Newsletter May 2025

New TEM

A new transmission electron microscope, a Hitachi HT7800 with a 20 MP Xarosa camera, will be installed beginning of June. The new microscope will be available for booking around week 34-35. The old Tecnai microscope will be dismantled on the 19th of May. During the time between dismantling and installation we are still able to accept samples for embedding and sectioning. If you are in need of urgent imaging, please contact Monika Hodik and Karin Staxäng for further information.

New Staff member

BioVis recruited a new staff member, Ross Smith, who will take over for a retiring colleague, Jeremy Adler. Together with Matyas, Ross will be responsible for providing Lectures, Introductions, courses related to Light Microscopy. Additionally, Ross will soon be offering Image Analysis services (pipeline scripting for various popular software platforms such as Python, Cell Profiler, Image J, IMARIS, and QuPath). Get in contact with Ross Smith to know more.

BioVis at BMC: Flow/LSM/IMARIS

A reminder to Researchers in need of Flow Cytometer (Cytoflex) and Confocal (LSM700). The Cytoflex LX(two) with 22 fluorescent channels and plate reader option is available. The LSM offers you Lasers 405, 488, 562 and 633 for excitation.

Additionally, we have now set up a small workstation which allows users to access the IMARIS software. As always book before usage.

IMARIS

BioVis is reviving its services for the 3D/4D visualization and analysis software, IMARIS. All customers using IMARIS must book it via iLab (under workstations). We have one Base license and several module licenses (Filament, Cells Viewer, Coloc, Lineage, Track, InPress, Vantage). IMARIS can be accessed from BioVis Workstations located in the Rudbeck and in the BMC facilities. Get in contact with Ross to know more or to arrange specialized connection needs.

Follow BioVis

BioVis has created several WhatsApp groups to efficiently exchange instrument-specific information with its customers. Join these groups to stay informed and get in contact with other customers. Links and details can be found on the Instruments or at the BioVis Lab doors. Newsletters are available on the BioVis homepage and LinkedIn.

FlowJo licences

BioVis purchased a 25-seat license for FlowJo, where an annual seat will cost 3775 SEK/year. BioVis will be administrating the seats, BioVis looks currently into the possibility for licences to rent out per quarter, the price here will be 2000 SEK. For more information contact Dirk Pacholsky.

• 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 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 ross.smith@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 is using iLab as its current Booking system.

Each customer to BioVis services (for Light Microscopy and Flow Cytometry) needs to have a valid account.

Make sure

• your Research group PI has a valid account including invoice details
• you are accepted to use your PIs invoice details and funding

The following documents give you more detailed information:

• Document for Research group PI Pdf, 114 kB.
• Document for Researcher (customer BioVis) Pdf, 139 kB.
• Document for external customers (not UU) Pdf, 132 kB.

Additional help

More detailed instructions can be found by clicking on the “HELP” link in the upper right hand corner or by navigating to our iLab Help Site. For any questions not addressed in the Helpsite, click on the “HELP” link in the upper right hand corner and submit a ticket, or email itsupport@uu.se or ilab-support@agilent.com.

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. Our data share computer is a public computer, all BioVis users will have access to your data there. We reserve the right to delete older data folders without prior notice if storage media owned by BioVis reach their capacity limits.

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.