Contributed Talks 3
Lambda Moses (California Institute of Technology)
Ellis Patrick (The University of Sydney)
Dario Righelli (Department of Statistical Sciences, University of Padova)
Lukas Weber (Johns Hopkins Bloomberg School of Public Health)
3:00 PM - 3:55 PM EDT on Wednesday, 29 July
Unsupervised analysis of transcriptome-scale spatial gene expression data in the human frontal cortex
VisiumExperiment an S4 class for 10x visium spatial gene expression
A comparison of spatial transcriptomics methods
Spatial analysis of in situ cytometry data
Moderator: Matthew McCall, Simone Bell
My research interests are focused on the development of novel tools and methodologies for multiple bulk and single cell Next Generation Sequencing data analysis, integration and visualization. I'm also interested in data and code sharing for reproducible research support.Перейти в профиль
I am a postdoctoral fellow in Prof. Stephanie Hicks’s group in the Department of Biostatistics at the Bloomberg School of Public Health, Johns Hopkins University. My research work is on statistical methodology, software development, and benchmarking for the analysis of high-throughput genomics data. Currently, I am mainly working with single-cell RNA sequencing and spatial transcriptomics data. My work is motivated by collaborative projects with researchers in various fields of biology. These collaborations show us where the interesting statistical problems lie, and let us contribute to fascinating scientific advances. I support open science principles, including free availability of code, software, and data resources, and publication of preprints. In my methodological work, I am a proponent of rigorous benchmarking against existing methods. I mainly work with the R programming language, and most of my software packages have been developed as part of the open-source Bioconductor project. I am also interested in teaching, especially R programming skills, and have been an instructor for several short workshops for Data Carpentry and Software Carpentry.Перейти в профиль
Welcome to the third contributed talk session. We have four wonderful speakers today. You should be getting a 10 minutes, 15 minutes. Please submit your questions by the possible pole and vote on other questions that you would like to have answered. Also, please remember to know which speaker the question is being addressed to the right person. And so, the first talked today is by Lucas Weber, got to talk about work. We've been doing on developing unsupervised analysis, five times for special transfer.
Just salad. I think the keynote talk before they start special transfer some background white, such an expression of each measurement from the connection on its website website showing this is a histology image of half a mouse pain. Then the way special transfer Comics works is for which color grid of circles. So I kind of across the tissue slide and measuring a gene expression, each class spots in the middle of this is showing a total gym pounds at age spots. Not in this experiment,
I've been Downstream of this, we can do all sorts of analysis, like, clustering on highly variable genes or looking at specific cell types. This is really being a night owl recently by several new technological platform, set up in a release that we've been working with David from the 10 X, 10 X, 10 X, busy and platform, which was actually released, like, last year he was somewhat schematics Mouse. Brain tissue slide slide on the right of showing the the workforce of the slide has four
separate areas. Each about six and a half. Each of us safely. Kotob spots. I've been after this analysis has a lot of similarities to single-cell RNA sequencing project. We assume that one spot is equivalent to one cell in our daughter. It was more like three sells Prescott on average Equity distribution from zero. After using this approximation, we could then reuse all sorts of back, doctor infrastructure and pipelines for analysis for a single cell experiment.
Structure, orchestrating single cell. Analysis online textbook, average. We couldn't go out for this work through an experimental collaboration. Really nice collaboration at The Institute for brain development. Poster Torres bring you some the new platform 20.69 layers between supervised and unsupervised. 3, your typical a total of 12 samples and total on the top, right? That's what the actual slide looks like at all star strain. Jeans are rich in your own special specifically. Galaxy S10.
