Not a confocal Q <bacteria in H2O>
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Rachael Lim |
Not a confocal Q <bacteria in H2O>
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi everyone! This is not much of a confocal question... But i would like to know if anyone here has knowledge or performed experiments dealing with bacteria found in water (tap water or filtered water)? I am interested in knowing if there is a fast way to detect bacteria in water by using a microscope. I have read that people normally culture them on agar prior to staining on slide for viewing with microscope. Are there any other available options? Please advise! Thank you! Regards, Shu Fen Malaysia |
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal The bacterial density in filtered water depends on the size of the filter (0.22 micron removing all bacteria). The bacterial density in drinking water (tap water) is typically low but can be measured. Filter the water through a 0.22 micron filter, then stain the filter with DAPI or acridine orange (DAPI is better), air dry the filter, then place a drop of immersion oil on a slide and put the filter on the drop. Put a coverslip on the prep and then examine using oil-immersion optics with epifluorescence. >Search the CONFOCAL archive at >http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > >Hi everyone! > >This is not much of a confocal question... But i would like to know if >anyone here has knowledge or performed experiments dealing with bacteria >found in water (tap water or filtered water)? I am interested in knowing if >there is a fast way to detect bacteria in water by using a microscope. I >have read that people normally culture them on agar prior to staining on >slide for viewing with microscope. Are there any other available options? > >Please advise! Thank you! > >Regards, >Shu Fen >Malaysia -- Robert J. Palmer Jr., Ph.D. Natl Inst Dental Craniofacial Res - Natl Insts Health Oral Infection and Immunity Branch Bldg 30, Room 310 30 Convent Drive Bethesda MD 20892 ph 301-594-0025 fax 301-402-0396 |
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Glen MacDonald-2 |
Re: Not a confocal Q <bacteria in H2O>
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In reply to this post by Rachael Lim
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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal there are methods to collect the bacteria by filtration onto membranes or to concentrate by centrifugation. You probably only need to culture if you need to expand the populations. If I remember correctly, Standard Methods for the Examination of Water and Wastewater, should be useful. Regards, Glen On Jan 6, 2008, at 11:12 PM, Rachael Lim wrote: > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Hi everyone! > > This is not much of a confocal question... But i would like to know if > anyone here has knowledge or performed experiments dealing with > bacteria > found in water (tap water or filtered water)? I am interested in > knowing if > there is a fast way to detect bacteria in water by using a > microscope. I > have read that people normally culture them on agar prior to > staining on > slide for viewing with microscope. Are there any other available > options? > > Please advise! Thank you! > > Regards, > Shu Fen > Malaysia |
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Cesare -ALEMBIC- |
not only confocal question - freeware BioImaging software
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
I apologize for not completely proper use of the list. Amazing softwares and images analysis tools have often only one big fault… they are very very expensive! Not always (unfortunately), but often (fortunately!) scientist, researcher, programmer or software developer build and allow free use of very interesting and useful free software or imaging tools. We are trying to get a free web-place where you can point out your favourite free software for the whole community. Freeware BioImaging Software Web-Case page (http://www.sanraffaele.org/58226.html?page=9#fs0). Please, if you have a free software to indicate send us an indication and we will be glad to publish it on the site! Thank in advance for your attention, suggestion and comment (all always welcome!) Best whishes Cesare ________________________________________________________ Dr. Cesare Covino Biologist - Light Microscopy Coordinator ALEMBIC Advanced Light and Electron Microscopy BioImaging Center DIBIT - San Raffaele Scientific Institute via Olgettina 58, 20132 - Milano - Italy Tel +39-022643-4636(others -4640, -4641) Fax +39-022643-4813 e-mail: [hidden email] ALEMBIC web page: www.sanraffaele.org/research/alembic |
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Nuno Moreno |
Re: not only confocal question - freeware BioImaging software
