[ome-users] BD Pathway plate import

[Melissa Linkert]

Hi Bram,

I've added better plate name parsing to the BD reader as of
Bio-Formats r6043, which you can view here:

https://skyking.microscopy.wisc.edu/trac/java/changeset/6043

This seems to work with the data that we have, but please let us know
if you find that the plate names are still incorrect.

Regards,
-Melissa

On Tue, Mar 16, 2010 at 10:01 AM, Chris Allan
<callan at lifesci.dundee.ac.uk> wrote:
> 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
>>>
>>
>
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