Hands-on introduction to targeted spatial transcriptomics data analysis
Hands-on introduction to targeted spatial transcriptomics data analysis
05/12/2024
06/12/2024
General context
In recent years, spatial transcriptomics technologies have become increasingly accessible to researchers with the emergence of a wide-array of commercially available targeted and untargeted approaches. While these technologies offer tantalizing opportunities to study extensive gene panels in their spatial context, the resulting data are often complex and answering research questions of interest requires a thorough understanding of spatial data analysis and the use of dedicated tools. To this end, this training will present a hands-on introduction into the analysis of targeted spatial transcriptomics data using the SPArrOW pipeline developed by the Yvan Saeys group (VIB).
In this course, we will teach you how to run the SPArrOW pipeline for targeted spatial transcriptomics data (i.e. imaging-based technologies such as Xenium (10X Genomics), MERSCOPE (Vizgen), Molecular Cartography (Resolve Biosciences), ...). Specifically, the following topics will be covered:
- How to read in the data outputted by the commercial vendors.
- How to optimize segmentation and allocate the transcripts to cells.
- How to cluster the data and create UMAPs.
- How to run the analysis on an HPC.
Participants should have some experience with Linux, and running jobs using the HPC/VSC. For those who lack these skills, we organize a Linux session and an HPC session on Wednesday November 27th in Ghent.
Participants should also have some experience with Python, Jupyter notebooks and conda environments. For those who lack these skills, we organize a Light Python session on Wednesday November 13th and 20th in Ghent.
Trainers
Arne Defauw
Arne holds a masters degree in Mathematics and a PhD in Physics. After his PhD he worked as a machine learning engineer in the industry, where he specialized in natural language processing. Now he works at VIB Spatial Catalyst, where he contributed to SPArrOW, a python library to analyse all types of spatial transcriptomics data. As a member of the Spatial Catalyst he also provides support for spatial omics data analysis and helps optimize bioinformatic tools for spatial analysis.
Frank Vernaillen
After working as a software developer in a company on physics-based modeling and 2D and 3D computer graphics, Frank joined VIB in 2016 to work on image restauration and registration of electron microscopy images, machine learning,... Via VIB's first imaging-based spatial proteomics platform, he got involved in spatial omics data analysis, and naturally joined the Spatial Catalyst when it was formed in 2023, to continue work on data analysis and development of analysis pipelines.
Julien Mortier
Julien obtained his PhD on phenotypic heterogeneity and stress responses in bacteria. In his postdoc at SciLifeLab, he developed a machine-learning based image analysis workflow to study phenotypes of bacteria under starvation conditions and he established an end-to-end workflow for Transposon Sequencing. Now he works at VIB Spatial Catalyst, where he provides support for spatial omics data analysis and helps optimize bioinformatic tools for spatial analysis.
Practical info
05 December 2024 - 06 December 2024
Leuven - Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium
05 December 2024 - 06 December 2024
Leuven - Campus Gasthuisberg
Leuven train station is approximately 4 km from the campus Gasthuisberg. Buses depart very regularly to the Gasthuisberg Campus from Leuven train station.
For tickets and up to date schedules visit website De Lijn or use the De Lijn App.
Exit at the very last bus stop ‘Gasthuisberg Campus) make sure not to exit at ‘Gasthuisberg Kliniek =
hospital)
Once you get off the bus, go to your right and go up the street until you see stairs to your left. Climb the stairs all the way up between two buildings. Look for the signs containing blue circles and white numbers and follow them all the way from 2 up to number 12. You will cross several buildings and the walk will take max. 10 minutes. When you reach number 12, you have reached O&N 5, where you can find the reception.
05 December 2024 - 06 December 2024
Leuven - Campus Gasthuisberg
The Gasthuisberg campus is west of the Leuven ring. Our buildings are situated behind the hospital (see black arrow near ‘RING NOORD’ on the map). If you come from the city center, you will arrive on campus from the east side (taking Mgr. Van Waeyenberglaan and roundabout Het Teken). If you come from Heverlee or Campus Arenberg, you will arrive from the west side (taking the Celestijnenlaan and Taborweg). When you arrive uphill at the intersection with the Rega Institute and the Red Cross building, you need to take the road down to the bicycle parking at Rega Institute (see map) where you can park. Next, follow the ‘Onderwijs & Navorsing blue route’ description below (start point is #9).
05 December 2024 - 06 December 2024
Leuven - Campus Gasthuisberg
You arrive via the E314 highway – EXIT 16
After 200 m, keep left to drive underneath the roundabout and into the tunnel.
Keep left and follow the arrows to Parking West.
You arrive via the Leuven ring road
At the roundabout, take the exit towards ‘Spoed / Ziekenhuis’.
Follow the ring around Campus Gasthuisberg and pass the entrance of SPOED.
Continue right until you arrive at a second roundabout.
Follow the directions for E314.
Near the Fire Brigade Station, make a U-turn and follow the directions for ‘Ziekenhuis’.
Keep left and drive downhill, underneath the roundabout and into the tunnel.
Keep left and follow the arrows to Parking West.
Next, leave the parking at level +1 using the big stairs near the vending machines.
Follow the red carpet and arrows to 'Onco Dagcentrum' to get to the O&N buildings. Take the stairs on your left after exiting Parking West. You are now in front of the O&N4 building; on the left you will find O&N5.