colocalization batch processing

[laurent barbe]

Hi all,

 

I am running colocalization test on stacks (12bit, 4 channels) using the
coloc. threshold plugin.

It works fine but now I need to run it on a large number of stacks; so I
basically want to batch process this operation, where I compare my channel
of interest to 3 others, leading to 3 sets of results (which I'd like to
automatically save) using the aforementioned plugin

I found some plugins dealing with stacks, but not yet able to compare one
channel to 2,3 others and to run a specific operation (in my case
colocalization threshold with specific options)

Is anybody faced this kind of situation before?

 

Thank you,

 

Laurent

 

______________________________________________

Laurent Barbe, Research Fellow

Royal University of Technology (KTH)

School of Nanobiotechnology - Dpt of Biotechnology

Roslagstullsbacken 21, 10601 STOCKHOLM

SWEDEN

Tel: [phone]

Fax: [phone]

 

[Michael Weber-4]

Dear all,

sorry for pulling old posts out of the grave, but I was wondering if
there was any progress in batch processing of colocalization analyis?

I am at the moment also seeking for a solution. I already tried to
simply automate the colocalization_threshold (plus the
colocalization_test) plugin via a macro, but apparently the threshold
plugin uses similar variables for the different channels, which makes it
difficult (impossible?) to hand them over from outside.

The routine wouldn't be that difficult in fact: load two images
(pre-selected tiff files in one folder), run the plugin, save the result
table, loop this, then do the same loop for the p-value calculation again.

Anybody an idea? This would really push things forward! :)

cheers,
Michael


laurent barbe wrote:

> Hi all,
>
>  
>
> I am running colocalization test on stacks (12bit, 4 channels) using the
> coloc. threshold plugin.
>
> It works fine but now I need to run it on a large number of stacks; so I
> basically want to batch process this operation, where I compare my channel
> of interest to 3 others, leading to 3 sets of results (which I'd like to
> automatically save) using the aforementioned plugin
>
> I found some plugins dealing with stacks, but not yet able to compare one
> channel to 2,3 others and to run a specific operation (in my case
> colocalization threshold with specific options)
>
> Is anybody faced this kind of situation before?
>
>  
>
> Thank you,
>
>  
>
> Laurent
>
>  
>
> ______________________________________________
>
> Laurent Barbe, Research Fellow
>
> Royal University of Technology (KTH)
>
> School of Nanobiotechnology - Dpt of Biotechnology
>
> Roslagstullsbacken 21, 10601 STOCKHOLM
>
> SWEDEN
>
> Tel: [phone]
>
> Fax: [phone]

[Gabriel Lapointe]

I modified the colocalisaqtion_test to solve this problem en make the
plugin usable in a headless environment. All you have to do is search in
the source code for the faulty variable and change it, ie. add a "_" at
the end. Recompile the plugin and your done. This might not be the
cleanest workaround but it work for me.

If your are interested contact me off list and I'll send you what I've
got. I might even have some time next week to look at the colocalisation
threshold.

cheers,
Gabriel

Michael Weber wrote:

> Dear all,
>
> sorry for pulling old posts out of the grave, but I was wondering if
> there was any progress in batch processing of colocalization analyis?
>
> I am at the moment also seeking for a solution. I already tried to
> simply automate the colocalization_threshold (plus the
> colocalization_test) plugin via a macro, but apparently the threshold
> plugin uses similar variables for the different channels, which makes
> it difficult (impossible?) to hand them over from outside.
>
> The routine wouldn't be that difficult in fact: load two images
> (pre-selected tiff files in one folder), run the plugin, save the
> result table, loop this, then do the same loop for the p-value
> calculation again.
>
> Anybody an idea? This would really push things forward! :)
>
> cheers,
> Michael
>
>
> laurent barbe wrote:
>> Hi all,
>>
>>  
>>
>> I am running colocalization test on stacks (12bit, 4 channels) using the
>> coloc. threshold plugin.
>> It works fine but now I need to run it on a large number of stacks; so I
>> basically want to batch process this operation, where I compare my
>> channel
>> of interest to 3 others, leading to 3 sets of results (which I'd like to
>> automatically save) using the aforementioned plugin
>>
>> I found some plugins dealing with stacks, but not yet able to compare
>> one
>> channel to 2,3 others and to run a specific operation (in my case
>> colocalization threshold with specific options)
>>
>> Is anybody faced this kind of situation before?
>>
>>  
>>
>> Thank you,
>>
>>  
>>
>> Laurent
>>
>>  
>>
>> ______________________________________________
>>
>> Laurent Barbe, Research Fellow
>>
>> Royal University of Technology (KTH)
>>
>> School of Nanobiotechnology - Dpt of Biotechnology
>>
>> Roslagstullsbacken 21, 10601 STOCKHOLM
>>
>> SWEDEN
>>
>> Tel: [phone]
>>
>> Fax: [phone]
>