Databinge Principles

  • Inclusivity: Databinge is a forum for everyone. We strive to provide a means to help others build their skills and further their projects while we do the same.  Creativity is maximized when researchers with diverse strengths work together.
  • Collaboration: Science is by its nature a community enterprise. Databinge encourages collaboration by working together starting early in the discovery process and using open data and code where possible.
  • Agility: New techniques, methods and approaches emerge continuously. Databinge strives to be responsive to this and enable adoption through collaborative workshops.
  • Sound Practice: Databinge strives to help improve practices including data and code management to further open science.

Data Champions Databinge:

  • Time: 12:30pm each Friday
  • Location: Online using Zoom

With Support from the Digital Alliance we have expanded Databinge as an online meeting to tackle coding and new approaches to data analysis while promoting sound Research Data Management Practice which supports our collaborations and Open Science Practices. The team, spanning the Centre for Brain Health, BCCHRI, ICORD and UVic, will be online via slack and zoom to discuss points of interest in detail and provide focused help. Contact a tutor (see bios here) via email for slack invites and zoom addresses. We recommend labs prep OSF projects in order to share data and code. Info on using OSF can be found here.

Databinge Recommendations on Exploratory Data Analysis and Visualization

At Databinge on Aug 26, 2022 we had a group discussion on best practices for Exploratory Data Analysis and Visualization. What follows below is a summary of the key points. Taken together these practices will:

  1. Save you time and frustration in conducting your current and future research projects and completing your program.
  2. Support (computational) reproducibility.
  3. Support the review process when it is time to publish results.
  4. Support the adoption of Open Science.

Initial Data Quality Control: Think about where you are in the data processing and analysis pipeline. This spans acquisition to raw data to processed data and all subsequently derived measures.  What is the raw data that you have obtained? It might differ from project to project.

  • Do initial quality control checks as close to the acquisition of the raw data as possible. Investing time and effort at this stage will mean fewer downstream doubts and follow-up experiments and an overall stronger conclusions later.  You will be confident that the rest of your analysis pipeline will have the best possible input.
  • Read through several literature sources and work through tutorials that use the quality control measures that you are thinking of applying to your data. You might decide that different sections from different pipelines suit your data and project the best; it’s always good to have a well-rounded understanding of the possible steps that you could apply (but don’t necessarily have to).

Sanity Checks and checkpoints: Try to establish steps in your pipeline where you can look for signatures indicating that the previous steps worked as intended. This could be accomplished by:

  • Examining one subject in depth in a multi-subject study
  • Having positive and negative controls
  • By using a high-quality open data set as input in addition to your own data

Record your steps and your code: Using your method of choice (e.g. code versioning on GitHub, ImageJ macro recorder, Slack channels, note taking software, or your lab book) ensure that you know the steps you took to arrive at your visualizations.  Exploring necessitates trying different ways to reach the best possible visualization, most of which will go nowhere, in a short time. It is easy to lose track and it can be frustrating to not be able to reproduce something potentially exciting. Be as comprehensive in the annotation of your steps as possible – someone with zero knowledge of your data or script should be able to at least get an idea of the steps you have taken (even if they don’t understand all of the theoretical underpinning).

Tools: The tools of choice depend on what data you are working with and, like the choice of programming languages, are often driven by what your research community routinely uses.  Options include Jupyter notebooks, R Markdown, MATLAB scripts, ImageJ macros, Napari, Open Science Framework and many more.  Certain software packages only work in specific programming languages. Databinge is a great forum to discuss the pros and cons of tools with people actively using them.

Community Advice on Data Presentation: Think about how you would like to show the data in presentations, papers and your thesis early on: the earlier, the better.  It is tempting to plot a lot of data when exploring but often simpler plots are needed to succinctly convey your message to others.  Get other researchers to look at your plots to see if you are conveying what you intend. Additionally, do not underestimate the power of the visual impact of your data. Spend a little time coordinating a colour palette that ties-in the overall experience of your poster or presentation. Often, it is helpful to have someone who is not deeply familiar with your work look at your visualizations as they will not have made the same assumptions as you or someone more familiar may have. This could be a lab member or through a forum like Databinge.

