Start here - basic information

BioVis NEWSLETTER September 2024

Welcome back to work and the second half of 2024. Below you find the news concerning BioVis

NEW BOOKING SYSTEM

We finally switched to iLab. In order to book BioVis services an iLab account is necessary for our independent customers.Make sure your Research group´s Supervisor has set up an account. iLab has partnered with Uppsala University, KI and KTH, which gives our customers easy access to other facilities. You find more information on our homepage under “START here”, menu iLabbooking.

NEW BioVis site at BMC

We finally can offer Flow Cytometry and Confocal Microscopy at the BMC. The Cytoflex S with 13 channels and the possibility to run either tubes or 96 well plates makes Flow Cytometry a breeze. The LSM700 with its 4 Excitation Lasers of 405/488/555/633 and two PMTs for emission collection awaits its customers. All customers who already received their introductions to the instruments and are situated at the BMC are invited to use the “BMC instruments”. Eager to get started and have not received an intro?

Light Microscopy

BioVis offers currently a total of 6 microscopes forWidefield -, Slide Scanning-, Confocal-, Superresolution- and Two-Photon Microscopy.

The new entry to our instrument portfolio is the Leica Stellaris 5, a versatile and user-friendly workhorse, for basic fluorescence imaging to advanced microscopy experiments. An instrument serving most user needs and especially designed to a wide variety of users from beginners to experienced. Sporting the White Light Laser option you can choose and tune in specific excitation wavelengths between 485-790nm. The system offers also the 405 Laser. For detection and collection of the fluorescent emission of your fluorophores, the system offers the free choice of emission bandwith. Fast overview images and images mosaics and stitching, XYYT are included. The Stellaris 5 offers also the TAU technique, time resolved imaging, where difference of fluorescence life times are revealed using fluorescently labeled or unlabeled samples.

Electron Microscopy

BioVis owns a Transmission Electron Microscopy and a sample preparation Lab. BioVis is looking for customers who are interested for FIBSEM, to explore your sample in XY and Z. We will use the FIBSEM situated at Ångström Lab.

Flow Cytometry

BioVis is offering now a total of three Analyzers and two Cell Sorter. The Cytoflex S (13 channels) as part of the BMC site, Cytoflex LX “LX ONE” and “LX TWO” (21 Channel) as part of the Rudbeck site. All three instrument have the plate reader option available. The “LX TWO” is the new instrument and has the same optical configuration as the “LX ONE”. The Sorter are at Rudbeck Lab with the Cytoflex SRT (14 channel) and the AriaIII (13 channel)

PhD Courses

PhD Course Introduction to Image Analysis, 9.30-4.30pm Oct 17, 18, 21, 22 ,23, 1.5 credits.

The IAS course is suitable for those beginning or wanting to start image analysis and is very hands on. There are two targets, understanding the fundamental of image analysis and learning how to use particular software, which we pursue in parallel. Initially working with ImageJ, the most popular scientific software, and then learning how to create macros to automate analysis. The course ends with the participants, working in groups, presenting their solution to a problem they are interest in.

The IAS course focuses on ImageJ and automating analysis by writing macros and is suitable for students beginning image analysis.

http://www2.medfarm.uu.se/utbildning/forskarniva/for_doktorander/kursanmalan1217.html

PhD course Methods for Cell Analysis, 2-10 October, 09:00-16:00, 3.5 credit

The course aims at postgraduate students, post-docs and research engineers who wants to learn more about Light Microscopy, Flow Cytometry and Electron Microscopy. The course is based on a lecture series and practical hands on sessions. Lectures will cover e.g. theory of fluorescence, its application in various light microscopy techniques and flow cytometry. Electron microscopy and latest technical achievements like super resolution are covered as well. The practical hands-on sessions include resources found at BioVis like laser scanning and two photon microscopy, flow cytometry and cell sorting, electron microscopy.

http://www2.medfarm.uu.se/utbildning/forskarniva/for_doktorander/kurs1011.html

Instrument Introduction Courses

BioVis offers monthly introduction courses, including lectures about the basics and details of each technique and instrument. You find more details following the link:

https://www.uu.se/en/research/biovis---biological-visualization/courses--introductions/instrument-introductions

EVENTs

FlowJo:

On October 1st (09:oo – 12:oo) BioVis will host a Virtual event on BD FlowJo.

Agenda

• Dimensionality reduction & clustering in your flow analysis
• FlowJo plugins
• FlowJo for Spectral flow
• Q&A

This event serves also the purpose to figure out, whether BioVis should offer FlowJo floating licences in its service portfolio, so that customer can pay by booked usage.

