Core Facilities

A core is an instrument or utility that is available to all groups at CMM whereas it is housed within one group. Usually, the CMM foundation invests in equipment and the running costs are covered by user fees. Instruments purchased by individual groups can through rent avelliations also be offered as core facilities. Read more about how to apply for CMM-supported core funding here.

There is a booking system and the Core is listed on the CMM website with a person responsible for the core. A user fee may be charged. If training is needed before operating the Core, a fee for such training may be charged. For more information and booking, see specific instructions listed for each core facility. 

The following core facilities are currently available at CMM (pages with detailed descriptions of each core will be available soon):

Bacterial laboratory

BC Platforms (Biocomputing)

ChemiDoc™ MP Imaging System

Glomax Multi Detection System

Flow cytometry

Functional Fluorescence Microscopy Imaging (fFMI)

IncuCyte

KIGene - genetic analysis and spatial biology

LICOR Odyssey CLx

Luminex

Mesoscale discovery platform

Neon Transfection System

Preparative Histo Core

Robotic System Biomek FX

Seahorse Extracellular Flux Analyzer

Single-cell library prep

Slide scanning

For booking of core facilities/instruments, meeting rooms, writing space and meeting equipment, please visit: booked.cmm.se

Flow Cytometry Core

 

DESCRIPTION:
Cell analysis and cell sorting by flow cytometry is a well established technique whereby rapid measurements of multiple cellular parameters such as light scatter and fluorescence are made on particles or cells as they flow through a sensing point forming the basis for selected populations to be analyzed and/ or sorted out. The CMM flow cytometry facility is equipped with:

 

Cell sorters: 

 

MoFlo Legacy with 2 lasers (488 and 635 nm)  

BD Influx with 5 lasers (488, 561, 641 405, and 355 nm)  

Up to six different cell populations can be sorted out simultaneously into tubes, or one population onto plates (including index sorting). 

 

Sony SH800 with 4 lasers (488, 561, 638, and 405 nm) 

Up to two different populations can be sorted out simultaneously into tubes, or one population onto plates (including index sorting).  

 

Analyzers: 

BD FACSVerse;  equipped with 3 lasers: 488nm, 635nm, and 405nm. 

BD LSR Fortessa;  equipped with 5 lasers: 488, 552, 640, 405, and 350 nm.  

Cytek Aurora; equipped with 4 lasers: 488nm, 635nm, 560nm, and 405nm.

Cytek Aurora; equipped with 3 lasers: 488nm, 635nm and 405nm.

 

Key applications include multicolor immmunophenotyping, cell cycle analysis, intracellular cytokine detection, apoptosis, cell proliferation analysis, and intracellular calcium measurement. Assistance and guidance in planning your experiments as well as suggestions for helping you achieve optimal results are available.

 

CONTACT:
Annika van Vollenhoven
Location: CMM floor 03, room 064
E-mail: annika.van.vollenhoven@ki.se
Phone: +46 8-517 75693
Address:
Flow Cytometry Facility
CMM L8:03
171 76 Stockholm

fFMI

Laboratory for functional Fluorescence Microscopy Imaging (fFMI)

 

The Laboratory for functional Fluorescence Microscopy Imaging (fFMI), Center for Molecular Medicine (CMM), offers training and efficient access to standard and advanced fluorescence microscopy imaging instrumentation for CMM and external users at all levels of experience. Our objective is to support research on molecular and cellular mechanisms underlying normal physiological and pathophysiological processes. To this aim, we enable fluorescence microscopy imaging of fixed and live cells, and quantitative biochemical studies in live cells using Fluorescence Correlation Spectroscopy (FCS) and Fluorescence Cross-Correlation Spectroscopy (FCCS). These techniques enable quantitative characterization of molecular interactions in live cells with high spatial (200 nm) and temporal (µs) resolution and single-molecule sensitivity.

Five dedicated systems are presently available in the Laboratory for Functional Fluorescence Microscopy Imaging (fFMI), L8:01, room 056.

Head of the Laboratory for functional Fluorescence Microscopy Imaging (fFMI)
Vladana Vukojevic, Associate Professor
Department of Clinical Neuroscience
Karolinska Institute

Contact: E-mail: vladana.vukojevic@ki.se; Phone: 070 306 06 48

Training:
Training is required for all first-time users at the cost of 1000 SEK. Training is limited to instructions on how to operate the system and use the software in order to acquire images, perform FCS measurements and export the results. Training does not include supervision in assay setup, assay preparation or result analysis. To schedule training sessions, contact us directly on the e-mail addresses above.

Costs:
Supervised use: 350 SEK/h for CMM users and 450 SEK/h for users outside of CMM. For new users, 5 supervised sessions are required, following the introductory training.
Unsupervised use during regular working hours (9-18 h): 100 SEK/h for CMM users and 200 SEK/h for users outside of CMM.
Unsupervised use outside of working hours (during the weekend and/or from 18-9 h): 50 SEK/h for CMM users and 100 SEK/h for users outside of CMM.
Service costs, including CMM IT costs, will be charged in accordance with the actual annual use.
Reagents have to be purchased by the user.