A programmatic approach: In tandem with feedback on your data presentation, work on a programmatic approach (e.g. macros, shiny apps, versioned Jupyter notebooks) to streamline the process of creating your visualizations.  This will save lots of time and ensure you treat each piece of data the same.  Strive for code that fails elegantly (e.g. warns you when the data input is not as expected).

Pre-Curtailment Databinge:

  • Time: 4:00-5:30pm each Friday
  • Location: Koerner F103
  • Food: Pizza at 4:30pm

Open to all UBC labs. Databinge is an interactive drop-in meeting for neuroscientists with the goal of furthering training and collaboration. Supported in part by the DMCBH and the Canadian Neurophotonics Platform, our goal is to promote collaboration and emphasize practical know-how via the use of UBC licensed and open-source software and sharing of protocols. Each Friday we will have an open house in which interested labs can have a data show-and-tell, problem-solving session, and/or technique presentation including interactive analysis using the facilities of the NINC. We encourage the use of MATLAB, ImageJ, Python, and LabView as well as cloud-based data storage/software archiving to facilitate sharing amongst labs.

Past Databinges:

13-August-2021 Brain-Tech 2021

This virtual event taking place during Databinge hours brings together students and researchers from diverse fields to brainstorm and prototype novel applications to support brain wellness. These applications may either improve brain wellness directly through the encouragement of healthy lifestyles or indirectly by contributing to the study and dissemination of brain wellness concepts. Researchers and students studying healthcare, neuroscience, computer science, and biomedical engineering are invited to contribute their unique expertise to this event. It is anticipated that winning teams will develop the concept for an app, software tool, or program that will aid the mission of the BC Brain Wellness Program.

For more information on the event, click here

To view project submissions, click here

30-April-2021 Neurodata Without Borders Presentation

Nuerodata Without Borders is a consortium of researchers and foundations that are dedicated to breaking down the obstacles to data sharing in the neuroscience community. Databinge will be hosting a special presentation on Neurodata Without Borders presented by Adrien Peyrache.

For more information on Neurodata Without Borders, please click here.

16-April-2021 iDISCO

A tool/procedure for rapid immunolabeling and volume imaging of biological samples

More information can be found here

19-March-2021 Special Guest Edward Yan

Edward Yan from the Murphy lab will be presenting his work on Neuropixel probes and high-density recording.

4-March-2021 Special Guest Shay Neufeld

Shay is the Data Product Lead at Inscopix where he leads a team in Vancouver, BC focused on building data analysis products and services for the neuroscience community. Prior to joining Inscopix, he worked as a Senior Data Scientist for Livestories (a small public health-focused analytics company in Seattle), as well as a Machine Learning Engineer & Product Consultant for Boston Children’s Hospital Technology & Innovation Development Office. Shay received a Ph.D. in Neuroscience from Harvard in 2017 where his research focused on investigating how neural circuits in the basal ganglia engender reinforcement learning & goal-directed behavior.

19-February-2021 UBC Digital Research Infrastructure Showcase

UBC Advanced Research Computing(ARC), in partnership with Djavad Mowafaghian Centre for Brain Health (DMCBH), will showcase UBC ARC digital research infrastructure: Sockeye and Chinook

More information on UBC ARC can be found here.

29-January-2021 Git and GitHub (Slides Included)

A presentation on Git and GitHub which a set of tools used for version control and project collaboration.

Slide Presentation

20-October-2020 TDT Fiber Photometry Workshop

Fiber photometry is a calcium imaging method for detecting neural activity.

11-September-2021 Calcium Imaging Data Processing Pipeline

Sam and Majid from the University of Lethbridge will join Databinge on Sept 11 to go over the pipeline they are employing to process calcium imaging data from in vivo two-photon microscopy. 

Their pipeline will make use of the Suite2p pipeline created by the Howard Hughes Medical Institute. More information on Suite2p can be found at

5-June-2020 Mathworks

MathWorks is the leading developer of mathematical computing software for engineers and scientists and is known for developing programs such as MATLAB. Aycan Hacioglu will be attending Databinge to discuss MATLAB resources and possible tutorial topics.