Indian surprised analysis in this project. We had a club Riders spots to to the northern lands. This is very labor-intensive work and in other contexts might not be possible at all, if that's not logical structure for sample results. This is showing butter for oil pipeline. Bursts, I'm looking for a specially. If I missed out of said, we can compare against the law. And we built this up by adopting, black Northwest Pipe lines for single-cell. RNA processing, about station, a feature selection
luxury, bus, during a testing for spice jeans, instead of just texting to see if I could improve performance. On. This is showing some of the results for did several styles of of David Ruffin analyses, including the completely unsupervised, on the left, side of the semi supervised analysis, work for where we use jeans from the manual annotation and separately. We also used from the church, Let me try to come up with different string, implementation to see if we could optimize this. So there are questions of which set of genes to use
special potions and cheese. And spinach case we can pay it is against the law and ground troops from the manual sanitation including the spatial coordinates slightly improved performance, spatial coordinates. I'm using the special D. Jeans did not improve performance very much at the highly variable genes. I'm finally at all. So let us find unexpected results which was very cool on the right here, with six months of the top 9 things from the last ones on the bottom, I want to start again, super fast
life line, which were specially variable, but not linked to the layers. And these are not change that are linked to lung specialist, immune cells, which were not really expecting to find in the store. I can pay for these unexpected ones in red at a high test statistic especially from now. And the last thing I just want to mention this, when I using this, as the basis for developing a longer and more comprehensive. And that's it. Thank you very much. Wonderful. Thank you for a very interesting talk starting us off for some of the attendees that baby came in late and this night openings. Feel
please submit your questions using the palpable pulse and make sure to dinner with us because they're asking you a question of the next talk is by Dario rebelling and she recorded one. Hello everyone. I'm better to get early and I'm opposed to work in the research lab at the apartment. If you have time to set University of Padua And today, as you can see, I changed a little bit my presentation talk because I extended the museum experiment class, with other classes. So we
decided to create a unique package statement, which gives multiple lists for classes for testicle toss. Potomac's several Technologies, which gives provides special Corps engineer of the cells to a reference in our case tissue or a portion of a tissue and moreover, they provide LOL so fast. It 20 seconds. Of course the number of a transcripts depending on the under under use it Technologies at the moment, the sex fish betta and at the next general experience of the
stomach's but there are several others and some others, they are, there are coming out of combines microscopy Imaging with insulation, combines a wheat stamp road bike routes in order to catch the coordinates of the cells and Nancy's, detected us the number to local organizing Sports transcript. These can be combined with with a single cell Ernie 60% to have a single cell multimodal integration. Baskets is a little bit different because the the tissue is placed on a on a trip with several spots
on it and why we didn't we catch the way? I made sure all the tissue on the, on the cheap CD, any application. He's made inside of each spot. So in the end we will be able to detect the spots next to its barcode and to have the abundance We started from the Single Cell experiment class because it's it sets a standard for any kind of single-cell. A bit of storage and Analysis in R Us in Bible doctor since the version 3.6 and it provides several attributes
for the handling of this kind of data. So small general for any kind of special experiment W designs for the besom data. At the moment, it is available on Justin Mega table, but we are on there by the end of the revisions. And if you're interested. The secret is available. Also on my T-top at the moment. It's from the Single Cell experiment and it wants to the basis for the special transcriptomics. Sorry, we implemented some attributes names. Special courts kicked out of the RX and why they are stored inside the G-Spot to All the Single
Cell experiment. And additionally, of course, we have designed for getting infecting, you do use these attributes. We are working still working on the aisle there. Other are three other other other methods for this class such as the sea Bond method, where we would be able to bind to a specialist pregnant objects. In order to give an example of usage, we used to go sell our data provided during an Ocotillo on for the Beast by integration worship. And the,
do you say she's available in this other repository name, spatial analysis. And you can find the 60s here in order to stand out to load the data from 5 and I'll just order them inside the Single Cell experiment for the single-cell RNA seek, and into the special experiment for the sexy and how to manage to play with the class here. After that to Extended Stay in this class with the situation with payment class because it was so nice provides multiple information such as for the spatial coordinates.
