Confocal -- Gear problem subtle but confirmed

Our Nikon service rep, Steve Fryer, took a look at the confocal yesterday and was able to replicate in a large z-stack the subtle abnormal behavior with the focus motor that has been observed by several users lately. He found that the steps in a z-stack occasionally would get very small for a few steps then "catch up" or come back to normal size. He cleaned and regreased the motor but felt that it may simply be a mechanical problem with no good solution. I'll be contacting the sales department to get a quote on a new focus motor, and at the same time will ask about getting a stage with XY motor control to allow some semblance of stereological sampling capability.

In the meantime, the recommendation is to watch your scans for this phenomenon, save your files as .ids format (for z-stacks), and report to me if and how often you observe problems.

Confocal -- Gear sticking problem?

A user reported to me that she noticed among many z-stacks in a row that a few times the z focus gears seemed to stick, such that 3 or 4 images were clearly in the same focal plane rather than different ones, but then the focus would change. She thinks it's a sporadic, unpredictable event, and didn't save the .ids files so that we could examine the images (she renders them and saves the resulting image).

I contacted our service rep, Steve Fryer, and he'll be coming to take a look on Wednesday afternoon next week. My recommendation for users is to watch your scans in case the focus motor behaves erratically, carefully engage the focus motor and check by trying to move the fine focus knob (gently), and SAVE .ids FILES FOR YOUR Z-STACKS. As I've probably mentioned to most users, even though they're large, they keep all of your data, so that you can judge if anything has gone awry, redo your projections, make new movies, make scale bars, and pick out the settings you used, just to name a few of the important reasons to save your .ids files.

If you are concerned about the amount of disk space this would take up, remember that DVDs are less than a dollar apiece and can store over 4 GB of data, which can be burning while you clean off the objectives at the end of your session. Talk to me if you have any questions or concerns about this.

Confocal and Zeiss -- Local Accounts deleted

I went in today and deleted all local accounts on the Zeiss computer and the Confocal computer. Thus, to access either of these computers, a Waisman logon is required. Please talk to me if you have any concerns or questions about this. All data from the Documents and Settings user folders was burned onto DVDs then deleted, but files that were elsewhere were left alone. If you need any of the data from the Documents and Settings folder (which would include anything on your desktop or in your My Documents folder), the dvds are in the small filing cabinet next to the confocal scope.

Since we are doing fine at the moment on disk space, I'll wait to clear off any other images or data from these computers until there is concern about this. The confocal computer currently has 75 GB free out of 250GB, and the Zeiss computer currently has 200 GB free out of 250GB, so I would say that the confocal computer will need clearing off in the next few months, but not the Zeiss for the forseeable future. An email will go out before I do this, and if possible, removed data will be compressed and burned to DVD, just in case.

Please make an effort to keep your hard disk usage to a minimum on these computers. Thanks.

RT PCR -- Beginning upgrade process

We are beginning the process of upgrading the ABI7500 real time thermocycler system from the computing standpoint. We would like to put the computer on the network, for several reasons, but the cost of getting the laptop imaged may not be worth it, especially since we would need to add RAM to the computer to be able to upgrade to the latest version of the software. Our ABI service rep said that the newest version of the software is very good, allowing for quick and easy export of data to Excel and PowerPoint, and with an improved interface. This upgrade is free if we download it, but we need to have enough RAM to run it.

So, Seprek (the CMN Core workstation computer) has been moved down to room T529 to be our experimental computer on which to try installing the upgrade and ensuring that the thermocycler software can complete runs without conflicts due to virus scanning. It has been reported that the software often has issues with Norton and other virus software, and with the computer on the network, we need to configure the virus scanning software (Symantec, in our case) to allow thermocycler software to run properly.

Ultimately, a different computer will run the software, either Quiberon, which we already have, a hand-me-down computer that has been de-commissioned from elsewhere in the building, the laptop (but upgraded and imaged), or perhaps a new computer. The laptop is still in the room, on top of the thermocycler (and connected to it), and we'll let users know how the upgrade process is going. Once the process is complete, all users will need to use Waisman logons to use the thermocycler. We will likely be changing to an hourly charge for thermocycler use at some point as well (probably July 1). Let me know if you have questions or concerns.

Real Time Thermocycler -- Seems ok

Our rep came today to check the machine due to our strange problem with the strip caps on the plate. He couldn't find anything wrong with the machine, especially the alignment. He did measure the block temperature and said it was a little hot (106 when it should be 105), nothing to worry about, and he adjusted it. He also found some contamination in four of the wells and cleaned that. He recommends we always use film with the plates and let him know if there are any further problems. He also noticed that many of the plates in the trash can by the machine have scratches all over the tops of the caps. If this was like this during the run, it would cause artifacts. We couldn't figure out where the scratches were coming from. Let me know if you know anything about this.

RT PCR -- strip cap problem

Last week, a user reported running some reaction plates on the Real Time PCR machine and having a problem with her strip caps popping off during the reaction. She noticed that the data from that column of reactions was messed up, so she's pretty sure it happened early in the reaction, probably during the initial 95 degree denaturation step. For her next reaction, she made sure all the caps were on tight, yet it happened again, with the caps in the very same column (#5).

It may have been a bad batch of caps, though it still would be weird that the problem happened twice in the same column. Please let me know if you've had a similar experience or if you have insight into this problem.

I spoke with technical support and our engineering rep at ABI, and they had the following advice: first they said to make sure we use the flat optical caps, not the domed (we already do). Next, they suggested using film instead of caps; we have some film and an application kit if anyone would like to use it. Lastly, the engineering technician said to go ahead and try running an empty plate using the RNAse P run to see if it happens again. He couldn't think of any explanation that involved a problem with the machine, but he's willing to come take a look at the machine on Monday.