[ome-users] BD Pathway plate import

[Chris Allan]

Thanks Bram. We'll chew on this and see if we can come up with a nice  
solution.

-Chris

On 16 Mar 2010, at 14:15, <b.gerritsen at nki.nl> <b.gerritsen at nki.nl>  
wrote:

> The folder structure is as follows:
>
> C:\Attovision\Users\<username>\Data\<experiment>\<acquisition>\
>
> Users normally write down the experimental settings such as which  
> cell lines have been used in the name of the experiment  
> (<experiment> field/folder), including the replicate number. Also  
> there is usually only one acquisition folder which contains all the  
> well folders (including Experiment.exp which BDReader uses). The  
> name of the plate should come from the <experiment> folder as the  
> <acquisition> part is automatically generated by the BD Pathway and  
> contains the date and the number of the acquisition.
>
> Example:
>
> C:\Attovision\Users\bgerritsen\Data 
> \SL_020707_BJET_14R1/2007-07-02_000/
>
> The name of the plate in omero should then be: "SL_020707_BJET_14R1"
>
> -Bram
> ________________________________________
> From: Chris Allan [callan at lifesci.dundee.ac.uk]
> Sent: Tuesday, March 16, 2010 2:32 PM
> To: Bram Gerritsen
> Cc: ome-users at lists.openmicroscopy.org.uk Microscopy
> Subject: Re: [ome-users] BD Pathway plate import
>
> If it's available somewhere we can extract it. Don't get too caught up
> in what BDReader.java does or does not do. Could you give us an idea
> of what the folder structure you have looks like and which directory
> and/or file specifically makes up the plate name? I assume this is a
> plate bar code?
>
> -Chris
>
> On 16 Mar 2010, at 13:14, <b.gerritsen at nki.nl> wrote:
>
>> The plate name, if one can call it that, is in the folder structure
>> of the BD Pathway and to my knowledge it is not in any of the files
>> that are processed by the BDReader.java.
>> ________________________________________
>> From: Chris Allan [callan at lifesci.dundee.ac.uk]
>> Sent: Tuesday, March 16, 2010 1:32 PM
>> To: Bram Gerritsen
>> Subject: Re: [ome-users] BD Pathway plate import
>>
>> That's all fine. What would you expect for the plate name? Is this
>> available in the plate file?
>>
>> On 16 Mar 2010, at 12:09, <b.gerritsen at nki.nl> <b.gerritsen at nki.nl>
>> wrote:
>>
>>> Hi Chris,
>>>
>>> The plate name is meta data, but the BDReader.java as it is
>>> currently in the bio-formats trunk uses the "Brand" field which
>>> won't change from one plate to another. If one imports many plates,
>>> they are all called "BD Falcon" for example. Of course the field
>>> could be changed in the corresponding plate file, but it might be
>>> useful to be allowed to specify the plate name during import.
>>>
>>> Kind Regards,
>>> Bram
>>
>