For registration please contact Dirk.Pacholsky@igp.uu.se email subject “FlowJo Oct1”

Stockholm: SuperResolution Microscopy:

Our Imaging Specialists at the Advanced Light Microscopy facility are inviting you to join their Advanced Light Microscopy Symposium covering super-resolution applications (STED, SMLM, MINFLUX). Time: 9-12am, September 13th / Place: SciLifeLab, AIR/FIRE, Tomtebodavägen 23A, Solna For more information and registration details follow the link: https://www.nmisweden.se/2024/08/15/scilifelab-symposium-in-advanced-light-microscopy/

• General Information

BioVis offers a wide range of different instruments. In general BioVis has three nodes: Electron Microscopy, Flow Cytometry (and Cell Sorting), Light Microscopy. More information is available under the Technology section.

We are mainly situated at Rudbeck Lab and have a small site at BMC. The BMC site offers one Flow Cytometer and (soon) one Confocal Microscope at B11, third floor. UU Campus card is needed to access the room. You reach the room following this mazemap link.

An Introduction to the Instruments given by BioVis Staff is priority for all customers, before using BioVis´Instruments independently.

Full Service can be booked, where BioVis staff is handling the customers´ processed sample on the Instrument.

An Acess card is needed to enter BioVis Premises.

Approved users have access to the facility 24 hours a day 7 days a week. However after 17:00, and during weekends, access is restricted to experienced users who are familiar with the instruments and can preform some trouble shooting themselves.

BioVis may be closed for all customer during shorter periods, concerning vacation. This will always be announced at least two months in advance giving you plenty of time to plan your experiments accordingly.

Report all instrument problems directly to BioVis staff and make a note in the logbook every time you have used an instrument.

Bring the consumables you will need to perform your analysis, like cell-strainers, tubes, glass slides and cover slips etc. They are not included in the fee.

• Entrance card & Access

In order to enter BioVis premises at Rudbeck Lab, you need to have a valid card. Customers of IGP and Rudbeck need only access granted on their existing cards. An access card can be obtained via BioVis. The access card is personal and must not be lent to a colleague. Access cards are given out to customers who have received Instrument introductions and use our instruments.

Please contact Jeremy.Adler@igp.uu.se for more details regarding access cards. Observe that your cards will be valid for one year in total. Have the access card form Excel, 13 kB. ready to be sent to Jeremy.

Since 240411 we have a FlowCytometer at the BMC, B11 third floor. See General Information menue for more details.

• Instrument Introductions

BioVis gives introductions to its instruments once per month. The introduction contain in-depth lectures and hands-on sessions on the instrument. Introduction to the instrument is a priority to be an independent customer. You can apply for introductions under Introductions.

BioVis will change its booking system to iLab, August 23. Customers and their PI need to have an iLab account.

A detailed description can be found in the document.

BioVis_iLab_Guideline_240805 Pdf, 691 kB.

For bookings in iLab use the link iLab bookings at BioVis

Instruments

BioVis offers a wide range of different instruments. In general BioVis has three nodes: Electron Microscopy, Flow Cytometry (and Cell Sorting), Light Microscopy. More information is available under the Technology section.

Services

• Flow Cytometry, Cell Sorting, Light Microscopy

BioVis offers its customers independ use of instruments or Full Service. For independent use of Instruments, customers are obliged to have been trained by BioVis staff. Apply for it under Instrument Introductions. Full Service can be booked. Here staff is handling the instrument, using your (processed) sample. BioVis offers also Consulting to discuss and guide projects concerning experimental design (in relation to instrument use).

• Electron Microscopy

BioVis offers its customer a full service mode from sample preparation to imaging.

Prices for Services

BioVis is mainly financed by the MedFarm Faculty of Uppsala University and service prices are subsidized for UU customers. A detailed price list can be seen below BioVis has a three level price setting: Uppsala University, Swedish Academia, Full cost price. Within this levels you will find Independent use and Full service, as well as different categories like Courses etc.

Acknowledgements

Our customers are obliged to acknowledge BioVis (and staff if applicable) inn case results are published where BioVis services were used.

Example: The BioVis platform of Uppsala University was used to conduct experiments using “technique /Instrument”, supported by “Staff name “.

• Biosafety

All work involving biosafety class 2 organisms on BioVis instruments must be performed according to Uppsala University regulations. You are obliged to inform us about any potential hazards.
The use of lentiviral vectors has been increasing because they allow highly efficient gene delivery in a wide variety of cell types. Samples of lentivirus-transduced cells pose a higher degree of hazard than other samples submitted for analysis. Have such samples in culture for one week so virus activity is ceased.

• Data storage

We cannot be held responsible for the misuse, loss and manipulation of data stored on our computers. You are allowed to store data temporarily on our computers. Always transfer your data to a trusted storage medium. Details on how to handle your data will be found on the instrument computer desktop. We export all stored data from instrument computers on a regular basis. We will always inform our users before this happens. Our data share computer is a public computer, all BioVis users will have access to your data there.

BioVis offers also courses in Image Analysis based on the usage of Image J. BioVis runs two PhD courses, Methods for Cell Analysis , and Introduction to Image Analysis Software.

You find more information under Courses.