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi! There are a few missing that I know Commercial Metamorph simplePCI neurolucida Free mevislab voxx2 bioimagexd infraview imagetool Regards, NM Cesare -ALEMBIC- wrote: > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear All, > I apologize for not completely proper use of the list. > > Amazing softwares and images analysis tools have often only one big > fault… they are very very expensive! > Not always (unfortunately), but often (fortunately!) scientist, > researcher, programmer or software developer build and allow free use of > very interesting and useful free software or imaging tools. > We are trying to get a free web-place where you can point out your > favourite free software for the whole community. > Freeware BioImaging Software Web-Case page > <http://www.sanraffaele.org/58226.html?page=9#fs0> > (http://www.sanraffaele.org/58226.html?page=9#fs0). > > Please, if you have a free software to indicate send us an indication > and we will be glad to publish it on the site! > > Thank in advance for your attention, suggestion and comment (all always > welcome!) > > Best whishes > > /Cesare > > / > > */________________________________________________________ > /**/Dr. Cesare Covino > /*Biologist - Light Microscopy Coordinator*/ > /**ALEMBIC* > Advanced Light and Electron Microscopy BioImaging Center / > /DIBIT - /San Raffaele Scientific Institute// > /via Olgettina 58, 20132 - Milano - Italy / > /Tel +39-022643-4636(others -4640, -4641) > Fax +39-022643-4813 > e-mail: [hidden email] > ALEMBIC web page: www.sanraffaele.org/research/alembic > <http://www.sanraffaele.org/58226.html> -- Nuno Moreno Cell Imaging Unit Instituto Gulbenkian de Ciência http://uic.igc.gulbekian.pt http://www.igc.gulbekian.pt phone +351 214464606 fax +351 214407970 |
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lechristophe |
Re: not only confocal question - freeware BioImaging software
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
all of these are free, some of them open source :
ImageJ and MAtlab plugins (ImageJ plugins are a huge world, the ImageJ site repository and the ImageJ wiki are a good starting point, but some of them are just mentionned in papers): http://www.cbl.ethz.ch/Downloads/index Paraview: http://www.paraview.org/HTML/Index.html a bunch of free medical imaging oriented software: http://www.ia.unc.edu/dev/download/index.htm ImageTrack (OSX, a bit outdated, but you can contact the author for recent betas): http://www.ohri.ca/programs/neuroscience/White_Matter_Injury/stysWeb/stysImageTrak.htm SINEMA (Single Particle Tracking, used for quantum dot labeling and diffusion measurements): http://www.lkb.ens.fr/recherche/optetbio/tools/sinema/ MIATool, a Matlab addon for microscopy: http://www4.utsouthwestern.edu/wardlab/index_files/MIATool.htm Imaging software from UCSB: http://www.bioimage.ucsb.edu/projects/ Drishti: http://sf.anu.edu.au/Vizlab/drishti/index.html HCA Vision for high content analysis: http://www.hca-vision.com/index.html Warning : I'm not sure it's free. Seems that they want to charge for it in the near future as the licensing is changing every other day And last, an extensive collection of links: http://www.cma.mgh.harvard.edu/iatr/display.php?spec=all Christophe Leterrier Postdoc INSERM UMR641 Neurobiology of ionic channels IFR Jean Roche - Mediterranee University Marseille, France On Jan 8, 2008 10:45 AM, Nuno Moreno <[hidden email]> wrote: Hi! |
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lechristophe |
Re: not only confocal question - freeware BioImaging software
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
and I forgot this webpage about 3D reconstruction from serial sections :
http://synapses.clm.utexas.edu/tools/index.stm
On Jan 8, 2008 11:22 AM, Christophe Leterrier <[hidden email]> wrote: all of these are free, some of them open source : |
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Michael Weber-4 |
Re: not only confocal question - freeware BioImaging software
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In reply to this post by Nuno Moreno
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hello Cesare, nice idea, I would add: commercial - Bitplane Imaris - Zeiss ZEN - Leica LAS AF - Olympus FV software - Nikon NIS Elements free - Leica LAS AF Lite - Zeiss ZEN LE - Olympus FV-Viewer - Bio-Formats for ImageJ My recommendation would be to take out the current versions (v4.1 etc.), since it's hard to keep it up to date. And several programs in the list are already available in newer versions ;). cheers, Michael > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Hi! > > There are a few missing that I know > > Commercial > > Metamorph > simplePCI > neurolucida > > > Free > > mevislab > voxx2 > bioimagexd > infraview > imagetool > > Regards, > NM > > Cesare -ALEMBIC- wrote: >> Search the CONFOCAL archive at >> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear All, >> I apologize for not completely proper use of the list. >> >> Amazing softwares and images analysis tools have often only one big >> fault they are very very expensive! >> Not always (unfortunately), but often (fortunately!) scientist, >> researcher, programmer or software developer build and allow free use of >> very interesting and useful free software or imaging tools. >> We are trying to get a free web-place where you can point out your >> favourite free software for the whole community. >> Freeware BioImaging Software Web-Case page >> <http://www.sanraffaele.org/58226.html?page=9#fs0> >> (http://www.sanraffaele.org/58226.html?page=9#fs0). >> >> Please, if you have a free software to indicate send us an indication >> and we will be glad to publish it on the site! >> >> Thank in advance for your attention, suggestion and comment (all always >> welcome!) >> >> Best whishes >> >> /Cesare >> >> / >> >> */________________________________________________________ >> /**/Dr. Cesare Covino >> /*Biologist - Light Microscopy Coordinator*/ >> /**ALEMBIC* >> Advanced Light and Electron Microscopy BioImaging Center / >> /DIBIT - /San Raffaele Scientific Institute// >> /via Olgettina 58, 20132 - Milano - Italy / >> /Tel +39-022643-4636(others -4640, -4641) >> Fax +39-022643-4813 >> e-mail: [hidden email] >> ALEMBIC web page: www.sanraffaele.org/research/alembic >> <http://www.sanraffaele.org/58226.html> > > -- > Nuno Moreno > Cell Imaging Unit > Instituto Gulbenkian de Ciência > http://uic.igc.gulbekian.pt > http://www.igc.gulbekian.pt > phone +351 214464606 > fax +351 214407970 |
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Cesare -ALEMBIC- |
Re: not only confocal question - freeware BioImaging software
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In reply to this post by Nuno Moreno
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Dear all, thank you for all your (numerous) private and public suggestions and indication. I'm discovering a World (cheap world fortunately) I'll update the page as soon as I can Just to specify, commercial softwares mentioned on the page are only commercial softwares we have, availables in our facility. I'm considering to open a new part with your indications about it. Please do not hesitate to contact me for errors, errors-link , update, etc for softwares indicated. Cheers, Cesare Nuno Moreno ha scritto: Search the CONFOCAL archive at |
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Judy Trogadis |
Re: not only confocal question - freeware BioImaging software
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In reply to this post by Nuno Moreno
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal That's actually Irfanview - not infraview - and a very useful program. Judy Judy Trogadis Bio-Imaging Coordinator St. Michael's Hospital, 7Queen 30 Bond St. Toronto, ON M5B 1W8, Canada ph: 416-864-6060 x6337 pager: 416-685-9219 fax: 416-864-6043 [hidden email] >>> Nuno Moreno <[hidden email]> 01/08/08 4:45 AM >>> Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi! There are a few missing that I know Commercial Metamorph simplePCI neurolucida Free mevislab voxx2 bioimagexd infraview imagetool Regards, NM Cesare -ALEMBIC- wrote: > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear All, > I apologize for not completely proper use of the list. > > Amazing softwares and images analysis tools have often only one big > fault* they are very very expensive! > Not always (unfortunately), but often (fortunately!) scientist, > researcher, programmer or software developer build and allow free use of > very interesting and useful free software or imaging tools. > We are trying to get a free web-place where you can point out your > favourite free software for the whole community. > Freeware BioImaging Software Web-Case page > <http://www.sanraffaele.org/58226.html?page=9#fs0> > (http://www.sanraffaele.org/58226.html?page=9#fs0). > > Please, if you have a free software to indicate send us an indication > and we will be glad to publish it on the site! > > Thank in advance for your attention, suggestion and comment (all always > welcome!) > > Best whishes > > /Cesare > > / > > */________________________________________________________ > /**/Dr. Cesare Covino > /*Biologist - Light Microscopy Coordinator*/ > /**ALEMBIC* > Advanced Light and Electron Microscopy BioImaging Center / > /DIBIT - /San Raffaele Scientific Institute// > /via Olgettina 58, 20132 - Milano - Italy / > /Tel +39-022643-4636(others -4640, -4641) > Fax +39-022643-4813 > e-mail: [hidden email] > ALEMBIC web page: www.sanraffaele.org/research/alembic > <http://www.sanraffaele.org/58226.html> -- Nuno Moreno Cell Imaging Unit Instituto Gulbenkian de Ciência http://uic.igc.gulbekian.pt http://www.igc.gulbekian.pt phone +351 214464606 fax +351 214407970 |