If you are interested in learning more about advanced fluorescence microscopy techniques and getting hands-on training at the instruments in our core facility, the next occasion of PhD course 2348: Functional Fluorescence Microscopy Imaging (fFMI) in Biomedical Research is November 18 – 29 2019. You can find more information about the course content at:

http://kiwas.ki.se/kicoursecatalogueHT19.pdf

http://kiwas.ki.se/katalog/katalog/kurs/3048

1. The ConfoCor 3 System

The ConfoCor 3 System, Carl Zeiss, Jena, Germany, is individually modified to allow fluorescence imaging with single-molecule sensitivity in live cells. This LSM 510 system consists of an inverted microscope for transmitted light and epifluorescence (Axiovert 200 M) with 6 objectives (5X Plan-Apochromat/0.16, 10X Plan-Neo/0.3, 20X Plan-Apo/0.75 with DIC capability, C-Apochromat 40X/1.2 NA W Corr, C-Apochromat 63x/1.2 W Corr, Plan-Apochromat 100x/1.40 Oil DIC), 3 lasers with 6 laser lines (Ar/ArKr laser with four lines 458, 477, 488 and 514 nm, HeNe 543 nm and HeNe 633 nm), HBO and Halogen lamps, 3 photomultiplier tubes (PMTs), scanning module LSM 510META modified to enable detection in the imaging mode by using silicone avalanche photodiodes (SPCM-AQR-1X; PerkinElmer) and FCS module with 3 detection channels.

Responsible: Vlad Radoi, PhD student; E-mail: vlad.radoi@ki.se; Phone: 073 647 81 04

First time users: If you are interested in using this system, please contact the responsible person for introductory training. System use without previous training is not allowed.

Booking ConfoCor3: Link to the booking system here

2. ConfoCor2 System

The ConfoCor 2 System, Carl Zeiss, Jena, Germany for quantitative in vitro studies of molecular interactions. The ConfoCor2 system consists of an upright microscope with the C-Apochromat 40X/1.2 NA W Corr UV-VIS-IR objective, 3 lasers (Ar laser with three lines 458, 488 and 514 nm, HeNe 543 nm and HeNe 633 nm), a Perkin Elmer APD detection system and computer working station.

Responsible: Dr. Ann Tiiman, Assistant Professor; E-mail: ann.tiiman@ki.se; Phone: 076 708 40 81

First time users: If you are interested in using this system, please contact the responsible person for introductory training. System use without previous training is not allowed.

Booking ConfoCor2: Link to the booking system here

3. mpFCS-alpha System

The mpFCS-alpha System is a state-of-the-art home built microscope specially designed for quantitative, scanning free ultra-fast confocal fluorescence microscopy imaging of fast dynamical processes in live cells. To this aim, the system relies on massively parallel Fluorescence Correlation Spectroscopy (FCS).

Responsible: Dr. Sho Oasa, Postdoctoral Research Fellow; E-mail: sho.oasa@ki.se

Phone: 072 287 09 53

First time users: If you are interested in using this system, please contact the responsible person for introductory training. System use without previous training is not allowed.

Booking mpFCS-alpha: Link to the booking system here

4. The mpFCS-beta System

The mpFCS-beta System is a state-of-the-art home built microscope specially designed for quantitative, scanning-free, ultra-fast confocal fluorescence microscopy imaging of fast dynamical processes in live cells by massively parallel Fluorescence Correlation Spectroscopy (FCS) and Fluorescence Lifetime Imaging Microscopy (FLIM).

Responsible: Dr. Sho Oasa, Postdoctoral Research Fellow; E-mail: sho.oasa@ki.se

Phone: 072 287 09 53

First time users: If you are interested in using this system, please contact the responsible person for introductory training. System use without previous training is not allowed.

Booking mpFCS-alpha: Link to the booking system here

5. LSM 880 Confocal Microscope (without AiryScan)

The LSM 880 Confocal Microscope (without AiryScan), Carl Zeiss, Jena, Germany consists of an inverted microscope for transmitted light and epifluorescence (Axio Observer 7) with 4 objectives: 10X air (Plan-Apochromat 10x/0.45 WD=2.0 M27), 20X air (Plan-Apochromat 20x/0.8 WD=0.55 M27), 25X multi-immersion (LD LCI Plan-Apochromat 25x/0.8 Imm autocorr DIC M27 for water, silicone oil, glycerine or oil immersion, WD=0.57mm at CG=0.17 mm), and 63X oil (C Plan-Apochromat 63x/1.4 WD=0.17 Oil DIC M27), all allowing simultaneous acquisition of transmitted laser light and differential interference contrast (DIC) imaging; 4 lasers with 7 lines for excitation at  405 nm, 458 nm, 488 nm, 514 nm, 453 nm, 633 nm; Halogen and Mercury short-arc reflector lamp (Illuminator HXP 120) for transmitted and reflected light, respectively; 3 detection channels of which two are multialkali photomultiplier tubes (PMTs) and one GaAsP detector; Scan module LSM 880 with high-speed scanners. Dedicated for imaging fixed samples. Can be used for imaging live samples with the microscope stage cell incubator (see Auxiliary equipment). Software ZEN 2.3 SP1 FP3 (black). To transfer your images to the CMM file server, follow the instructions at: https://10.129.28.247/web/guest/service_catalogue/itservices/access-home-folder-windows#unmanaged

