Image set library for image analysis algorithm benchmarking

[Leonardo Guizzetti]

Hello IJ users,

I wonder if any of you know of open data sets that contain images of cells
with various compartments stained (e.g., cytoplasm, nucleus, ER, Golgi)
which can be used to benchmark image analysis or segmentation algorithms?
The purpose of this is to see if there are accepted data standards to use
for these tasks, prior to testing a particular algorithm against my own
data.


I look forward to your help,

Lenny Guizzetti

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[Leon Espinosa-3]

maybe you can try the Broad Institute Database:

http://www.broadinstitute.org/bbbc/



Le 10 sept. 2014 à 17:47, Leonardo Guizzetti a écrit :

> Hello IJ users,
>
> I wonder if any of you know of open data sets that contain images of cells
> with various compartments stained (e.g., cytoplasm, nucleus, ER, Golgi)
> which can be used to benchmark image analysis or segmentation algorithms?
> The purpose of this is to see if there are accepted data standards to use
> for these tasks, prior to testing a particular algorithm against my own
> data.
>
>
> I look forward to your help,
>
> Lenny Guizzetti
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

... [show rest of quote]

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[Leonardo Guizzetti]

Thank you Leon,

I will have a look into that database. Some of those data sets may be
useful to me.

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[Dimiter Prodanov (imec)]

Hello,

It is a good starting point. Are there other resources?
May be we can also use the ImageJ wiki for this.

Best regards,

Dimiter Prodanov

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[ctrueden]

Hi Lenny,

> I wonder if any of you know of open data sets that contain images of
> cells with various compartments stained (e.g., cytoplasm, nucleus, ER,
> Golgi) which can be used to benchmark image analysis or segmentation
> algorithms?

How about:
http://www.cellimagelibrary.org/

Regards,
Curtis

On Wed, Sep 10, 2014 at 10:47 AM, Leonardo Guizzetti <
[hidden email]> wrote:

> Hello IJ users,
>
> I wonder if any of you know of open data sets that contain images of cells
> with various compartments stained (e.g., cytoplasm, nucleus, ER, Golgi)
> which can be used to benchmark image analysis or segmentation algorithms?
> The purpose of this is to see if there are accepted data standards to use
> for these tasks, prior to testing a particular algorithm against my own
> data.
>
>
> I look forward to your help,
>
> Lenny Guizzetti
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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[Leonardo Guizzetti]

Hi Curtis,


> How about:
> http://www.cellimagelibrary.org/


This is a good suggestion, and it seems that data sets are in beta on their
website with one data set available.
Thank you,
Lenny

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[Cammer, Michael]

Interesting.  All raw data used to be available for download.  I used this back in 2011-2013 and always could download the raw data.
I recommend contacting them.
===========================================================================
Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical Center
Cell:  914-309-3270   note that we do not receive messages left at 212-263-3208
http://ocs.med.nyu.edu/microscopy & http://microscopynotes.com/


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Leonardo Guizzetti
Sent: Wednesday, September 17, 2014 11:37 AM
To: [hidden email]
Subject: Re: Image set library for image analysis algorithm benchmarking

Hi Curtis,


> How about:
> http://www.cellimagelibrary.org/


This is a good suggestion, and it seems that data sets are in beta on their website with one data set available.
Thank you,
Lenny

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