Composite_Palette - Interactive adjustment for CompositeImages

[Michael Ellis]

Dear List

I've been recently been developing some ImageJ plugins and although  
probably primarily of use to our existing SmartType and SmartCapture  
customers, they may be of some general interest so hence this post.

PlugIns
    - Composite_Palette - Interactive adjustment for CompositeImages
    - SmartType_Readrer - Reads SmartType karyotype files storing  
chromosome boundaries in the ROI Manager
    - Barrel_Shifter - Barrel shift for images

Probably the plugin of most utility is the Composite_Palette for  
Interactive adjustment of the levels for CompositeImages (byte and  
short only).



The plugins are available at http://www.dsuk.biz/DSUK/ImageJ_PlugIns.html

It's certainly been an interesting learning exercise and at some point  
I may share some of the source code for the more interesting aspects  
like how to introduce threading to improve user interface  
responsiveness in a manner that avoids all those nasty gotcha's that  
using threads can introduce (and in a manner that is easy enough  for  
dummys like me!)

Feedback and bug reports appreciated!

P.S. Next feature on the list for Composite_Palette is copy and paste  
the histogram settings between images. After that, channel  
registration and other features may follow - watch this space!



Michael Ellis
Managing Director
Digital Scientific UK Ltd.
http://www.digitalscientific.co.uk
[hidden email]
tel: [phone]
fax: [phone]

Sheraton House
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[Gabriel Landini]

On Tuesday 08 Jun 2010  14:47:14 you wrote:
> I've been recently been developing some ImageJ plugins and although
> probably primarily of use to our existing SmartType and SmartCapture
> customers, they may be of some general interest so hence this post.

Since this was missing from the message (found it in the website) I see that
the plugins contact a database somewhere without telling the user to check for
features that are already enabled.

Could you please clarify what information from the user do you log when the
plugins connect to the database, and why?

For example, what does the hidden file sdbcache file store?

Thanks

G.

[Michael Ellis]

Gabriel,

Yup the message got screwed up somewhere along the line. I was about  
to send out a plain text version but another list user has identified  
some other problems with the plugin not running so I am trying to sort  
it all out now.

In answer to your question, NO information is logged.

The online database is just a list of what features can run against  
what security keys.

The plugin reads this database and then compares it against the  
security keys that are held. The security keys are gathered from local  
information (e.g. the machine local address, the MAC address if you  
are running Java6, the system properties for user.name).

This security information is not logged anywhere, either locally or on  
our website.

The sdbcache is just a local encrypted copy of the online database  
that is intended for use when the online version is inaccessible.

I hope this explains what is going on. I'll be adding this information  
to the website to make it publicly available.

Can I ask if you succeeded in getting the Composite_Palette to run as  
I have one person (to my knowledge) that finds it fails.

Regards -- Michael Ellis



On 8 Jun 2010, at 15:17, Gabriel Landini wrote:

> On Tuesday 08 Jun 2010  14:47:14 you wrote:
>> I've been recently been developing some ImageJ plugins and although
>> probably primarily of use to our existing SmartType and SmartCapture
>> customers, they may be of some general interest so hence this post.
>
> Since this was missing from the message (found it in the website) I  
> see that
> the plugins contact a database somewhere without telling the user to  
> check for
> features that are already enabled.
>
> Could you please clarify what information from the user do you log  
> when the
> plugins connect to the database, and why?
>
> For example, what does the hidden file sdbcache file store?
>
> Thanks
>
> G.

Michael Ellis
Managing Director
Digital Scientific UK Ltd.
http://www.digitalscientific.co.uk
[hidden email]
tel: [phone]
fax: [phone]

Sheraton House
Castle Park
Cambridge
CB3 0AX


The contents of this e-mail may be privileged and are confidential.  
It may not be disclosed to or used by anyone other than the  
addressee(s), nor copied in any way.  If received in error, please  
advise the sender and delete it from your system.

[Gabriel Landini]

On Tuesday 08 Jun 2010  15:57:31 you wrote:
> I hope this explains what is going on. I'll be adding this information
> to the website to make it publicly available.

Yes, that is a good idea.
 
> Can I ask if you succeeded in getting the Composite_Palette to run as
> I have one person (to my knowledge) that finds it fails.

I tried it and it runs, but I was expecting to load a 8bit stack and be able
to assign each channel to a slider. Not sure it was the way it was intended to
be used.

Cheers

G.

[Michael Ellis]

Dear List

I've been recently been developing some ImageJ plugins and although  
probably primarily of use to our existing SmartType and SmartCapture  
customers, they may be of some general interest so hence this post.

PlugIns
    - Composite_Palette - Interactive adjustment for CompositeImages
    - SmartType_Readrer - Reads SmartType karyotype files storing  
chromosome boundaries in the ROI Manager
    - Barrel_Shifter - Barrel shift for images

Probably the plugin of most utility is the Composite_Palette for  
Interactive adjustment of the levels for CompositeImages (byte and  
short only).

The plugins (and pictures) are available at http://www.dsuk.biz/DSUK/ImageJ_PlugIns.html

It's certainly been an interesting learning exercise and at some point  
I may share some of the source code for the more interesting aspects  
like how to introduce threading to improve user interface  
responsiveness in a manner that avoids all those nasty gotcha's that  
using threads can introduce (and in a manner that is easy enough  for  
dummys like me!)

Feedback and bug reports appreciated!

P.S. Next feature on the list for Composite_Palette is copy and paste  
the histogram settings between images. After that, channel  
registration and other features may follow - watch this space!

P.P.S. (Apologies for repost but previous post to list seemed to only  
result in a graphic being posted and the text being lost so here is a  
picture free plaint text version that should get through)

P.P.P.S I would like to thank Bill Mohler and Gabriel Landini for  
their patients and assistance with this endeavour.

P.P.P.P.S As soon as possible I will add a list of known bugs and  
features to the website (thanks Bill, for your input here)


Michael Ellis
Managing Director
Digital Scientific UK Ltd.
http://www.digitalscientific.co.uk
[hidden email]
tel: [phone]
fax: [phone]

Sheraton House
Castle Park
Cambridge
CB3 0AX


The contents of this e-mail may be privileged and are confidential.  
It may not be disclosed to or used by anyone other than the  
addressee(s), nor copied in any way.  If received in error, please  
advise the sender and delete it from your system.



Michael Ellis
Managing Director
Digital Scientific UK Ltd.
http://www.digitalscientific.co.uk
[hidden email]
tel: [phone]
fax: [phone]

Sheraton House
Castle Park
Cambridge
CB3 0AX


The contents of this e-mail may be privileged and are confidential.  
It may not be disclosed to or used by anyone other than the  
addressee(s), nor copied in any way.  If received in error, please  
advise the sender and delete it from your system.