Re: Public bank of bio-images

Posted by Silas Leavesley on Aug 24, 2017; 2:52pm
URL: http://imagej.273.s1.nabble.com/Public-bank-of-bio-images-tp5019258p5019259.html

Hi Adrián,

We discussed this some at the Cyto 2017 conference in our 3D image
analysis workshop.  What would be really useful, I think for you and a
lot of others, is if there were test sets of representative image data
that could be used to benchmark new algorithms.  Ideally this would
include different modes, dimensions, etc. (e.g., 2D, 3D, timelapse,
spectral, etc.).  To my knowledge there isn't a comprehensive set of
reference image sets out there for use in benchmarking.  However, there
are certainly example image sets that could be downloaded from different
group websites.  A couple examples I can think of:
-Human Cell Atlas.  There are a bunch of images - you will want to do
some digging through the web site to familiarize yourself with how it's
structured and what types of images you are looking for:
http://www.proteinatlas.org/humancell
-Image Data Resource.  Again a bunch of data sets and you will want to
take some time to orient yourself with the data:
http://idr.openmicroscopy.org/about/
-Data from Cell Profiler tutorials.  These are smaller data sets
intended to demonstrate a specific analysis pipeline:
http://cellprofiler.org/

Hopefully some of these will be helpful, and there's likely even more
out there, this is just what I thought of off the top of my head.

Best regards,

Silas



On 8/24/2017 9:36 AM, Adrián Villalba wrote:

> Dear ImageJers,
>
> I found on the imageJdocu webpage this database of images (
> http://sipi.usc.edu/database/). Does anyone know if there is something
> similar to a database from bio-images that i can use in Fiji to test macros
> and something related? I mean, if i can use public images rather than my
> own microscope images (bright or fluorescence).
>
> Thank you very much!
>

--
Silas J. Leavesley, Ph.D.
Professor
Department of Chemical and Biomolecular Engineering
Department of Pharmacology
Center for Lung Biology
University of South Alabama
150 Jaguar Drive, SH4129
Mobile, AL 36688
ph: (251)-460-6160
fax: [phone]
web: http://www.southalabama.edu/centers/bioimaging
google scholar: http://scholar.google.co.uk/citations?user=knkwcj4AAAAJ
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