Microscope news

2006-03-27 The AxioImager Z1 has been repaired (a lot of parts have been exchanged) and the HBO Lamp has been replaced with an new version. I hope both will function now. 
So far, I have tested the system using several slides.

A new component on the system is a motorized attenuator for the flourescent light. This can be useful if your have DAPI staining that is too bright and thus would require exposure times of less than 10 msec that are not handled very well by the camera. I have created a new set for multidimensional aquisition called DAPI-20. This lets only 20% of light through (It is the setting number 7 when the experiment "all-reverse" is selected).

I have also recalibrated the Apotome.

There are also two new software modules available: "Channel unmixing" and "automatic measurements". These modules are rather complex. I need to dig into these a bit more and will let you know how to use them sometimes later.

The known problem with Cy5 on this system:
The Cy5 filter cube on this setup is a "tight" one (Ex: 640/30, Em: 620/40), thus preventing any bleedthrough from the "red" channels. The disadvantage is that some of the Cy5 signal is lost, thus reducing sensitivity. I have asked for an offer for another filter cube that has a wider excitation window and a long-pass emission filter (cost around 900 Euro).

What is still not working is the motorized filter wheel for the transmitted light path. Zeiss is informed about this problem.

2005-11-15 The confocal is working again, at least partially.
The UV-laser is still not adjusted and cannot be used yet, but otherwiese everything else should be working (hopefully).
If you want to use the system, please make sure that you sign into the confocal reservation system available here:
2005-11-09 1

I have repaired the Uniblitz shutter on the "old-Apotome".
Please let me know if you experience problems with that equipment now.

The confocl is still out of order. Herr Vieten, how is in charge of getting it fixed, was ill the last two weeks and wants to inform me about the possibilietes of repairing it soon.
I have moved the licence-dongle for Axiovision around a little bit.

Right now, time-laps aquisition is only possible at the Axioimager ("new apotome")
The Axioimager also contains the Insight 4D Module. You will not find the 3D button in Axiovision on the old Apotome any more.

If you want to perform some three dimensional operations, like z-projections, either use ImageJ (installed on the old Apotome), or transfer your data to the Imager-Computer on which the Insight 4D-modul in Axiovision is now residing

Tomorrow, Wednesday, September 27, we expect Herr Vieten from Leica to repair the confocal.

As a consequence, usage of the Apotome microscope might not be possible when he his assembling things on the neighboring confocal microscope.

Please plan your experiments accordingly

On the Axioplan imaging microskop ("old Apotome"), the second camera (Axiocam MRm) is temporaly not avaiable.
Please let me know if you need it desperately and one can arrange to put it back (it is at the moment on the microscope next to Juergen Dohmens office until a new camera has arrived.)


Problem: Axioscope and bad resolution pictures:

Possible solutions:
1. When taking pictures with the color camera, adjust the light to get exposure values that are above 10 ms.
I would think something around 15-30 ms is a good value, but you might need to test this for yourself.
If you choose shorte exposure times, the camera might have problems with color balance and/or resolution.

2. Make sure that you have choosen the maximum resolution (under the frame tab, select highest pixel number and standard color

News about the confocal microscope

The confocal is up and running, altough several things are not implemented yet (UV-laser, FRAP/FRET-Module) and some Problems exists (field rotation above 45 degrees does not work, some Z-dimensioning is not correct).

If you want to use the confocal, you need a detailed instruction.
This can take some time when you use the confocal the first time.

For each new user, some basic instruction how to turn the  machine ON and OFF have to explained. In addition, software training might be required.
As we do not have an imaging center and a person who could provide that training on a professional level, each user has to learn it from other users.
I thus will create a list of users that new users should contact for help on using this machine.
This list of users can be found at:

(I have updated the Leptin-link pages and have provided links to these sites under the Imaging categorie)

There is also a link to a html site dedicated to the confocal:
On this page, you find important informatons on reserving the confocal, startup and shut-down procedures

 Microscope-news website.

I have made a website in which all these microscope news will be collected for reference. The link is on the link-page:


Today, we (the Zeiss-represenative and myself) made some interesting observations that you should take into account when taking multichannel pictures.

I noticed that the Alexa 647 channel get overexposed when taking multichannel pictures on the Axioimager. That is why I asked Zeiss to come and find the problem.

It turned out that the problem is not in any hardware or software but that the Alexa 647 fluorochrome gets "half-activated" by short wavelength UV-light (although the physics behind this are not clear or documented, but that is our explantation for the moment).
If you take a multichannel picture and use DAPI, this will result in "half-activation" of Alexa 647. When you then take the picture in the 647 channel, you get a brighter picture compared to a single image in the 647 channel (that is without UV-activation).

To avoind overexposure of the 647 channel by this effect, please use the settings file "All-channels-647" instead of "All-channels". The difference between these is that the order of channel has been changed such that DAPI will be the channel that will be taken last.

The problem with the parafocality is solved. The problem was a loose 40 X length that changed its position over time.

The ProGres (Kontron) is working again (I had to switch the system to a different computer)
The Camera is now operated by the computer that contains the data of the comptuer formerly known as "Leptin G3". The computer originally at this place can now be found in the computer room (3.08).

The AxioImager Z1 ("new Apotome") had connection problems that somtimes caused misbehaviour (unpredictable moving of the stage causing damage to the observed objects).
I have now replaced the connector cable and used a different port for connections. It is not clear if this will solve the problem, only time and usage will tell.
As requested before: Report any unusual behaviour to me (best via E-mail) and write it in the log book.