It provides XY in tissue. The definition of the pixel. And I have four columns and four rows and additionally, it provides multiple in different formats and 222 interchange between these images, you need some skill factors. So that's why we provided also the methods for handling with this other and we got this other attributes. And we provided also a message or within the same repository. But with a different name here in this case has become a neurologist and whilst others provided by the Connex available on the
site site. And it's a very high number of different format. So we show how to load these data and how to store them into the resume experimental object. Finally we used our special experiment across into the Single Cell multimodal experiment, tab a bike on Doctor package SS, meaning to mention by Marcel Ramos in the bathroom slab and it wants to and keep access to multiple data sets of single-celled or multi-celled nmtc with a set and I provided to contribute to this package. I contributed by implementing
the dysfunction for storing the sexiest plus single-cell, RNA 60% The main idea is to have one single function for each for each kind of data. We have this sick fish function, you can select the the dataset of your interest by a dog, eat a type argument. In this case, the name of this is a sexy smile speedworld cortex and each of these function return Subutex experiment indeed. As shown in the figure, the sexiest Lita are stored in the special statement by the Single Cell Ernie, 6 days into the Single Cell
experiment and we combine them into an experiment objects. The next t-shirt, we willing to allow, including throw it out of me with you between the special experiment classes and some other external worse such such as the package of a kangaroo Albrecht and some other scripts for the spatial disorientation developed by the Sheila got some fire. Additionally, we want to implement some dedicated. The attributes and methods for networks because networks interaction is a very important
stuff during the speech analysis and we want to be a package for the week. 6, x samples. We are working on some other specific tasks such as in order to release them. Another Thank you for your attention. And if you have any questions, I will be here for depression and answers session. Thank you. Wonderful. Thank you for another great Arthur's sister's. Today is Linda Lou will be speaking. My name is Lambda and I'm a grad student at Caltech are in biology. And so basically this project over to
the effort to write a review paper and Staples So here are the birthdays of the inside. The state of Base was presentation. I will show some highlights from the analysis of the metadata, as well as just a little bit about the about the data from different from a special trip to mix Technologies from Niles crane on Princeton Salton, single stall, and the SAR SAR they tools for 4 Christmas Armistice Day. Analysis package has also Valentine who used to be a postdoc in our lab. Database of literature in singles. And
about 10 days, to find some friends and Smith are under 6 year. Old database for this project is the first inspector who performed there are over from the papers in the state of base and include some historical. Literature of to show some historical context getting cold and pale abilities species and tissue else. That's programming, languages used to to perform the down screaming out with me and to build houses tools and the other There's a seat in this is dedicated just for us
all the code and the notebooks for the analysis, are our friends and our packs from Union St and it's only available from our laps are the popularity of truck driving languages must be old and wear specially because 4 or later captured microdissection, just too much. And always now it's even colder of Cam explored interactively on our Civics weld on from this to your l. Reduce the number of Publications / pretending and the security of the remarkable growth of this
field especially since 2018, and Christopher quite long. So if it's number Publications, in the case of any interest in this for quite long, interest in collecting data, or developing the technology to collect data and spatial transcriptomics. What was kind of a head of the interest in Indianapolis? This whole burden has been catching up recently. Do some research with sections of human brains and do like a thick soles or like a grid notebook. Young done in the first half of the 2010s, we saw some of them were from their methods starting produced in
the previous talking to stations or just because you are fish and St. Worcester State of Trance, abusive 2016. Then we'll have all these new technologies. I'm so so so, so, so, so our, which of these Technologies are busy and which are a businessman with a resolution for single. The resolution ones. And myrrh fish were used more. More recently Young with me, for all these different methods, compare versus the number of transcripts captured Purcell, and for the
very best method of cells in your looks like the captions do not ask me to transcripts and the comparable to Wild Acres plus a person more Technologies read the stuff to fish plus here at the same one and though, Are there many other technologies that are similar resolution. Even more transcripts install is still our provider using it? Possible to use these single-celled, a special technology to profile like a like a ten thousand genes. However I will call me when we used to do profile, select
channels jeans Penn Station, message to profile like over like oh without those few outliers, the number of cells isn't really much greater than like a typical male. So so why? Because I just four of those, no power resolution bears in the pipeline design for line. For these methods are, there is sufficient enough or Universal enough. One reason, another reason why I see you. The probe mean, if your profile, so many genes are expensive. You're supposed to be served all day. So how about get analysis shows that the
which type of the analysis are cheaper than most interested in overtime and has tools? Compass to West Virginia operational hours from Mike Alvarado 3 using the single some special technology that the most popular ones are actually designed for integrating the spatial data with housing authorities. Think they do, nothing else like a storm or more packages for Explorer. Is it didn't Alice has such a study although and after utilities for SD data and he also likes
raw logo start and then something specific for their own technology select for which What Champion? Plug across different Technologies and Assurance, don't sell them directions and so long. And Summary of the highlights of the Indian houses. Yalta. Also suggested the killing of a special going to technology. Can be challenging and discovers that, I need your help earlier. So damn it stinks by noon or 4 for his support for for this for fun. So afraid, sociological an unusual project. So yes, and thank you for listening and that he questions.
