BEGIN:VCALENDAR VERSION:2.0 PRODID:icalendar-ruby CALSCALE:GREGORIAN BEGIN:VEVENT DTSTAMP:20260720T125024Z UID:848a28b3-dec1-46d9-bf04-1d4385beca6a DTSTART:20260603T090000Z DTEND:20260605T170000Z DESCRIPTION:## Overview\n\nSpatial transcriptomics is a rapidly evolving te chnology that allows researchers to study gene expression within the spati al context of tissue architecture. This course provides a practical introd uction to the analysis of both sequencing-based and imaging-based spatiall y resolved transcriptomics (SRT) data\, combining theoretical background w ith hands-on exercises using mostly the `R`/[Bioconductor](https://www.bio conductor.org/) ecosystem. Participants will gain an understanding of expe rimental design\, data preprocessing\, and downstream analysis workflows. Through lectures and guided practicals\, the course aims to equip particip ants with the skills needed to perform their own spatial transcriptomics a nalyses and interpret the results in a biological context.\n\n## Audience\ n\nThis course is designed for PhD students\, postdoctoral and other resea rchers in the life sciences from both academia and industry who are seekin g to understand and analyze spatial transcriptomics data.\n\n## Learning o utcomes\n\nAt the end of the course\, the participants are expected to:\n\ n- **Explain** the principles and describe applications of both sequencing -based and imaging-based spatially-resolved transcriptomics (SRT)\n- **Ide ntify** potential pitfalls and limitations of SRT experiments and analysis workflows.\n- **Define** applications for cell segmentation and apply fre quently-used cell segmentation methods\n- **Assess** and interpret raw out puts and spatial metadata files\, understanding their structure and releva nce for downstream analyses.\n- **Define** important aspects of quality co ntrol\, feature selection\, dimensionality reduction and differential gene expression to SRT data and apply those. \n- **Clarify** various spatial s tatistics and their application to biological questions.\n- **Use** freque ntly-used methods to analyze multi-sample SRT experiments.\n\n## Prerequis ites\n\n### Knowledge / competencies\n\n**Participants must have basic kno wledge in UNIX\, R\, dimensionality reduction\, clustering and Next-Genera tion Sequencing (NGS) techniques.**\n\nThis course is part of the [Omics D ata Analysis learning path](https://www.sib.swiss/training/learning-paths? path=omics-data-analysis). To get the most out of this course\, you should meet the learning outcomes of [Single-Cell Transcriptomics with R](https: //www.sib.swiss/training/course/ISCTR)\, [Introduction to bulk RNA-Seq: Fr om Quality Control to Pathway Analysis](https://www.sib.swiss/training/cou rse/IRNAS)\, [NGS - Quality control\, Alignment\, Visualisation](https://w ww.sib.swiss/training/course/NGSQC)\, [First Steps with R in Life Sciences ](https://www.sib.swiss/training/course/FSWRR) and [UNIX Fundamentals](htt ps://www.sib.swiss/training/course/2012_UNIXF). Upon completion of this co urse\, you may wish to attend the [\nIntroduction to Sequencing-based Spat ial Transcriptomics Data Analysis\n](https://www.sib.swiss/training/course /SBSRT).\n\nIn summary\, participants must already have a basic knowledge in:\n\n- Next Generation Sequencing (NGS) techniques\n- Analyzing gene exp ression data\n- Dimensionality reduction (PCA\, UMAP)\n- Graph-based clust ering \n- R (evaluate your R skills [here](https://docs.google.com/forms/d /e/1FAIpQLSdIyeuabd_ZOWXgI1MWHapmaOMu20L9ESkLDZiWnpmkpujyOg/viewform?usp=s f_link))\n- UNIX (self-assess your skills with the e-learning course [UNIX Fundamentals](https://www.sib.swiss/training/course/2012_UNIXF)\, and thi s [quiz](https://docs.google.com/forms/d/e/1FAIpQLSd2BEWeOKLbIRGBT_aDEGPce 1FOaVYBbhBiaqcaHoBKNB27MQ/viewform?usp=sf_link))\n\n### Technical\n\nAtten dees should have a Wi-Fi enabled computer. An online R and RStudio environ ment will be provided. However\, in case you wish to perform the practical exercises on your own computer\, please take a moment to install R (>\; 4.5) and Rstudio before the course.\n\n## Schedule – CE(S)T time zone\n \n## Application\n\nThe registration fees for academics are **300 CHF** an d **1500 CHF** for for-profit companies.\n\nWhile participants are registe red on a first come\, first served basis\, exceptions may be made to ensur e diversity and equity\, which may increase the time before your registrat ion is confirmed.\n\nApplications will close on **20.05.2026** or as soon as the places will be filled up. Cancellation after **20.05.2026** will no t be reimbursed. Please note that participation in SIB courses is subject to our [general conditions](https://www.sib.swiss/legal-documents).\n\nYou will be informed by email of your registration confirmation. Upon recepti on of the confirmation email\, participants will be asked to confirm atten dance by paying the fees within **5 working days**.\n\n## Venue and Time\n \nThis course will be streamed.\n\nThe course will take place at the Unive rsity of Zurich\,.\n\nThe course will start at 9:00 CET and end around 17: 00 CET.\n\nPrecise information will be provided to the registered particip ants in due time.\n\n## Additional information\n\nCoordination: Geert van Geest\, SIB Training group.\n\nA **Certificate of Attendance** will be sen t provided you were present at the course\, whereas a **Certificate of Ach ievement** recommending 0.75 ECTS will be sent provided you passed the exa m.\n\nYou are welcome to register to the SIB courses mailing list to be in formed of all future courses and workshops\, as well as all important dead lines using the form [here](https://lists.sib.swiss/mailman/listinfo/cours es).\n\nSIB abides by the [ELIXIR Code of Conduct](https://elixir-europe.o rg/events/code-of-conduct). Participants of SIB courses are also required to abide by the same code.\n\nFor more information\, please contact [train ing@sib.swiss](mailto://training@sib.swiss). SUMMARY:Introduction to Spatial Transcriptomics Data Analysis URL;VALUE=URI:https://www.sib.swiss/training/course/20260603_ISTDA END:VEVENT END:VCALENDAR