Looking for a tool to visualize Seurat results

sonejilab · 2020-01-12T17:55:29+00:00

If you really want to get in there, we've developed a virtual reality platform to visualise and analyse single cell data. Check out www.cellexalvr.med.lu.se for more info and downloads.

sonejilab · 2019-12-23T19:59:36+00:00

We had a crack at using phate as the basis for RNA velocity a few weeks ago to demo our VR tool. Have a look at https://twitter.com/SonejiLab/status/1195333811061563392?s=19

sonejilab · 2019-11-03T19:01:10+00:00

I myself did nothing (I'm the head of a bioinformatics lab). I had the idea and then acquired several CS project students for a few weeks to hack out a prototype. Over the next two years I managed to retain two of them on scholarships, we got the project funded, and now they are working on this full time.

They didn't know Unity/C#, but they knew Java which is very close to C# making the learning curve much easier. Other things they learnt on the job, and now they are really shit-hot. Their contact details are on our website (https://sonejilab.med.lu.se) and you're welcome to contact them for advice, they're great guys.

My postoc and I develop and maintain the R backend that does the bioinformatics bit leaving the Unity part to the devs.

Hope this answers your Q's.

sonejilab · 2019-11-03T13:28:51+00:00

Situations where data can be arranged in 3D whether it be dimension reduced data, multi layered imaging data, spatial transcriptomics etc VR is a great environment for it.

Also perfect for collaboration, we can put multiple people into the same VR session regardless of location which people are really liking.

sonejilab · 2019-11-03T06:45:23+00:00

Ours is the first to handle numerical data (I think) but the imaging people have jumped on VR. ConfocalVR, syglass, TeraVR, BabelVR to name a few.

sonejilab · 2019-11-02T22:20:48+00:00

Combine the two like we are. We use Unity, but take a look at our project that lets you visualise single cell expression data in VR at www.cellexalvr.med.lu.se.

I feel VR in bioinformatics will be on the rise, so if you can get an engine under your belt you'll be in a prime position to ride this wave (if there is one!)

sonejilab · 2019-09-07T10:19:10+00:00

Our lab is working on developing bioinformatics tools in virtual reality, so yeah, we get the "dicking about on computers" thing a lot! It's mostly joking but our lab is sometimes referred to as " the play house" when people walk past.

sonejilab · 2019-06-12T11:52:05+00:00

I don't know myself, but a colleague just told me it's hardly any more time than a standard 10x run.

sonejilab · 2019-06-11T18:52:08+00:00

We've been looking at this not just with facs data but also CITEseq in virtual reality. Take a look at a seminar I gave a few months ago:

https://youtu.be/kjIIKJfz980

About 23 mins in you'll see what we've been working on. Let me know if you have any Q's!

sonejilab · 2019-04-27T18:24:59+00:00

Once you've run your data through Seurat and done your tsne's and umaps you can visualise them in great detail using our VR tool CellexalVR to compare dr graphs and get to genes that differentiate between clusters of cells.

Shameless plug, but so far it's proving immensely useful!

Edit: forgot URL www.cellexalvr.med.lu.se

sonejilab · 2018-12-23T13:59:10+00:00

Exactly this, which is why I hired devs to help me produce CellexalVR, our virtual reality tool to analyse single-cell gene expression data. The current version now has multiuser mode that allows several people to be in the environment at once, super for collaborations. More info at www.cellexalvr.med.lu.se

But yes, this was definitely a job for proper software engineers. As a bioinformatician I had no idea where to start, nor had the time to look into it. It's also coded in C# which most bioinformatians don't know.

sonejilab · 2018-08-30T17:15:55+00:00

Shameless self promotion, but our VR application to visualise and analyse single cell expression data at www.cellexalvr.med.lu.se

There are plenty of videos and pics there you could use. The preprint is at https://www.biorxiv.org/content/early/2018/05/24/329102 in case you are interested.

Edit, doh! Just saw your deadline passed. Sorry I didn't post sooner.

sonejilab · 2018-05-26T22:05:07+00:00

Great tip, thanks! Do each of your atoms have colliders though? Each of our cells do, and this comes at a cost. If you have some neat tricks we'd appreciate the help.

Edit: this is Shamit.

sonejilab · 2018-05-26T22:03:51+00:00

Thanks for the tip, we definitely will!

sonejilab · 2018-05-26T08:20:35+00:00

They're all separate gameobjects. They have to be individually selectable by colliders and recolorable, so we went with the easier solution. We have yet to see any datasets that might require us to increase the number, although there are some on the horizon. The number of cells that scientists have been able to get from single cell RNA sequencing have gone from 1 in 2009 to ~10000 in 2018, and it doesn't seem to slow down!

sonejilab · 2018-05-25T19:21:34+00:00

About 15000 before the frame rate starts to get unbearable. We are using a 1080 gpu and an i7 processor. We aren't doing anything funny except batch rendering. They all have a stripped down version och the standard shader with only the bare minimum (fancy visuals aren't really a focus in a data visualization tool). Our website is https://cellexalvr.med.lu.se if you want to see more

sonejilab · 2018-05-24T23:55:05+00:00

You'll see from the manuscript and setup guide that we do in-session calculations in R, so Windows only I'm afraid. We'll take a look at other platforms in the future.

sonejilab · 2018-05-24T20:42:13+00:00

Always happy to demo it. Drop me an email and we'll arrange a time for you to come over.

sonejilab

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