Responsible: Dr. Sho Oasa, Postdoctoral Research Fellow; E-mail: sho.oasa@ki.se

Phone: 072 287 09 53

First time users: If you are interested in using this system, please contact the responsible person for introductory training. System use without previous training is not allowed.

Booking LSM 880: Link to the booking system here

Auxiliary equipment: Microscope stage cell incubator consisting of heating Insert P, a solid heating element with uniform heat distribution and a high thermal conductivity, the CTI-Controller 3700 digital, with an IR absorption based CO2-sensor for continuous monitoring of CO2 concentration in the circulating air stream, and the Tempcontrol 37-2 digital, temperature regulator with two independent channels designed to maintain cells at the desired temperature and under desired atmosphere on a microscope stage.

 

Preparative Histo Core

BioClinicum J8:20, Theme Cardiovasc, division of Vascular Surgery

 

Single-cell Library Preparation Core

Single-cell facility at CMM is strived to provide both full service and advanced equipment access on the self-service base for single cell library preparation.

We currently run Smart-seq2 plate-based full-length protocol, and 3’-tagged droplet sequencing using 10X Chromium Single Cell Controller.

We also welcome users to set up their own automation protocols using our equipments.

 

 

Other available equipments are:

Tecan Fluent Robotic System (an automated solution for genomic workflows)

Mantis Nano Dispenser

Agilent bioanalyzer

Pippin Gel Extraction Prep System (DNA Size Selection for PCR fragments and NGS, 100bp – 1.5kb).

 

Descriptions:

 

Tecan Fluent Robotic System (an automated solution for genomic workflows)

Tecan fluent 780 at single cell core facility is an advanced automated workstation which can help you with fast dispensing, transferring or removing low volumes of liquids (0.5 μl to 125 μl in the 384-well format, and 0.5 μl to 500 μl in the 96-well format) with high accuracy. It equips with either 8-channel FCA arm or 384/96-multi channel arm which allows various workflows. A separate robotic gripper arm is used for moving plates on the worktable and acquire plates on the deck. Currently, Smart-seq3 protocol is in-built to perform bead purification and liquid transfer. You are welcome to design and optimize your own assays on it! For more technical and practical detail, please visit https://lifesciences.tecan.com/fluent-laboratory-automation-workstation and contact Peri Noori (peri.noori@ki.se).

 

Pippin Gel Extraction Prep System (DNA Size Selection for PCR fragments and NGS, 100bp – 1.5kb).

 

 

The facility is located at CMM L8:01 room 052.

 

Contact 

Peri Noori, for more information and introduction.

E-mail: peri.noori@ki.se  

 

Scientific advisors

Qiaolin Deng

E-mail: qiaolin.deng@ki.se

 

Eduardo Villablanca

E-mail: eduardo.villablanca@ki.se

Slide scanning and image analysis

 
Slide_Scanner_Core_Facility.JPG

Using the Hamamatsu NanoZoomer Slide Scanner, we are able to digitalize whole microscope slides. These “virtual slides” can be viewed at any computer using the free software NDP View. On the webpage ndpserve.com (click “sign in as guest”) you are able to see some examples of scanned slides.

The benefits of Virtual Microscopy include:
1. Enjoy superior work ergonomics
2. Forget about slide degradation during long-term storage
3. Annotate slides without affecting their contents
4. Many possibilities for software-aided image analysis

CMM staff can view their scanned images via \storage.cmm.ki.setankprojectsby-labelNDP Scanning (copy and paste the link for proper redirection)

The user fee is SEK 100 per slide scanned for CMM user (having CMM account) and Team Cancer users. for external users at Karolinska Institutet the cost is 150 SEK per slide and for extern users outside Karolinska Institutet the cost is 200 SEK.

Your slides for scanning should be clean without any precipitation of mounting medium on the slides. If your slides are not clean for scanning, we will charge you for additional 20 SEK /slides.

Slides for scanning can be dropped off every workday between 08:30 and 09:30 at BioClinicum: J5:30, Room U210 05 6500, expedition 6. Scanned slides will be ready depending on the number of slides for scanning between 3-5 working days.

Download this the order form where you can also find more information about slide preparation: 

 

Location

BioClinicum: J5:30, Room U210 05 6500

 

Contact person

Afsar (Maral) Rahbar

E-mail: afsar.rahbar@ki.se