13-March-2020 Predicting Task Outcomes From Mesoscale Brain Activity

Learn about modeling to predict task outcomes in Murphy lab automated imaging.

6-March-2020 Brain Functional Organization, Connectivity And Behaviour

Meeting Report.

28-February-2020 Dual-Modality Microfluidic-Based Calcium Imaging Setup In C. Elegans

Learn about a new rig being constructed in the Rankin lab.

21-February-2020 No Databinge Scheduled (Ubc Winter Break)

Time to hit the books (or slopes).

14-February-2020 Veta: An Open Source Tool For Combining Tms With Behavioural Tasks

Learn about this software

7-February-2020 Expansion Microscopy Update (Slides Included)

Update on current protocols and imaging results using expansion microscopy at UBC

Slide Presentation

31-January-2020 Github, Osf, And The Brain Circuits Cluster (Slides Included)

Review of the Dynamic Brain Circuits cluster resources and overview of activities in 2020.

Slide Presentation

6-December-2019 Pydynamo (Slides Included)

An open-source Python application for analyzing the dynamic morphometrics of neuronal arbors over time

Slide Presentation

29-November-2019 Postponed

Postponed due to TransLink Strike.

22-November-2019 Version Control With Git (Slides Included)

The basics of version control with git using GitKraken.

Slide Presentation

15-November-2019 Allen Institute Showcase Symposium Discussion (Slides Included)

Discussion about the Allen Institute Showcase Symposium held Nov. 11-12, 2019

Presentation 1

Presentation 2

Presentation 3

8-November-2019 Deeplabcut And Beyond (Slides Included)

DeepLabCut: “a software package for animal pose estimation”. A presentation about phase space analysis, motion mapper, and applications in neural encoding.

Slide Presentation

25-October-2019 No Presentation Scheduled (Sfn)

No presentation due to Society for Neuroscience (SfN) 2019.

18-October-2019 No Presentation Scheduled (Sfn)

No presentation due to Society for Neuroscience (SfN) 2019.

11-October-2019 Bioimage Informatics 2019 (Slides Included)

Report on BioImage Informatics 2019.

Slide Presentation


4-October-2019 Multiplexed Fluorescent In Situ Hybridization Assays

27-September-2019 Postponed

Postponed due to Climate Strike.

20-September-2019 Voltage Imaging (Slides Included)

Voltage imaging and report on the 2019 Frontiers in Neurophotonics Summer School.

Slide Presentation

13-September-2019 Cshl Statistical Methods For Functional Genomics (Slides Included)

Report on the CSHL Statistical Methods for Functional Genomics course.

Slide Presentation

6-September-2019 Jupyterhub (Slides Included)

Introduction to the new JupyterHub on the DMCBH computer cluster.

Slide Presentation

31-May-2019 Neurophotonics Raspberry Pi Preview (Slides Included)

Hands-on workshop with pis. To be presented at Neurophotonics Summer School in QC.

Slide Presentation

26-Apr-2019 Optical Sensors For Metabolism (Slides Included)

2-photon imaging.

Slide Presentation

18-Apr-2019 (Thursday) Mesoscale Calcium Imaging Analysis

calcium imaging analysis with Matlab.

5-Apr-2019 Jupyter & Binder (Slides Included)

Introduction to Python tools, Jupyter Notebook and Binder.

Slide Presentation

29-Mar-2019 Jess & The Simple Western Platform: Why You Should (Almost) Never Have To Perform A Traditional Western Blot Ever Again

Meeting Report.

22-Mar-2019 Designing And Using Advanced Multiphoton Imaging Systems In Neuroscience (Slides Included)

Meeting Report.

Slide Presentation

15-Mar-2019 Comprehensive Imaging (Slides Included)

Functional imaging of an entire neuron.

Slide Presentation

8-Mar-2019 Serial-Scanning Laser For High-Throughput Optogenetic Stimulation (Slides Included)

Opto for automatic experiments.

Slide Presentation

1-Mar-2019 Chips For Sub-Cellular Ca2+ Analysis (Slides Included)

Code for analyzing astrocyte calcium signals among other things.

Slide Presentation

8-Feb-2019 Berkeley Advanced Imaging Methods Workshop (Slides Included)

Meeting report.

