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.
Monday, April 21, 2008
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.
Monday, April 7, 2008
FACSCalibur -- FlowJo license not to worry
FlowJo users: our license is set to expire on Friday, but not really. I just contact them each year and they give us a new serial number for the year. I should receive that soon and there should be no lapse in our license. Let me know if you have any problems, and just ignore the message that the license is about to expire. Thanks!
Tuesday, April 1, 2008
Confocal - access Viewer and Thumbnailer installers on MyWebSpace
University of Wisconsin users (with NetIDs) can now access the installers for the C1 Viewer and Thumbnailer from MyWebSpace. Just log into it (http://mywebspace.wisc.edu/xythoswfs/webui) then search for NetID jxconnor, folder named confocal. Open the folder, and the installers should be there. Let me know if you have any problems.
Newsletter sent out and on web site
The 4th issue of the CMN Core newsletter went out today, detailing the changes and news since the last issue about a year ago. It is also posted on the website on the News page.
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