I was able to partially remove the remote focus controller from the confocal, but am waiting for our rep to come finish removing it for shipping to Oregon. The manufacturer will repair it and ship it back as quickly as possible.
Z-stacks will not be possible until it's back, but capturing single images, including channel series (frame lambda) should be fine. I have a few sessions booked this week, and will let people know if there seem to be any problems. I would expect us to be up and running again for z-stacks by around the 21st or so (of May), but will update the blog as I hear back about it.
Saturday, May 10, 2008
Calendars -- Event privacy considered
At the monthly CMN Core meeting, I raised the issue of event privacy on the CMN Core calendars. Thus far, I have been making sure all events are public, meaning anyone can see your name and timeslot. I've gotten the sense that some users would prefer not to have their names quite so public and would prefer privacy. From my end, the problem is that I definitely need to know who's signed up for which timeslot, and I think it benefits other users to be able to see who's before or after them in case of schedule changes at the last minute.
If we designate an event to be private, then all those authorized to self-schedule on the calendar can see the details, but not the general public. They can see the details when logged into Google, though when viewing the calendar via the CMN Core web pages, one often needs to click reload to get the details to appear. The general public and anyone not logged into their authorized Google account for viewing the calendars simply sees the word "busy" for each private event.
I've recommended that we increase privacy by having reservations be private on CMN Core calendars. So, I'll send out an email about this when I'm ready to implement it, then will consistently make sure events are made private, except for service events. Those who consistently use Google and are frequently logged in may not notice much, but others will see the word "busy" instead of names. Let me know if there are questions or concerns.
If we designate an event to be private, then all those authorized to self-schedule on the calendar can see the details, but not the general public. They can see the details when logged into Google, though when viewing the calendar via the CMN Core web pages, one often needs to click reload to get the details to appear. The general public and anyone not logged into their authorized Google account for viewing the calendars simply sees the word "busy" for each private event.
I've recommended that we increase privacy by having reservations be private on CMN Core calendars. So, I'll send out an email about this when I'm ready to implement it, then will consistently make sure events are made private, except for service events. Those who consistently use Google and are frequently logged in may not notice much, but others will see the word "busy" instead of names. Let me know if there are questions or concerns.
Thursday, May 1, 2008
Confocal -- focus motor to be sent for repair
I got information from our Nikon rep and then the manufacturer of our focus motor as to the best way to get it repaired. We'll be sending it out next Friday, May 9, for repairs and should have it back by the end of the following week. As far as I know, we should still be able to capture images just fine, but not z-stacks.
Monday, April 21, 2008
GeneSifter - License to be purchased, cost $75/month or less
We have decided to purchase a license for GeneSifter software.
This software is used to analyze microarray data and is considered very user-friendly and extremely useful. The main benefits over other microarray software are that it is web-based (so your lab can use it anywhere), well-supported, and intuitive to use. It does statistical analyses using the R statistical language, picks out differentially expressed genes with various statistical algorithms, performs cluster and pathway analysis, corrects for multiple comparisons, has one-click gene summaries, identifies biological themes, allows searches by function, and provides ontology reports. The gene annotations combine information from GenBank, UniGene, LocusLink, The Gene Ontology Consortium, Affymetrix NetAffx, Homologene, and KEGG. More info can be found at www.genesifter.net.
Note that P30 Projects (those listed on the Waisman Center Core Grant) receive subsidies for CMN Core services and also for services (such as microarray runs) at the Biotechnology Center.
We decided to get a one year license and allow investigators to gain access to the software by committing to up to $100/month for 12 months. The more investigators commit, the lower the price is for everyone. We currently have four investigators ready to contribute to the license, so for now the cost is $75/month. One more will bring it down to $60/month, and two will bring it down to $50/month. If anyone is interested in trying out the software or in contributing to the license to gain full access, just contact me.
This software is used to analyze microarray data and is considered very user-friendly and extremely useful. The main benefits over other microarray software are that it is web-based (so your lab can use it anywhere), well-supported, and intuitive to use. It does statistical analyses using the R statistical language, picks out differentially expressed genes with various statistical algorithms, performs cluster and pathway analysis, corrects for multiple comparisons, has one-click gene summaries, identifies biological themes, allows searches by function, and provides ontology reports. The gene annotations combine information from GenBank, UniGene, LocusLink, The Gene Ontology Consortium, Affymetrix NetAffx, Homologene, and KEGG. More info can be found at www.genesifter.net.
Note that P30 Projects (those listed on the Waisman Center Core Grant) receive subsidies for CMN Core services and also for services (such as microarray runs) at the Biotechnology Center.
We decided to get a one year license and allow investigators to gain access to the software by committing to up to $100/month for 12 months. The more investigators commit, the lower the price is for everyone. We currently have four investigators ready to contribute to the license, so for now the cost is $75/month. One more will bring it down to $60/month, and two will bring it down to $50/month. If anyone is interested in trying out the software or in contributing to the license to gain full access, just contact me.
Confocal -- mercury bulb alignment and field of view
On Friday, I had our service technician come to help figure out what was going on with a concern about the field of view. Essentially, a user has been looking at cells in the dentate gyrus of mouse sections -- granule cells specifically -- and finds that the field of view looks much larger than on the widefield fluorescence scope in his lab. This makes the cells look very small and harder to count, and images captured with the entire field of view don't "look right" because they seem zoomed out.