Slide Presentation

30-November-2018 Fiber Photometry (Slides Included)

Learn about the Raymond lab’s new fiber photometry rig.

Slide Presentation

16-November-2018 Post Sfn Discussion

Share what amazed you most at SfN 2018.

9-November-2018 Deeplabcut (Slides Included)

Come learn about a new machine learning approach for movement tracking.

Slide Presentation

26-October-2018 Slap Microscope (Slides Included)

Come learn about a new approach for fast 2p imaging.

Slide Presentation

19-October-2018 Sql Database (Slides Included)

Come learn how to organize your data.

Slide Presentation

12-October-2018 Neural Networks (Slides Included)

Come join the discussion on artificial neural networks.

Slide Presentation

5-October-2018 Canadian Neurophotonics Platform (Slides Included)

Ellen Koch will tell us about the current state of neurophotonics and what she learned at the course in Laval last summer.

Slide Presentation

28-September-2018 Advanced Research Computing Resources At UBC (Slides Included)

Representatives from Advanced Research Computing at UBC will be joining us to talk about available High-Performance Computing and data storage resources available to researchers on campus at UBC and through WestGrid and Compute Canada.

Slide Presentation

21-September-2018 Imaging Structure And Function In The Nervous System- Highlights And Emerging Technologies (Slides Included)

Tristan Dellazizzo Toth will tell us about his experience at the Cold Spring Harbor course he took this summer.

Slide Presentation

More Info

16-Mar-2018 Janelia Meeting Report Frontiers In Microscopy Technologies (Slides Included)

Discussing an overview of the Janelia Spring Conference on Frontiers in Microscopy Technologies and Strategies for Bioimaging Centers Network.

Slide Presentation

09-Mar-2018 Mclust Spike Sorting (Slides Included)

Tetrode sorting using Mclust to improve sorting over single cells significantly as well as over stereotrodes.

Slide Presentation

02-Mar-2018 Minion Sequencing

MinION, the only portable real-time device for DNA and RNA sequencing

Not Available

23-Feb-2018 Video Rate Flim

Fluorescence lifetime imaging microscopy at video-rate speeds.

Not Available

16-Feb-2018 Crispr (Slides Included)

An overview of how CRISPR functions, its role and the possibilities that it opens.

Slide Presentation

02-Feb-2018 Gibson Cloning (Slides Included)

Joining fragments of DNA.

Slide Presentation

17-Nov-2017 Sfn Tech Pitch

$50 Starbucks gift card to best SFN tech pitch (other than Deisseroth or Boyden labs since we all know how great they are), $25 for the second place. 5 minutes max, no slides only talking and whiteboard, at least 5 pitches lined up for a contest to occur.

Not Available

03-Nov-2017 Dreadds (Slides Included)

Designer Receptors Exclusively Activated by Designer Drugs.

Slide Presentation

20-Oct-2017 Illustrator/Inkscape (Slides Included)

Using software such as Inkscape and Illustrator to create vector graphics for figures.

Slide Presentation

13-Oct-2017 Blender (Slides Included)

A talk on the benefits of rendering for creating figures and basic understanding of algorithms to calculate pixel colour value.

Slide Presentation

02-Jun-2017 Summer Workshop On The Dynamic Brain (Slides Included)

An in-depth overview of the Summer Workshop on the Dynamic Brain

Slide Presentation

09-Jun-2017 Hpc (Slides Included)

Short tutorial on how to use linux/unix tools to run code on the centre’s new computer cluster

Slide Presentation

26-May-2017 The Shell (Slides Included)

The Unix Shell


19-May-2017 Linux Survival Guide (Slides Included)

A guide on using Linux.

Slide Presentation

12-May-2017 Bayesian Stats (Slides Included)

A theory in which the evidence about the true state of the world is expressed in terms of “Degrees of Belief” know as Bayesian Probabilities.

Slide Presentation

28-Apr-2017 Stats Primer (Slides Included)

Basic statistical tests like the t test are used by almost all neuroscientists but how do they work and allow us to make inferences from our data? What are the assumptions? What are the differences between commonly used t tests?

