Category Archives: OMX V4 blaze

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.

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

Joystick arrived for OMX V4

A newly developed joystick is installed on the OMX-V4, it allows navigating through a sample, mark and start acquisition/mosaic. It is a bit fast but with practice will help you find the best cells more efficiently.

Few new features are implemented during the last service visit (for example: laser power tuning), ask CCI staff to inform you before working on the machine. Again, be sure to keep the OTFs of April 2018 for the reconstructions.

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) 

OMX filter drawer error

On the OMX imaging system, channel alignment is repeatedly disturbed by incorrect placement of the automated filter drawer (which sets in every time at startup) . A GE scientist is coming to solve this issue (in the week of February the 29th). Until then the filter drawer will be fixed to the BGR position to maintain correct aligning settings. We can work with it to image many but not all of your favourite dyes. Please take this into consideration.