Earlier in the week, I had taken our calibration grid slide that I use to calibrate the Zeiss and we put it on the scope to see if there was any calibration issue. We were able to get an image of the calibration grid in the red channel and a granule cell in the green channel, and indeed the cell we were looking at appeared to be only about 5 um in diameter. The PI checked the literature and found these cells to generally be described as at least 10 um in diameter.
After much discussion with the rep, we concluded that indeed our confocal tends to have a larger default field of view than many other scopes, which can be reduced if desired using the Zoom or Crop feature of the Navigation menu. Talk to me if this is of concern to you or you'd like to learn more about it.
Later that day, we found that the mercury bulb was again out of alignment. This is the second or third time this has happened, and we are very puzzled as to how this could occur. I called our service technician back and asked him to come check it out, both to get it back in optimal alignment and see if he could find any reason for it to be going out of alignment without anyone intentionally touching the knobs. This mystery remains unsolved at the moment.
Earlier in the week, I had taken our calibration grid slide that I use to calibrate the Zeiss and we put it on the scope to see if there was any calibration issue. We were able to get an image of the calibration grid in the red channel and a granule cell in the green channel, and indeed the cell we were looking at appeared to be only about 5 um in diameter. The PI checked the literature and found these cells to generally be described as at least 10 um in diameter.
After much discussion with the rep, we concluded that indeed our confocal tends to have a larger default field of view than many other scopes, which can be reduced if desired using the Zoom or Crop feature of the Navigation menu. Talk to me if this is of concern to you or you'd like to learn more about it.
Later that day, we found that the mercury bulb was again out of alignment. This is the second or third time this has happened, and we are very puzzled as to how this could occur. I called our service technician back and asked him to come check it out, both to get it back in optimal alignment and see if he could find any reason for it to be going out of alignment without anyone intentionally touching the knobs. This mystery remains unsolved at the moment.
Friday, April 11, 2008
Seminar -- What's New in the CMN Core -- went well and will be held again soon
On Wednesday at 11 am, I gave an hour long seminar titled, "What's New in the CMN Core". I gave an overview of the equipment and services that are available as well as updates on what we've upgraded, plan to upgrade, or are anticipating difficulties with. I'll be giving the talk again sometime soon, since many people weren't able to make it on such short notice (both the neuroscience program and Waisman Center didn't get announcements out as early as would be ideal). I'll also be putting the talk on the web site for download.
There will also be more talks in the CMN Core seminar series, with topics including Flow Cytometry analysis using FlowJo software, planning and carrying out a confocal or stereology project, and image analysis using ImageJ and MATLab software. Please let me know if there are other seminar or workshop topics you'd like to see in the series.
There will also be more talks in the CMN Core seminar series, with topics including Flow Cytometry analysis using FlowJo software, planning and carrying out a confocal or stereology project, and image analysis using ImageJ and MATLab software. Please let me know if there are other seminar or workshop topics you'd like to see in the series.
Confocal -- Mercury bulb went out of alignment -- fixed now
We started having a strange problem on Wednesday morning with the confocal. When looking through the eyepiece, only a blobby looking area in the center was illuminated (and very brightly). The rest of the field of view was relatively dark. As I was hurriedly preparing for the seminar, I didn't have time to check out the problem thoroughly. I had the user try the confocal, to see where in the light path the problem was, and it appeared that the problem was also in the laser light path in addition to the mercury light path. I called our scope service rep and he said he would try to get someone to come take a look.
I checked back several times later in the day, and the users that were scheduled used the confocal and reported that it worked fine (the confocal light path being fine, and the view in the eyepiece still abnormal). Then on Thursday, I was able to take a minute to check the mercury bulb alignment and it was way off. There are three knobs for adjusting the positioning of the bulb, and it was the one farthest forward that needed adjustment to get it back in alignment. Hopefully, no one is intentionally touching this knob, as it disrupts the mercury illumination for all users. Contact me if you have questions about this or would like for me to show you how to get the mercury bulb back in alignment (or what knobs NOT to touch).
Another strange phenomenon this user reports is that at 40X, often the field of view appears zoomed out, his cells of interest appearing very small. I'm looking into getting a fluorescent micrometer slide of some sort, to be able to check this type of thing out. In the meantime, let me know if you observe this same phenomenon.
I checked back several times later in the day, and the users that were scheduled used the confocal and reported that it worked fine (the confocal light path being fine, and the view in the eyepiece still abnormal). Then on Thursday, I was able to take a minute to check the mercury bulb alignment and it was way off. There are three knobs for adjusting the positioning of the bulb, and it was the one farthest forward that needed adjustment to get it back in alignment. Hopefully, no one is intentionally touching this knob, as it disrupts the mercury illumination for all users. Contact me if you have questions about this or would like for me to show you how to get the mercury bulb back in alignment (or what knobs NOT to touch).
Another strange phenomenon this user reports is that at 40X, often the field of view appears zoomed out, his cells of interest appearing very small. I'm looking into getting a fluorescent micrometer slide of some sort, to be able to check this type of thing out. In the meantime, let me know if you observe this same phenomenon.
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