entropy of Phase Congruency (EPC) - Entropy of the Image (EDIS) - Mean Gradient Magnitude of the Image (MGDIS) ---
**Author:** ![mboerrigter](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/mboerrigter/32/92_2.png) [@mboerrigter](https://awg.osdr.space/u/mboerrigter)\ **Post date:** [December 16, 2024, 10:23pm UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429/51 "2024-12-16T22:23:39Z")
Thank you Lauren! ---
**Author:** ![mboerrigter](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/mboerrigter/32/92_2.png) [@mboerrigter](https://awg.osdr.space/u/mboerrigter)\ **Post date:** [December 24, 2024, 1:34am UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429/52 "2024-12-24T01:34:25Z")
Is anybody aware of any other open source datasets featuring DNA damage and light microscopy for comparison purposes? ---
**Author:** ![evartsb](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/evartsb/32/250_2.png) [@evartsb](https://awg.osdr.space/u/evartsb)\ **Post date:** [December 25, 2024, 5:28pm UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429/53 "2024-12-25T17:28:38Z")
Hi @mboerrigter I have been looking for one also and have not found one that is an exact fit for our use case. It has been a while since I looked though. I’ll try again over the holidays. ---
**Author:** ![anuiris](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/anuiris/32/1358_2.png) [@anuiris](https://awg.osdr.space/u/anuiris)\ **Post date:** [January 6, 2025, 9:51pm UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429/54 "2025-01-06T21:51:56Z")
The DeepFoci paper here lists development of a dataset. They may be able to share this data upon request. > **[DeepFoci: Deep learning-based algorithm for fast automatic analysis of DNA...](https://www.sciencedirect.com/science/article/pii/S2001037021004840)** > > DNA double-strand breaks (DSBs), marked by ionizing radiation-induced (repair) foci (IRIFs), are the most serious DNA lesions and are dangerous to hum… ---
**Author:** ![evartsb](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/evartsb/32/250_2.png) [@evartsb](https://awg.osdr.space/u/evartsb)\ **Post date:** [January 14, 2025, 6:55pm UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429/56 "2025-01-14T18:55:35Z")
Hi Parham, We would be happy to have you join the team! send me your email address and I’ll add you to the list. We meet monthly on the second Wednesday of each month at 12 PM ET. ---
**Author:** ![svcostes](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/svcostes/32/33_2.png) [@svcostes](https://awg.osdr.space/u/svcostes)\ **Post date:** [May 29, 2025, 3:52pm UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429/57 "2025-05-29T15:52:15Z")
**Hi everyone,** I wanted to make sure the AI AWG Microscope subgroup is aware that the complete set of DNA damage imaging data in mice (OSD-366) is now available here: 🔗 [NASA OSDR: Open Science for Life in Space](https://osdr.nasa.gov/bio/repo/data/studies/OSD-366) For each dose, time point, and animal, about 800 cells have been imaged. These are packaged into two zip files per condition—one for raw data and one for spot detection using the wavelet algorithm I developed. - 15 strains - ~5 animals/strain (3M, 3F, with some loss) - 3 radiation types - 3 dose levels (0, low, high) - 4 time points (4, 8, 24, 48 hrs) = ~2,700 conditions × 800 cells = **~2 million cells** The microscopy benchmark dataset we released on AWS a few years ago is just a subset of this. This new release includes full 3D stacks of 53BP1 in `.ics` and `.ids` formats (rather than projections), allowing for full 3D spot detection. I’m excited to test the classifier we’ve been building on this expanded dataset, which now includes other radiation types like Argon. We should also be able to observe the Poisson distribution for Argon, though the dose increments are smaller—perhaps allowing us to distinguish it from Fe. [@AIMLawg](https://awg.osdr.space/groups/aimlawg) ---
**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:** [May 29, 2025, 8:05pm UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429/58 "2025-05-29T20:05:09Z")
EPIC. Cheers and thanks Sylvain @svcostes 🚀 I hope other AWG members [@ALSDAawg](https://awg.osdr.space/groups/alsdaawg) [@MultiOmicsAWG](https://awg.osdr.space/groups/multiomicsawg) [@AnimalAWG](https://awg.osdr.space/groups/animalawg) check out this gigantic imaging rodent spaceflight study 🙂 ⬆ ---
**Author:** ![Fgaze](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/fgaze/32/2012_2.png) [@Fgaze](https://awg.osdr.space/u/Fgaze)\ **Post date:** [May 29, 2025, 8:05pm UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429/59 "2025-05-29T20:05:20Z")
Hi everyone, Is there any meeting planned for that time? Thank you Best Regards, Fae Gaze Biostatistician\> Machine Learning Researcher| Computational Biologist Advancing AI in biomedical research [faegaze@precisionbioai.com](mailto:faegaze@precisionbioai.com) [GitHub](https://github.com/FaGaze-DataSciencBioinformatics) | [LinkedIn](https://www.linkedin.com/in/fae-g-11a1201b0/) _Please note: Due to active research and collaborations, replies may occasionally be delayed._ ---
**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:** [May 29, 2025, 8:19pm UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429/60 "2025-05-29T20:19:28Z")
Hi @Fgaze Fae, Yes! This group on microscopy and DL has been meeting for a while. I believe the next meeting is June 11th. You should see the meeting invite in your calendar: [https://awg.osdr.space/upcoming-events](https://awg.osdr.space/upcoming-events) You can ping-chat with @evartsb who leads the collaboration. I believe they are in the manuscript phase. Unsure Cheers -Ryan ---
**Author:** ![evartsb](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/evartsb/32/250_2.png) [@evartsb](https://awg.osdr.space/u/evartsb)\ **Post date:** [June 2, 2025, 3:50pm UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429/61 "2025-06-02T15:50:54Z")
Great news !! Big thanks @svcostes and GeneLab! Can’t wait to explore the new data! We can discuss this at our next meeting on 6/11! @lauren.sanders @svcostes - What is the best way to programmatically access the data ? Via the OSDR API, or are there plans to add this data to AWS data registry? ---
**Author:** ![evartsb](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/evartsb/32/250_2.png) [@evartsb](https://awg.osdr.space/u/evartsb)\ **Post date:** [June 3, 2025, 1:38am UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429/62 "2025-06-03T01:38:31Z")
Interesting new paper providing insights into mechanisms of RAD51 HR: **eLife Assessment** “This **landmark** study describes the structure of the human RAD51 filament with a recombination intermediate called the displacement loop (D-loop). Using cryogenic structural, biochemical, and single-molecule analyses, the authors provide **compelling** evidence on how the RAD51 filament promotes strand exchange between single-stranded and double-stranded DNAs. The work will be of interest to the community of homologous recombination and DNA repair, as well as genome stability more generally.” > **[Structural mechanism of strand exchange by the RAD51 filament](https://elifesciences.org/reviewed-preprints/107114v1)** @svcostes @lauren.sanders [@AIMLawg](https://awg.osdr.space/groups/aimlawg) ---
**Author:** ![Fgaze](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/fgaze/32/2012_2.png) [@Fgaze](https://awg.osdr.space/u/Fgaze)\ **Post date:** [June 17, 2025, 11:24pm UTC](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429/63 "2025-06-17T23:24:34Z")
Hi, Thank you for leading this group I have been working in this field. I am very interested in joining this group and would like to collaborate. [Previous page](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429.md?page=2) [Next page](https://awg.osdr.space/t/dna-damage-microscopy-image-classification-project/429.md?page=4)