ZIP with demo files and slide presentation

21-Apr-2017 Resamapling, Bootstrap, And Permutation Testing Part 2. (Slides Included)

A discussion of resampling techniques to estimate standard error and confidence intervals as well as do hypothesis testing. These methods are very useful for exploring your data and make few assumptions about the underlying distribution.

ZIP with demo files and slide presentation

07-Apr-2017 Resamapling, Bootstrap, And Permutation Testing Part 1. (Slides Included)

A discussion of resampling techniques to estimate standard error and confidence intervals as well as do hypothesis testing. These methods are very useful for exploring your data and make few assumptions about the underlying distribution.

ZIP with demo files and slide presentation

31-Mar-2017 Rstudio (Slides Included)

RStudio is a free and open-source IDE for R, a programming language for statistical computing and graphics.

ZIP with demo files and slide presentation

24-Mar-2017 Data Analysis (Slides Included)

A discussion of key guiding principles for any rigorous and honest data analysis. These principles were fueled by years of analyzing mostly behavioral and electrophysiology data, but should extend to all analyses. Topics include: Why Bayesian analyses are (now) awesome, why Frequentist analyses are useful, why Frequentist statistical philosophy is nonsense, and the critical importance of failure.

Slide Presentation

17-Mar-2017 Graph Theory (Slides Included)

Learn about how graphs can help you understand brain networks and how you can use computers to analyse the produced graphs.

Slide Presentation

10-Mar-2017 Aavs (Slides Included)

Adeno-Associated Virus!

Slide Presentation

03-Mar-2017 Computer Vision (Slides Included)

Crash course on Computer Vision.

ZIP with demo files and slide presentation

24-Feb-2017 Light Sheet Microscopy

Light Sheet Microscopy.

Not Available

17-Feb-2017 Gcamp (Slides Included)

Imaging brain activity with Calcium Imaging.

Slide Presentation

10-Feb-2017 Mouse Genetics (Slides Included)

Everything you wanted to know on mouse genetics.

Slide Presentation

03-Feb-2017 Machine Learning (Slides Included)

Machine Learning with MatLab.

ZIP with demo files and slide presentation

27-Jan-2017 Flim (Slides Included)

Fluorescence lifetime imaging microscopy.

Slide Presentation

20-Jan-2017 Spike Sorting

Sorting Spikes.

Not Available

09-Dec-2016 Deconvolution

Deconvolution. Sharpening images.

Not Available

02-Dec-2016 Lab View

Developing with Lab View.

Not Available

25-Nov-2016 Raspberry Pi (Slides Included)

Basics on Raspberry Pis and their Cameras.

ZIP with demo files and slide presentation

04-Nov-2016 Imagej Macros (Slides Included)

Simple ways to automate your image analysis using the indispensable ImageJ.

Slide Presentatioin

28-Oct-2016 3d Models With Solidworks (Slides Included)

Learn the basics of 3D modelling in Solidworks.

Slide Presentation

21-Nov-2016 App Development In Python (Slides Included)

Tips and tricks to building a scientific app using PyCharm.

Slide Presentation

14-Nov-2016 Mendeley And Ref Management (Slides Included)

How-to guide to manage papers and references with Mendeley.

Slide Presentation

07-Oct-2016 Git And Github (Slides Included)

Learn git for software version control.

Slide Presentation

30-Sep-2016 Animations And Illustrations

A discussion of different software (notably inkscape and blender) used to create animations for science communication.

23-Sep-2016 Intro To Databinge

Open to all UBC labs. Databinge is an interactive drop-in meeting for neuroscientists with the goal of furthering training and collaboration. Supported in part by the DMCBH and the Canadian Neurophotonics Platform, our goal is to promote collaboration, emphasise practical know-how via the use of UBC licensed and open-source software, and sharing of protocols. Each Friday we will have an open house in which interested labs can have a data show-and-tell, problem solving session, and/or technique presentation, including interactive analysis using the facilities of the NINC. We encourage the use of MatLab, ImageJ, Python, and LabView as well as cloud-based data storage/software archiving to facilitate sharing amongst labs. Located at Koerner F103, anyone interested can drop-in and experience Databinge. Presenters offer demo files to aid in the understanding of large topics, and pizza is handed out at 4:30pm every meeting.