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New excitation filters for Nikon microscope 1 and 2

On Wednesday 11 July new excitation filters have been installed in the filter wheels for microscope 1 and 2. For microscope 1 the old filters are also still available but have now a different postion in the filterwheel. For microscope 2 all filters have been replaced with equivilent filters with a diferent coating, allowing more light to reach your sample.

Nikon microscope 1

old filternew filter
484DF15 485DF15
555/25 560/DF40
395/10 400/15

Nikon microscope 2

old filternew filter
400DF15 365QM35
475AF40 470QM50
525AF45 525QM45
560AF55 560QM55
630AF50 630QM50

If the replacement of filters causes problem for your imaging, please contact the microscope manager.

Upgrade Nikon-TIRF microscope; Now Nikon microscope 3 (with TIRF)

The Nikon TIRF microscope in MSB 388 has recently been upgraded with a LED light source for the wavelengths 365nm, 490nm, 565nm and 635nm. Also a dual filter block for excitation with 490 nm and 565 nm has been included in the upgrade. This filter block can be used for both LED and TIRF imaging and will allow fast live cell imaging. The system also has a Perfect Focus system to keep your cells in focus during long term cell imaging and is equipped with a very sensitive Andor iXonEM+ EMCCD DU 885 camera (pixel size 8µm x 8µm). This upgrade makes this microscope an excellent choice for multi position live cell imaging, both fluorescence and brightfield (for example wound scratch assays). The system takes also slides and can be used as a standard fluorescence microscope on fixed material. It replaces Nikon microscope 3 in the Henry Wellcome Building and will be renamed Nikon microscope 3 (with TIRF). For further info see: Nikon3 (with TIRF)

User group meeting 24 October 2011; Data analysis using Volocity
10-11 am

During this user group meeting PerkinElmer will show their latest release of Volocity. Volocity is not only used for image acquisition but also for 2D, 3D and 4D image analysis and quantification. It can ready most file formats, also from other microscope manufacturers. Have a look at: http://www.perkinelmer.com/pages/020/cellularimaging/products/volocityquantitation.xhtml or http://www.perkinelmer.com/pages/020/cellularimaging/products/volocity.xhtml. The analysis package include, for example, co-localization calculations and distance measurements between channels. Large number of files can be analysed in batch.

After the user group meeting there will be the opportunity to have a session with a product specialist from PerkinElmer on the microscope or data analysis computer to answer your specific questions. This gives you as user the opportunity to find out how to analyse your microscope images or if there is an easier way to analyse your microscope images.

Important: To get an idea if there is interest from the users for this user group meeting and the individual sessions, PerkinElmer has setup an online survey. Please follow this link: http://www.surveymonkey.com/s/BDSLG7R. It takes less than a minute to fill out this survey. Please do fill out this form!

Imaging Equipment Presentation for CRF building on 12 September 2011

Dear All

CBS is in the process of finalising what equipment would be best suited to the users of the new state-of-the-art in vivo imaging facility due to be available in the Imaging Suite in the CRF Building. Apart from MRI, we are in the process of establishing other in vivo imaging modalities within the CRF through funding provided by the Wellcome Trust Capital award.
Following on from the presentation we had in July from Caliper Life Sciences I have organised for a further 2 presentations. There will be a presentation from Ben Atkinson from Intelligent Imaging Innovations for an intravital microscope system followed by a presentation from Marcus Salmon form Perkin Elmer for an in vivo imaging system.

Date: 12th September
9.30 - 10.30 Ben Atkinson, Intelligent Imaging Innovations
11.00 - 12.00 Marcus Salmon, Perkin Elmer
Location: The Frank & Katherine May Lecture Theatre in the Henry Wellcome Building

User registration form

Since the AIF is now part of CBS we have to be able to give information about use of the Imaging Facilities to the CBS, College and funding bodies when they ask for it. To be able to collect the necessary data the AIF will introduce a user form. Please download this form, print it and fill it out, sign it and send it to the manager of the AIF (internal post: Kees Straatman; CBS/Biochemistry). From the 1st of August all users of the Facility have to have submitted this form if they want to use the facilities. Obviously, when you won't use the facilities after the 1st of August you don't have to fill out the form.

FACS software Demonstration

There will be a flow cytometry analysis software demonstration of 'Kaluza software' in the Hodgkin Building (Toxicology Unit Seminar Room) on Tuesday 24th May at 10.30. Everybody who is interested is welcome. For further information please visit: http://www.coulterflow.com/bciflow/kaluza.php

Adrian Building power shut down 12/2

Dear all,

During the major electrical power shut-down on December 19th 2010, several serious issues were identified which will require a further electrical power shut-down to both the Adrian and the Bennett buildings to rectify these. The necessary parts are now available and the day we are proposing to carry out the remedial work is Saturday, 12th February 2011, the actual power shut down would be approximately 08:00 to 17:00hrs.
If this is going to cause you an insurmountable problems please contact either Bill Brookes 252 2309 or Steve Rees 252 2194 to discuss further.

