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Hi Brian,
We use the aperio only to scan large batches of slides. The viewer
software is only used to extract the area of interest for further
analysis. I have not used the aperio analysis software (though people i
have spoken to say it is alright but very pathology specific). All our
analysis is performed in MetaMorph as it is more than powerful enough
for what we want, and i am very familiar with the scripting interface to
write any sort of custom analsis we may want.
At the moment you need to extract a tiff image out using the aperio
viewer for metamorph or anything else to be able to use it. I have heard
rumours of MetaMoprh supporting the aperio file format (svi) soon.
1GB (or bigger) are not too much f a problem on a computer with enough
grunt. MetaMorphs only limitation is that the image cannot be any bigger
than 32,000 x 32,000 pixels.
The current plan for funding a new scanner is to hit up internal funding
sources we have access to (and potentially fill in gaps with small
grants etc.)
The systems i have tested so far are sitting around the $200-300,000
mark
I am currently leaning towards the MetaSystems VSlide as it can do both
bright field and fluorescence, can have up to 880 slide loader, can do
imaging with immersion objectives and can handle very large files thanks
to an Imaris backbone. It also has very advanced tissue recognition and
filtering.
Cheers
Cam
-----Original Message-----
From: Confocal Microscopy List [mailto:[log in to unmask]]
On Behalf Of Armstrong, Brian
Sent: Wednesday, 18 May 2011 9:34 AM
To: [log in to unmask]
Subject: Re: Slide Scanner
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Hi Cam, thanks for the reply.
So I guess the Google-Earth-like software of Aperio is nice for viewing
images, but what about analysis by Metamorph, or other? How do you
analyze a 1GB image?
To whom will you aim the proposal for your new scanner?
Do you think you could fund it through a grant, or is this internal?
What do you expect to the system to cost?
I hear differing opinions about Aperio, support, leasing, analysis is
weak and geared towards pathology, etc..
I think that the Leica SCN400 sounds nice, and Definiens seems powerful,
but both are expensive.
What system do you favor?
Sorry about all the questions. Thanks for offering your opinion.
Brian D Armstrong PhD
Assistant Research Professor
Light Microscopy Core
Beckman Research Institute
City of Hope
Dept of Neuroscience
1450 E Duarte Rd
Duarte, CA 91010
626-256-4673 x62872
http://www.cityofhope.org/research/support/Light-Microscopy-Digital-Imag
ing/Pages/default.aspx
-----Original Message-----
From: Confocal Microscopy List [mailto:[log in to unmask]]
On Behalf Of Cameron Nowell
Sent: Tuesday, May 17, 2011 3:29 PM
To: [log in to unmask]
Subject: Re: Slide Scanner
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Hi Brian,
Pretty sure you didn't mean your question to go to the whole list but
thought i would chip in anyway. Hope you don't mind.
A slide scanner is an amazingly powerful tool when coupled with high
powered image analysis. We have access to an Aperio scanner for scanning
standard histology slides and we also have a fluorescence scope set up
to be able to scan four slides (multiple areas of each) at once in up to
seven channels if required.
Both systems give phenomenal images and provide a great deal of
information when crunched through MetaMorph (or a similar program). We
have done classification of macrophage populations in whole mouse lung,
counted stem cells in the whole mouse colon, counted neruons through
whoel brain slices to name just a few.
I am currently in the early stages of putting a proposal together for
the purchase of a more high throughput fluorescent scanner. One that can
take ~100 slides in a loader and do all its magic without having to
change out the slides every couple of hours from our current setup.
The one thing to be aware of in this whole process is that the image
files are huge!!!!! We are talking a gigabyte or more per slide
depending o the scan area and the objective used.
Feel free to contact me off list for anything, or ask question here so
everyone can foloow along.
Once again sorry for hijacking your email
Cheers
Cam
Cameron J. Nowell
Microscopy Manager
Centre for Advanced Microscopy
Ludwig Institute for Cancer Research
PO Box 2008
Royal Melbourne Hospital
Victoria, 3050
AUSTRALIA
Office: +61 3 9341 3155
Mobile: +61422882700
Fax: +61 3 9341 3104
Facility Website
-----Original Message-----
From: Confocal Microscopy List [mailto:[log in to unmask]]
On Behalf Of Armstrong, Brian
Sent: Wednesday, 18 May 2011 2:28 AM
To: [log in to unmask]
Subject: Slide Scanner
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Hello Julio, do you have a slide scanner in your core?
Do you think a slide scanner is a good match for a research microscopy
core facility?
I would appreciate your opinion.
Cheers,
Brian Armstrong PhD
Light Microscopy Core
Beckman Research Institute
1450 East Duarte Rd
Duarte, CA 91010
626-256-4673 x62872
http://www.cityofhope.org/SharedResources/LightMicroscopy/LightMicroHome
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