Category Archives: Organization issues

Leica SPE2 40x HCX oil objective defect

The 40x oil on the Leica SPE-II CLSM showed severe chromatic aberration in Z for UV fluorescence. The objective is removed from the system and its aberration is being validated on another Leica machine in the UU campus. We probably need to repair or replace it. Our objectives are very costly and vulnerable, please handle them with care. A microcourse on how to prevent lens damage is given by dr. Waters (link). We notice a great number of scratches on the top beveled end of all lenses, please realize that these are often generated by collisions to the bottom edge of a sample holder. Please make sure lenses are lowered before rotating the turret and realize that moving the stage at some point will get the lens too close to the sample holder edge.

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

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

The CCI is closed for all purposes with exception for people that need to finish essential experiments and the work performed on corona at the virology subdepartment. We are one week in this setting now and hope everybody is safe at home trying to get a workroutine.

Great initiatives to learn microscopy related (and unrelated)  courses are collected here and on ibiology or MOOCs, this may be the best time to upgrade knowledge on FIJI, Python, R, machine learning, etc.

When you desperately need to use our equipment, please use common sense to keep distance and apply to strict hygiene rules. Register (at reception and on-line) for security staff to know who is in the building at any time. Offices are spacious so a minimum of 1.5 m distance between persons is easily done. For the microscopy spaces, please check the on-line booking system before entering. If someone is already in the area, try to minimize the time to co-occupy a room.

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. Make sure microscope parts that people touch are cleaned with 70% EtOH wetted cloths.
    1. Knobs on the scopes (focus, xy-table, condenser), remote joysticks, touch screens, etc
    2. Oculars (clean the rubber rings, use the lens papers to clean the lens itself)
    3. Microscopy table
    4. Mouse, keyboard, on-off switch PC
  3. Please do not (re)use the common lab coats, use your own to work in the labs
  4. Wear gloves or wash hands before and after your work, do not touch your face
  5. Work alone on a microscope, so co-operation (one doing microscope hardware, the other the PC) is not recommended.

We leave some electronic equipment running since they require continuous cooling, please do not shut down the already running equipment without notifying us (R.Wubbolts@uu.nl).

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

Kindest regards,

CCI staff

Richard Wubbolts

Esther van ‘t Veld

Soledad appointed, Cryostate moved and supported by Judith in NG O.53

Soledad Ordoñez-Alvarez has been appointed for 2 days a week as a new staff member of the CCI. She specializes in instructing new users and adds expertise in image analyses to the CCI.

Unfortunately, Rob Bleumink had to retire. Since we miss his expertise in cryosectioning (as for countless other issues), we moved the cryostate to the Nieuw Gildestein building in room O.53 under the expert guidance of Judith Hendriks (department Dier in Wetenschap en Maatschappij j.c.j.mhendriks@uu.nl). She will take care of instructions and access to the cryostate. Please contact her to arrange this.

BioImaging Winter meeting and Imaris Workshop

BioImaging Utrecht will have a winter meeting on Wednesday 21st of February  from 10:00 to 11:00. It will be followed by an IMARIS workshop at the Stratenum (MCR). Georgia Golfis will outline the program at 11:00 -12:30 (Rm STR3.108) and she will train groups to work with own datasets in the afternoon. The next day, Thursday the 22nd a workshop to all  Imaris users will be given (RM STR 2.106). Registration for the workshop is required by mail to Livio (L.Kleij@umcutrecht.n). Highly recommended for Imaris users!! (Announcement PDF).

 

BioImaging Utrecht events autumn 2017

The BioImaging Utrecht  community (link) has a number of events planned that are highly recommended.

Hardware Microscopy demonstrations.

Demonstration of the re-scan confocal (link) at the UMCU was only last week (contact Corlinda if you want to know how good it was). Additional product demonstrations are planned:

29th of September:
CeniBra / Yokogawa representatives will give talks on a spinning disk desktop machine, the CQ1 (link) that should be well suited to image and analyse organoid containing volumes.

4th of October
Leica will host lectures (link) on their high end imaging systems on the 4th of October (especially their new DMi8S TIRF live imaging setup) – Lukas Kapitein and Philip Tinnefeld will lecture on TIRF use in their labs, no doubt spectacular work will be shown. Hands-on workshops will continue the next day.

The Utrecht Image Contest (link)

This year Utrecht microscopists are again invited to send in their most beautiful and/or artistic image in jpg format to compete for the prestigious title of the best Utrecht Microscopy Image in the Electron Microscopy or Fluorescence microscopy categories. In addition, a printout by pArt of Science (link) and a prize of 200 Euro (provided by Carl Zeiss) can be won. Please supply image with microscope information and a brief scientific description to : meetings@bioimaging-utrecht.nl

ImageJ/FIJI workshop (BioImaging Utrecht_ImageJ beginners 2017)

At this workshop, image analyses experts in the Utrecht imaging community will train you to learn using ImageJ/FIJI and give you an idea how to start analyzing (microscopy) images in general. Highly recommended for microscopists. Good to realize that image analyses will usually make your image acquisition better and will help you focus on the actual measurement of imaging process. Registration deadline October 1st (ImageJ_beginners_registration form 2017).