Use of Openlab

Openlab has been withdrawn for image acquisition and has been removed from the license server. Openlab has been replaced with Volocity. However, if you still want to use Openlab for data analysis there are two license dongles available. Both Tara and Kees have one. Contact one of them if you want to use Openlab.

A problem is that the Power Mac in the analysis room of the HWB has problems with the power supply and fails in most cases to start up. You can use for the moment the computer for Nikon3 for data analysis using Openlab. You can also use a Mac in your own lab if you download Openlab from the PerkinElmer website and arrange the use of one of the license dongles. Users who want to use Volocity for data analysis should use the computers in the analysis room.

Huygens Image Contest 2010

SVI ask you to submit your favorite microscopical Huygens image or movie to the contest. They will all be shown on their website, so you will all be winners.

The prize for the best image is a fully functional one year valid Huygens Essential or Professional software license. This image will also be printed on their Christmas card, which will be send to all our customers worldwide. Thus, global eternal fame is yours!

Closing date for sending images is November 20, 2010.
The SVI team will inform the winner before December 1, 2010.

You can upload the image file (max. 1Gb) here: upload

Of course, you're more than welcome to submit more than one image. With uploading you agree that SVI can use the image for commercial and educational purposes.

Acceptable entries include:
1. a deconvolved or 3D renderered image, or movie created with Huygens!
2. the microscopical parameters
3. a short description of the imaged object
4. your name and institute address

The SVI team

DAPI filter change on Nikon2 and Nikon3

As you might have noticed the DAPI/Hoechst excitation filter on Nikon2 (filter 5 in the filter wheel) gave very poor quality signal. I have temporary replaced this filter with the equivalent from Nikon3. However, the original filter was a 365WD50 excitation filter and the replacement is a 400DF15 excitation filter. This means that the signal will be a little weaker than it originally was, but much better than in the last few weeks, as well as that the whole field of view is now illuminated again. For the time being I have put the old filter from Nikon2 in the filterwheel for microscope Nikon3, till we have purchased a replacement filter for Nikon2.

Images for Ibidi calendar

Ibidi is printing a calendar with beautiful cell images. They have started with this last year and are looking for nice images for next years calendar, ideally (but not necessarily) taken in an ibidi chamber. To give you an idea what they want: Please follow link to calendar.
The deadline for image submission is Friday 15 October.
If you think you have some nice images that can be used please contact Kees at krs5@le.ac.uk.

Centre for Core Biotechnology Services (CBS)

Since the first of June 2010 the Advanced Imaging Facilities have become part of the new formed CBS. This means that the SEO for advanced microscopy has moved from the department of Biochemistry to the CBS. However, for the moment this will have no effect on the way the facilities opperate and the SEO will still be in room 3/65 in the Henry Wellcome Building. The supporting technicians for the different imaging systems maintain part of the different departments.
Aim of the CBS is to make the different facilities and services within the college of Medicine, Biological Sciences and Psychology more visible and to provide a financial framework for the different facilities and services as well as to provide for a framework to grow and adapt the core services to meet changing research needs in the college.

The core services included in CBS are:
• Protein and nucleic acid chemistry laboratory (PNACL)
• Geneta
• Imaging
• Electron microscopy
• Protein expression (Protex)
• Mechanical Workshop
• Containment level III
• Bioinformatics (B/BASH)

In terms of administration the CBS will be considered as a Centre with line management and budgetary control over the core research facilities. The Centre is chaired by Professor Andrew Tobin and the Secretary to the CBS Management Group is Anna Harding.

Data storage

As several people have been aware, we try to roll out a 10TB data storage service in collaboration with IT Services for storage of microscopy data, including back-ups. The microscopy part of this project is funded via CIF. A pilot project was started in August 2009 with data testing in late 2009. From the point of view from microscopy the actual testing was successful. Unfortunately, a software problem on the actual Sun server causes major problems and at the moment we are still not able to use the data storage. IT services are in close contact with Sun to resolve this problem but till now without success. We hope that this problem is resolved soon and microscope user can start using this new storage within the Advanced Imaging Facilities.

This data storage is now up and running. Please follow link.

