New Hard Drive to temporarily backup data, new Cy5 cube

The NIKON system has been updated again, a 2 TB hard drive is installed that allows temporary storage untill you verified dataintegrity . We will imply an automated sync-system  to move data from the C:\ drive to the new F:\ drive when the system is not in use.

A new cy5-cube has been placed in the 3rd A1R filter wheel set to allow sensitive imaging of far red dyes in the GaAsP detector, and outperforms the old filtercube several fold.


Secundary Antibodies supply discontinued

We are going to discontinue the service to provide secundary fluorescently labelled antibodies. It was useful to maintain a relatively fresh stock that is continuously probed for functionality, this way users did not need to worry about out-of-date fluorescent antibodies. However, this service is too expensive to keep, and if users keep stocks as 50% glycerol solutions in -20 C freezers long term storage is very stable. The problem of drying and getting aggregates of non-functional antibodies is minimised by this procedure. Our advice is to generate a stock of secundary antibodies and share this among department members (one or two persons responsible for the ordering, aliquotting and distribution clarifies cost streams and inventory overview). A handy tool to keep track of inventories is supplied as freeware by Quartzy.


About imaging chambers

Users need to purchase their own stocks of imaging chambers, we were lucky to obtain a set of chambers from IBIDI and they perform well on our systems. We also have good experience with WPI 3 cm Fluodishes (having a 8 mm or 23 mm imaging well), initial problems with Labtech chambered coverglas slides are solved. Low cost solutions using ATTOfluor cell chambers clamping 25 mm round cs from Marienfeld are also available. It should be noted that mounting cs sometimes induces tension in the clamped cs which is released in an unpredictable manner, resulting in a loss of focus. Remember that objectives of high end imaging systems are calibrated to work with #1.5 (or 0.17 mm) thick glass coverslips.

Lastly, the TOKAI hit heater setup will be updated to allow better fluid replacement during imaging in the coming weeks.

CCI app launched as html-app

To help users I have developed a HTML app (see QRcode below, for now- we are still in testing phase) to log mic setings and send to the user by mail, booking is also included and a checklist to guide STORM imaging is in there as well. Handy for keeping track of some settings you would like to have available before you start a new imaging experiment, making a rule in mailing programs can keep these mails toghether, if you prefer. Native app for Android, Apple and Windows will follow if the app functions well. We noted that some users show personal info on the booking site, beware that this is a public site and anyone can see this (editting is restricted to users though).


QR code

QRcode for CCI -app


Posts Before November 2013

dd October 2013

The A1R/Storm system is running  satisfactory, we keep testing its capacities. NIS software has been updated to the latest 4.2 version with quite some improvements. Also the SPE2 has been serviced and software was updated. Please contact us if you have difficulties.

dd June 2013

The NIKON A1R/STORM system is running. A1R CLSM live cell imaging is performing quite well, we await filter changes to optimally image gfp / rfp variants. The STORM is still in its testing phase, especially dual/triple color imaging is challenging. The AFM has moved to the CCI and is operational, contact Bart Gadella for further info.

dd April 2013

The NIKON A1R/STORM system has been installed and the first imaging validations are being preformed. Please ask staff if you are interested to image on the machine. We will evaluate the time schedule and need for you to do your experiment on the machine.

dd March 2013: 

A new state of the art microscope will be installed, the NIKON A1R/STORM system. We will be trained in the coming weeks on the A1R CLSM, the TIRF and STORM options.

The AFM from the B&C department will be moved to the CCI.

dd Jan 2013:

new Leica cryostate 3050S replaced the broken IRAS cryostate, thanks to collaborive effort of IRAS, DWM,Pathobiologie, I&I and GZD. Thank you all on behalf of the users for the continuation of this functionality at the CCI.

dd 2012

The OME image database on a LINUX server (with kind help of Aart deGroot) is working fine. We are exploring ways to properly implement it into the network to have central collection of the microscope data. We aim to store these for about half a year so users can acces the files easily and arrange definite storage capacity of their own.