The last talk in this session is by Ellis, Patrick Delta's pics of the Olson signs. These technologies will enable what time is talk, give me a big picture of you with two analytical methods, special relationships. On The Rise here, we have a standard 3D image of cells and some color and tissue Imaging Technologies that I ever characterize cells with tens hundreds. Thousands of our pricing The ability to deeply fiends hot cells, the locations of ridiculous. Number of different cells hives.
So what are some of the key questions we can? Ask special, I mixed up first as these Technologies estimate, for the true composition of cells in a tissue second Lady, and probably most relevant light out of steel types. They might be interacting with In this toy figure, we can say that the red and blue cells seem to be near each other. So, extending this, if you're able to quantify how cells a localized, need a tissue. Fortunately, there are a range of statistical methods. If we have the technology like steak fish or IMC able to
identify cells at a Titan, the side of an x and y coordinate, we can use some special Arrangement that sells A1 class of summary statistic especially attracted or pulse rate Java number so hot. On the right, you can send lcross function, summarizing spatial association between cd11c, positive cells function is the cells are randomly distributed throughout the tissue. How about the black is what we observe in a Dada. This indicates of this cell type has to be localizing in the same region since I child be.
Function or any other measures specialization a measure of the association and one t-shirt. But doesn't tell us how that Association right here, we have some data from one of the Bode Miller Group by the Scripps Inn by Sloan diabetic individuals and individuals that have recently developed on the association is the area between the L function and it's diagonal line. In this darkness that effectively have multiple images represented in the box, plot. Xbox One
game sales and T-Mobile sales. There are some complications the formerly testing if they change the random. Your food plot measure of spatial association between the cell types. This number of cells decreases. This shouldn't be surprising, is the variability increases as we have less information. So we proposed modeling this relationship. Of course, if I design my own simulation for testing, the child has an association between the number of cells including beneficial. so, with these tests we never best method to test if a child
What type of wire from the state map of changes in association? Is that we consider them my beach instead of the results. You said, because of this, we also propose a method to summarizing Broad patterns of spatial association between multiple cells. You're not examples. Ideally we'd like to be out in five regions where red and blue cells localized and regions of tissue way. Red green and purple cells. The Priestly describing a method to every cell recalculate
summary to how close that sell these two other cell types. And then we can mend type this Association Matrix Camillus tried this method in an awesome God, set from Gary Allan's group where they applied codex Imaging with 33, use that method to Costco, sells and localization costumes. How is David hate math represents the relative enrichment of each cell type in each of the regions? First thing we can say is if we use that method to identify classes of cells, that end with each other and five classes
difference between a 26 different cell types. Portland. If we compare the regional costumes that we identified on the left hand, to those who will manually out of tied up with all of this to the manuscript on the rod to do a reasonable job is replicating, the extra a Tyson and said there was some strong advantages to the elk rut functions, provide the opportunity for sale cost function includes summary statistics of a rind r. I t i want to reduce the impact of large-scale
tissue structure on the clock during this is possible. I'd like to quickly finished my really talented post-grad student who spearheaded a lot of questions and actually I session cheese, please keep the questions coming in and we'll get through as many as we can. The first question is for Lucas, how did you include the spatial coordinates in your unsupervised cluster? I just saw him in the simplest possible way which was basically pick up Lighting on two more Columns of the
features for XY coordinates. We are starting a 50/50 restaurant with scaling the X & Y coordinates. Range Rover, comparable to the top PC. I want to talk to you now. Can you see? Special experiment. Class also holding morphology information, sell masks, or even images. Yes, I think that's we can handle this because the information is stored in to ask, for vectors dataframe, that can load any kind of us could work. But you can, at the moment, we didn't load images. Seen our classes. We just order the deposit. So it's it's up to do with user
to, to load the data at the moment. But in the future, we want to do better handle and try to find better ways to store Day. Images also became ideas. I think The next one isn't so much a question, but I think we should check that out Museum. St. Get her 3 phone. And is made a note, I don't know if you can see it in the store. I think you called it, a sociological analysis. What was the thing that you could have found the? Most surprised they were the most different