New Nikon objectives

Two 60x/1.4 Plan Apo VC objectives and two 100x/1.4 Plan Apo VC objectives are now available for use on the Nikon microscopes in the HWB. Information about these objectives can be found on the Nikon website. Measurements showed that these objectives are around 30% more light efficient than our old objectives. This means that if you do QUANTITATIVE imaging and you have to compare your data with data collected earlier you CANNOT use these objectives! You can identify the objectives by the addition of the letters VC.

Although these objectives have the description DIC on them we don't have the proper DIC filter sets to use on our microscopes as this is different on the more modern systems.

Workshop 2009

In the last week of August the Microscope facilities run a series of workshop in collaboration with GENIE and several industrial partners. This year’s workshops were considered a great success. Pictures from the workshop can be found here and photos from the diner via this link.

Microscopy workshops:
24th August 2009: Immunolabelling
25th-27th August 2009: Fluorescence microscopy
28th August 2009: Quantitative fluorescence based screening
For more information follow this LINK

Imaging non-adherent cells


Giora Bar-Akiva of Cell Kinetics Ltd., Israel, visited the University on 26th of February introducing their CKChipTM platform. This technology "enables fluorescence-based imaging of thousands of individual living cells, each held at a given position"...." The CKChipTM system effortlessly deposits single living cells of any kind into wells arranged as a matrix." This matrix can be recognized by their software what will allow analyzing single cells even if the system has been taken off the microscope, put back in the incubater before other timepoints are taken to compare with the first image.
The image shows EL4 cell labelled with calcein (green) and CD8 cytotoxic T lymphocytes (blue) on the CKChip. Green cells are alive, blue cells are dead. The number of dead cells will increase over time. Image courtesy of Cell Kinetics Ltd.
For more information please visit the Cell Kinetics website. If you are interested in testing this system please contact Dr. Kees Straatman so we can order one tester kit for several groups within the University.

CIF funding

The faculty wide imaging bid to CIF has been awarded by the University. This bid includes hardware and software upgrades for the Nikon microscopes, a network server for image storage, a MP confocal laser microscope, a Biolumnescence system, a confocal laser scanning microscope for the Robert Kilpatrick Clinical Sciences Building (Royal Infirmary) and a laser TIRF microscope as well as a FACS machine (cell counting), gel imager and luminescence/fluorescence imager. The expectation is that these systems will be purchased during 2009. These new systems will expand and improve our facilities significantly bringing in major new technologies that will allow us to pursue our strategic vision of maintaining Leicester at the forefront of international academic and clinically-relevant research.

New Nikon microscope

Dr. Kayoko Tanaka (Biochemistry) has recently been awarded a BBSRC grant which includes funding for a fluorescence microscope for the microscope facilities equipped with a high sensitive camera. After testing different systems it was decided to go for a Nikon microscope. This microscope will employ LEDs instead of the classical mercury-vapour lamp as fluorescence light source. LEDs are very stable, long lasting, good for live cell imaging and the microscope can be used as soon as the LEDs are switched on. The stage will be a motorized piezo stage for fast Z acquisition with encoders for accurate multiposition imaging. An environmental chamber will be included. As camera the Andor iXon EM-DU897 is chosen. There is already room created in the Biochemistry microscope room for an extra microscope. The plan is that microscope 3 will move soon to the new created space and the new microscope will go behind the curtain.

Quantitative Fluorescence Microscopy Based Screening. Workshop 23 September 2008

Gain hands on experience in automated quantification of fluorescent microscope pictures at a one-day professional course on Quantitative Fluorescence Microscopy Based Screening. This course is organized in collaboration with GENIE, the Centre for Excellence in Teaching and Learning in Genetics, Olympus Life and Material Science Europa GMGH and Olympus UK Ltd and includes the use of the new Olympus scan^R screening station.

9.30 – 10.00 am Registration and coffee
10.00 – 11.00 am Introduction to cell screening and image analysis
11.00 – 12.30 pm Using the scan^R station
12.30 – 13.30 pm Lunch and Q&A
13.30 – 14.30 pm Practical 1: data acquisitions
14.30 - 15.30 pm Practical 2: data analysis
15.30 – 15.45 pm Coffee
15.45 – 16-45 pm Practical 3: data analysis
16.45 - 17.00 pm final remarks and closing

Designed for industry R&D scientists and the academic community. Maximum 12 places available. Costs: Standard rate £250; Academic rate £85. To apply for this course please visit: http://www.le.ac.uk/genetics/genie/courses/index.html.
Members of research groups who pay the annual access charge for microscopy please contact Dr. Kees Straatman to apply for this course. There are a limited number of places for FREE!

OpenLab license server

Unfortunately, the OpenLab License server has broken down and the License server has temporarily been installed on computer 2. The server runs under administrator account in the background. Therefore, computer 2 should not be switched off! Users can still use computer 2 for data analysis as well as the attached scanner.