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Judy Trogadis |
Re: not only confocal question - freeware BioImaging software
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In reply to this post by Cesare -ALEMBIC-
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Forgot another commercial one - Neurolucida, a 3D reconstruction and quantitative analysis program from MicroBrightfield. Initially developed for neuroscientists, we are using it to reconstruct blood vessels. Judy Judy Trogadis Bio-Imaging Coordinator St. Michael's Hospital, 7Queen 30 Bond St. Toronto, ON M5B 1W8, Canada ph: 416-864-6060 x6337 pager: 416-685-9219 fax: 416-864-6043 [hidden email] >>> Cesare -ALEMBIC- <[hidden email]> 01/08/08 4:14 AM >>> Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear All, I apologize for not completely proper use of the list. Amazing softwares and images analysis tools have often only one big fault... they are very very expensive! Not always (unfortunately), but often (fortunately!) scientist, researcher, programmer or software developer build and allow free use of very interesting and useful free software or imaging tools. We are trying to get a free web-place where you can point out your favourite free software for the whole community. Freeware BioImaging Software Web-Case page <http://www.sanraffaele.org/58226.html?page=9#fs0> (http://www.sanraffaele.org/58226.html?page=9#fs0). Please, if you have a free software to indicate send us an indication and we will be glad to publish it on the site! Thank in advance for your attention, suggestion and comment (all always welcome!) Best whishes /Cesare / */________________________________________________________ /**/Dr. Cesare Covino /*Biologist - Light Microscopy Coordinator*/ /**ALEMBIC* Advanced Light and Electron Microscopy BioImaging Center / /DIBIT - /San Raffaele Scientific Institute// /via Olgettina 58, 20132 - Milano - Italy / /Tel +39-022643-4636(others -4640, -4641) Fax +39-022643-4813 e-mail: [hidden email] ALEMBIC web page: www.sanraffaele.org/research/alembic <http://www.sanraffaele.org/58226.html> |
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Bill Miller-3 |
Re: not only confocal question - freeware BioImaging software
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In reply to this post by Judy Trogadis
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Many Photoshop compatible plugins work with Irfanview as well At 11:24 AM 1/8/2008 -0500, Judy Trogadis wrote: >Search the CONFOCAL archive at >http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > >That's actually Irfanview - not infraview - and a very useful program. >Judy > >Judy Trogadis >Bio-Imaging Coordinator >St. Michael's Hospital, 7Queen >30 Bond St. >Toronto, ON M5B 1W8, Canada >ph: 416-864-6060 x6337 >pager: 416-685-9219 >fax: 416-864-6043 >[hidden email] > > > >>> Nuno Moreno <[hidden email]> 01/08/08 4:45 AM >>> >Search the CONFOCAL archive at >http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > >Hi! > >There are a few missing that I know > >Commercial > >Metamorph >simplePCI >neurolucida > > >Free > >mevislab >voxx2 >bioimagexd >infraview >imagetool > >Regards, >NM > >Cesare -ALEMBIC- wrote: > > Search the CONFOCAL archive at > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear All, > > I apologize for not completely proper use of the list. > > > > Amazing softwares and images analysis tools have often only one big > > fault* they are very very expensive! > > Not always (unfortunately), but often (fortunately!) scientist, > > researcher, programmer or software developer build and allow free use >of > > very interesting and useful free software or imaging tools. > > We are trying to get a free web-place where you can point out your > > favourite free software for the whole community. > > Freeware BioImaging Software Web-Case page > > <http://www.sanraffaele.org/58226.html?page=9#fs0> > > (http://www.sanraffaele.org/58226.html?page=9#fs0). > > > > Please, if you have a free software to indicate send us an indication > > > and we will be glad to publish it on the site! > > > > Thank in advance for your attention, suggestion and comment (all >always > > welcome!) > > > > Best whishes > > > > /Cesare > > > > / > > > > */________________________________________________________ > > /**/Dr. Cesare Covino > > /*Biologist - Light Microscopy Coordinator*/ > > /**ALEMBIC* > > Advanced Light and Electron Microscopy BioImaging Center / > > /DIBIT - /San Raffaele Scientific Institute// > > /via Olgettina 58, 20132 - Milano - Italy / > > /Tel +39-022643-4636(others -4640, -4641) > > Fax +39-022643-4813 > > e-mail: [hidden email] > > ALEMBIC web page: www.sanraffaele.org/research/alembic > > <http://www.sanraffaele.org/58226.html> > >-- >Nuno Moreno >Cell Imaging Unit >Instituto Gulbenkian de Ciência >http://uic.igc.gulbekian.pt >http://www.igc.gulbekian.pt >phone +351 214464606 >fax +351 214407970 |