from what you expect when you started on a really good question. okay, so one thing yours, I was really surprised and I just think like a, Sweden has played a very big role in this even though they did not play a very huge role in life. Atlas's before, which is the historical context from, which is a rose. Yeah, I think so. Yeah, I think it's also how widely you later capture microdissection has been used. It's also very while using plants like the plane part wasn't very expected. Are you Alexa the more? The more Malden likes to come see where I can fish
with methods are more focused on humans advice. Yacht. Recall, can you give more info on the computed on polygons and what distance measure was used to scan shapes? Okay, I'm so I figure thing I do. I assumed it was used technology. We've got the resolutions, we had a segment sells, I'm sorry if we can segment the cells, use polygons just type it. The center of the XY center of the segmented, self-analysis the sky functions are since they're just taking radius has
around around to the sentence of the cells. And so you can do that are for a range of distance. The 7Up, doing any polygon, stop weather sells touching were just looking at Distances between senses. I saw her going back to the Lucas. You mentioned that the histology image matches with the total Jean count example in standard distribution center, technical variability, technical variability. In fact, this is so weird. I am now not to try to develop message.
Dario, how would you deal with different quality versions of histology images? In our case, we have low medium and high about 15 images in the future. We might have super high several thousand gigabytes. Images, still be part of the object or links to say. Aw, is also say, you have an image of mask. Where do you store Yeah, as I could before, we just store the parts now, or the Leafs whatever you want, and it's up to go to the user to load the images, but of course, he's the one that has
to do with that object. We can work together to do it and And I'm sorry that was part of the question was how to deal with your friend resolutions of histology images. Oh, I don't think it's a problem to, to do to store these kind of different quality version of the celebrity images of talking to us. We can store them as data into into the spatial coordinates because any kind of object can be stored there. Next question is for Ellis, is it possible to calculate the underlying lcross using non-euclidean
distances? I can imagine very boundary situations manifold where you putting would be problematic. Truth possible drive. So guess what is the answer? It is. The maybe you might want to think about using different distance metric. I'm at one of the great things about shuttles that technique. I'm sorry, calculating a lot of the sky Pro cell crust Options at least thought about these kind of boundary situations and so you can put wipes in for enter fix like I said the tissue, you know, but
you're dieting you can put whites in to in terms of cell density and all those kinds of things. I think a lot of that Whiting structure, that's in the functions of the accounts, to those kinds of issues. But if that answers If not, I'm sure the person that send me to follow up with you use for unsupervised analysis. So we used to the fact, the doctor I'll stop by playing with you and standard single cell by conductor clustering python. Sorry, I didn't see any benefit on having all facts for the spot level data and say pseudobulb Slayer level beta.
I think that's you. Can you, can you repeat the question? Try reading our functions isn't all facts for the spot level data and say so I have pink up a little bit about this, but maybe you can text. As it is. But of course, I think better about this this one. Thank you. Next question is for LS. It's a follow-up from the first question that you take the centroid, how can you account for a long skinny sells like, neurons versus small round leukocyte, or Starship astrocyte? And their side, the questioner
would love to chat more and he's also looked at some of these days, maybe that's why did the reality, is you caught? So then these things I'll just point. It really comes down to the question. You're trying to ask if you're really interested in a cell, if it's Ross neighborhood, who sells averaged over all of those sales in all of the image. Not I don't think it really matters to all types. I don't think it's necessarily going to help you with those kind of beat broad
summarize Association across the hall tissue. All right, so maybe the last question first, and Lucas is what defines a layer in space or how would you think about it when cell types of shared across the fishing? Yeah, so what exactly is on my route? If we're interested in conditional, sell times for additional Downstream analysis on that. Or if we just sit down, Well thank you for all four speakers again for a very interesting session, we're halfway through the expense should be to talk sessions for this one. So
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