Microscope workshop April 2008

On Tuesday the 8th and Wednesday the 9th of April 2008 a microscope workshop was organized to introduce the new microscope facilities in the Department of Genetics, part of the imaging facilities of the School of Biological Sciences. During this workshop the name of the new facility was unveiled: The Wolfson Foundation Light Microscopy Facility. On Tuesday morning there were 4 talks followed by a lunch sponsored by Olympus UK.

Dr. Kees Straatman, University of Leicester; Imaging and analysis.
Dr. Ferenc Müller, University of Birmingham; Quantitative mapping of promoter enhancer interaction specificity by automated spatial reconstruction of reporter gene activity in virtual zebrafish embryos. (Example of use of Scan^R)
Professor Clive Bagshaw, University of Leicester; TIRF Microscopy: a comparison of optical arrangements.
Dr. Werner Kammerloher, Business Manager BioAnalytics, Olympus, Germany; Closing gaps in fluorescence and luminescence imaging

In the afternoon and the next day demonstration were given on the different microscope system in the microscope suite, the Olympus FV1000 confocal laser scanning microscope, the Cell^R/Scan^R system and the cytological imaging system as well as on a demo TIRF system. Several product specialist of Olympus were present to make these demonstration a success.

Workshop confocal FV1000

Rosy Manser (Olympus; middle) demonstrates the Olympus FV1000 confocal laser scanning microscope.

Workshop TIRF

Professor Clive Bagshaw (left) and Dr. Dmitry Cherny (middle) have a closer look at the TIRF demonstration system under the watching eye of product specialist Raj Hathiwala (Olympus).

Workshop CellR

Participants during the Scan^R system demonstration.

If you have missed this opportunity to get a closer look at the new imaging facility, you can always make an appointment with Dr. Kees Straatman to get an explanation of the working and options of the microscope systems, including screening and analysis of your samples.

Nikon 4x objective (February 2008)

A new 4x objective for the Nikon microscopes is bought by Prof. David Critchley and Dr. Kath Clark and is available in the Biochemistry microscope room. It is a CFI PLAN FLUOR DL 4X PhL objective with NA=0.13.

New microscopes installed (Autumn 2007)

In the last few weeks new microscopes have been installed in room G1 of the Adrian Building. The Olympus confocal laser microscope, the Scan^R/Cell^R system for live cell imaging and to analyze slides and the advanced cytological system are now operational and training session can be booked. Contact krs5@le.ac.uk.

Microscopy Management Committee (August 2007)

The first meeting of the newly convened Microscopy Management Committee has been held on the 2nd of August. The price for microscope use in 2008 has been decided in this meeting. See Charges for more details.

Committee members:
Dr. Kees Straatman (SEO for advanced light microscopy in the School of Biological Sciences)
Dr. Andrew Fry (Biochemistry)
Prof. David Twell (Biology)
Prof. Nick Hartell (CPP)
Dr. Nicola Royle (Genetics)

Luminescence microscope (August 2007)

FV200Recently Olympus demonstrated their new Luminescence microscope LV200 in the Adrian Building. The system will allow you to follow gene expression at cell level.

We imaged using exposure times from 100 ms up to 30s, dependent on the objective used. All normal objectives used on a 'normal' microscope can also be used for this system.

If you missed the demonstration but would like more information, please follow this link or contact Kees Straatman (krs5).

New microscopes (May 2007)

Three Olympus systems have been ordered for the microscope suite in the Adrian Building. These systems are funded by a Wolfson Foundation grant to professor Tony Brooks. The idea behind these systems is to replace a confocal laser scanning microscope that has left the department and secondly to make quantification of microscopy data easier by automatisation and use of specialized software.

System one is the FV1000 confocal laser scanning microscope on an inverted IX81 fully automated microscope with 405, 457, 488, 515, 559 and 635 nm laser lines. For information about this system use the provided link.

System two is a combined Scan^R (without plate loader) and Cell^R system on an inverted IX81 microscope. This system doubles up as a live imaging system using dishes/multi-well plates or as a high throughput screening station.

Cyto systemThe third system is a cytological system on a BX61 automated microscope equipped with an imaging system from Spectral Imaging (via GT Vision), including HISKY (BandView/FISHView), CGHView, MultiSpecies, SPOTScan and RELOScan (right). The stage is adapted with the ScanView Platform which will hold 8 slides.

Together with these three systems the Bitplane Imaging Processing software package (Imaris, MeasurementPro, Track, Coloc, Search) and the deconvolution suite Huygens Essential (SVI, The Netherlands) is purchased.

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