Category Archives: Olympus-Leica wide field system

Leica SPE-II, NIKON A1R/TIRF/STORM, Olympus-Leica wide field system, OMX V4 blaze, Organization issues, Uncategorized, Zeiss LSM880 NLO Multiphoton

Walking directions during reboot of the CCI labs

Working on the Leica SPE2:

Entry: General entrance AG East 1 st floor, direct right turn to access the Confocal room O.161, knock before entry and apply to the hygiene rules that are supplied. A second person can be present in the room yet distance of 1.5 m should be kept at all times.

Exit: Leave following the same path.

Working on the Olympus histology microscope:

Entry: General entrance AG east 1 st floor, direct right turn to access the O.161, knock before entering and turn left and avoid coming close to the people working here. Only one person on the microscope.

Exit: Leave following the same path or move through the ML-2 lab space if someone enters when you are still in the narrow room

Working on the OMX:

Entry: General entrance AG east 1st floor, enter ML-2 lab from the corridor. Knock before entering, max 1 person in the OMX rooms (laser station room, workstation room). The corridor in the ML-2 space is co-occupied, so be careful to move through it and notify others that you are coming though.

Exit: same route.

Working on the NIKON:

Entry: General entrance AG east 1st floor, enter ML-2 lab from the corridor. Knock before entering, max 1 person in the NIKON-A1R room. The corridor in the ML-2 space is co-occupied, so be careful to move through it and notify others that you are coming though.

Exit: same route.

Working on the Zeiss LSM 880 NLO:

Entry: General entrance AG east 1st floor, enter ML-2 lab from the corridor. Knock before entering, max 1 person in the Zeiss LSM880 room. The corridor in the ML-2 space is co-occupied, so be careful to move through it and notify others that you are coming though.

Exit: same route.

Hardware issues, NIKON A1R/TIRF/STORM, Olympus-Leica wide field system, OMX V4 blaze, Organization issues, Zeiss LSM880 NLO Multiphoton

Centre for Cell Imaging safety instructions during the restart in the SARS-CoV-2 crisis

The CCI is re-opening for microscopy from the 19th of May 2020. We hope everybody is safe at home trying to get a work routine partly at home and for essential work in the lab.

Great initiatives to learn microscopy related (and unrelated)  courses are collected here (https://www.rms.org.uk) and on ibiology or MOOCs, this may be the best time to upgrade knowledge on FIJI (or follow excellent bioimage analysis course by Robert Haasse), Python, R, machine learning, etc.

When you use our equipment, please use common sense to keep distance and apply to strict hygiene rules and follow the walking directions as outlined here. Book equipment on-line (we are improving the Reserve-a-Scope to better function from home). For now, please ask us to book equipment for you. Additionally, register at the building entrance for security staff to know who is in the building at any time.

We are going to implement video connections (via MS Teams to share screens or webcams) to train and assist people when problems occur, please contact us if you have smart ideas about this.

Since our environment is shared with many different people, take notice of extra precautions you must take.

  • For the microscopy spaces, check the on-line booking system and knock before entering rooms. Minimize the time to co-occupy a room or corridor. Work alone on a microscope, so co-operation (one doing microscope hardware, the other the PC) is not allowed. Likely, the share-screen approach can help provide an alternative way to work together. Workstations can be used but allow us to accommodate the maximum persons present in the offices
  • Bring Your Own box with items you need to work at the CCI. Apart from samples, these should include:
    1. Lab coat (we removed ours to prevent shared use)
    2. Gloves (if you need them to work in hood or add things, but do not use gloves to handle the equipment, they must remain clean at all times)
    3. EtOH 70% flasks as backup for the stocks we provide
  • Make sure to close the system(s) when you are done, likely you are the last to image any time of the day.
  • Take time to clean the workspace before and after your visit.
    1. Make sure surfaces are cleaned with 70% EtOH (bottles are present in the lab)
    2. Keyboards are wrapped in saran wrap, please clean them before and after use.
    3. Make sure microscope parts that people touch are cleaned with 70% EtOH wetted cloths.
        • Knobs on the scopes (focus, xy-table, condenser), remote joysticks, touch screens, etc
        • Oculars (clean the rubber rings, use the lens papers to clean the lens itself). Eyelashes frequently contact the lenses (we know because of mascara deposits), beware of this.
        • Microscopy table
        • Front end of the microscope body
        • Mouse, keyboard, on-off switch PC/monitors
  • Wash hands before and after your work, do not touch your face

Above all, stay safe and stay at home when possible, according to the government and UU guidelines.

Kindest regards,

CCI staff

Bioimaging Utrecht, Leica SPE-II, NIKON A1R/TIRF/STORM, Olympus-Leica wide field system, OMX V4 blaze, Software, Zeiss LSM880 NLO Multiphoton

April 4: ImageJ Advanced workshop

The Bio-Imaging Utrecht community organizes an ImageJ/FIJI workshop for experienced users on Tuesday the 4th of April. Previous sessions were very well appreciated and they allow you to interact with experts in IJ coding. You can learn image analyses automation and the experts can help you find, tweak and apply the proper plugin(s) for you specific question. It is highly advised for microscopists who use FIJI but have problems overseeing the large analyses possibilities offered by the platform. Register using the form attached here (deadline 17th March) 

Hardware issues, Leica SPE-II, NIKON A1R/TIRF/STORM, Olympus-Leica wide field system, OMX V4 blaze, Organization issues

DATA storage testing

A StorSimple backup system has been  implemented by ITS.  We have tested it for a couple of months and it seems to perform well. The extra network drive is available on all imaging machines (except for the Zeiss NLO system, that will be connected to the net in the coming weeks) and can be found at O:\Research\CCI\#equipment\##user##.  Writing on the drive  can only be done on our machines, users will be able to read only from these drives so data will be available but secured. We are implementing a secure logon system for users to read data from this drive.

 

Hardware issues, Leica SPE-II, Olympus-Leica wide field system, Organization issues, Zeiss LSM880 NLO Multiphoton

Reoganization of the CCI

Due to the renewal of  equipment, we will reoganize the CCI drastically.

First, the space that will host the multiphoton system is being prepared. This is a collaboration with the WKZ, see earlier posts about this. This system will be placed in room O122. The co-ordinator of work on this machine will initially be Nienke Vrisekoop. We will facilitate instruction, authorisation and general surveillance of the device.

In preparation of this, the Olympus microscope has been moved to O123A, see an earlier post about this.

Second, we need to fit the OMX system within our limited space which has proven to be a major task. Currently, we plan to move the SPE2 system to the wetlab (room O101) are reserve it for maximally ML1 work. The OMX will then occupy room O124 and O124A.

To do this reorganisation and restore arrears of maintenance on the airconditioning units, we will face disturbance in the CCI day-to-day business in the coming weeks/months. Watch this space for updates.

Olympus-Leica wide field system

Upgrade Olympus/Leica microscope

The Leica color camera on the Olympus microscope setup has been upgraded due to great efforts of Rob and financial support of the IRAS, we are very grateful for this improvement of the CCI.

One of the new features is live stitching. While moving the xy-table during image acquisition, the LAS software will choose appropriate timing of snap shots that build up a stitch in a live preview.

Ask Rob for further details and other features of the upgrade.