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Russell Spear |
Re: not only confocal question - freeware BioImaging software
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In reply to this post by Judy Trogadis
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi I also use Thumbs Plus Pro not free but cheap from Cerious Softward (no commercial intrest) some image manipulation and databasing. Russ Russell N. Spear Sr. Research Specialist Dept. of Plant Pathology Univ. of Wisconsin 1630 Linden Dr. Madison WI 53706 voice 608.263.2093 fax 608.263.2626 |
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Jason Swedlow |
Re: not only confocal question - freeware BioImaging software
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In reply to this post by Judy Trogadis
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Cesare et al:
A few more: **** The Open Microscopy Environment (http://openmicroscopy.org) releases open source (i.e., free and available!) software for biological microscopy. Our released packages include: -- OME Server-- a Perl-based for visualising, managing, and analysing microscope images and metadata. It includes a web browser interface, a threshold segmentation and tracking application (called "findSpots"), a MatLab interface, support for VisBio, LDAP, BioFormats and much more. -- OMERO-- a Java-based server/client system for visualising, managing, and annotating microscope images and metadata. See the movies at http://openmicroscopy.org/howto for more info. -- Bio-Formats-- a Java library for reading and writing popular microscopy file formats capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats (maintained in collaboration with LOCI, http://loci.wisc.edu/). -- OME-TIFF-- a specification and libraries for standardised image files for biological microscopy. More info on all of these is at http://openmicroscopy.org **** LOCI are releasing a number of other useful packages, including WiscScan, VisBio, and 4D DataBrowser. See http://loci.wisc.edu/ for more info. **** The Vale Lab at UCSF is releasing MicroManager (http://micro-manager.org/), an open source package for imaging and control of automated microscopes on multiple platforms. All of these are active development projects that respond to users' requests and needs. The different websites provide facilities for download and feedback. Use and abuse, and let us know what you think! Cheers, Jason On Jan 8, 2008 4:28 PM, Judy Trogadis <[hidden email]> wrote: Forgot another commercial one - Neurolucida, a 3D reconstruction and quantitative analysis program from MicroBrightfield. Initially developed for neuroscientists, we are using it to reconstruct blood vessels. -- ************************** Wellcome Trust Centre for Gene Regulation & Expression College of Life Sciences MSI/WTB/JBC Complex University of Dundee Dow Street Dundee DD1 5EH United Kingdom phone (01382) 385819 Intl phone: 44 1382 385819 FAX (01382) 388072 email: [hidden email] Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/ Open Microscopy Environment: http://openmicroscopy.org ************************** |
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Cesare -ALEMBIC- |
Freeware BioImaging Software Web-Case (Vers. 2.0)
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In reply to this post by Cesare -ALEMBIC-
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Dear All, further to my mail last December, we are delighted to publish a new version of ALEMBIC Freeware BioImaging Sofware Web-Case direct link http://www.sanraffaele.org/58226.html?page=9 or, from Alembic home page, www.sanraffaele.org/research/alembic --> page 'software' following a large number of indications, we have completely rebuild the page. Now softwares are divided in 8 macro-categories in order to allow a friendly and quick reference. In the last update we have more than 40 entries....!!! Thanks for all the (numerous) private and public suggestions and indications. If you have a free software to indicate, we would be glad to publish it on the site! Please, do not hesitate to contact me for errors, errors-links , updates, etc for softwares indicated. Enjoy it! Cesare _______________________________________________________ ALEMBIC Advanced Light and Electron Microscopy BioImaging Center DIBIT - San Raffaele Scientific Institute via Olgettina 58, 20132 - Milano - Italy Tel +39-022643-4635/36/40 Fax +39-022643-4813 e-mail: [hidden email] home page: http://www.sanraffaele.org/research/alembic ********************************************************************** Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi ("Ricerca sanitaria") il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [hidden email] o vai sul sito w w w . 5 x m i l l e . o r g |
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