[ome-devel] Leica SP5 Matrix Screener

[Rubén Muñoz]

Hi Melissa,

Hope this helps. All the file names, including the folder names are configurable. 
What I sent you were the default settings, as you can see below. 

Please let me know if I can help with anything.

Regards,
Rubén 

ImageName: the first token (see sample: ... Image) 
LoopCount: the Loop token (see sample: ... L0000) 
Slide: the number of the slide (see sample: ... S00) 
WellX: the well position (see sample: ... U00) 
WellY: the well position (see sample: ... V00)
PPos: in case we found multiple positions in a image 
RPos: a possible rotation of the image (SP5 only) 
LamPos: if we make a lambda emission scan 
XTPos: in case we make a XT scan
TSPos: T Slice series 
LamExcPos: if we make a lambda excitation scan 
JPos: the job position (see sample: ... J01) 
XPos: the X scan field position (see sample: ... X00) 
YPos: the Y scan field position (see sample: ... Y00) 
TPos: the logical time position (see sample: ... T0000)
ZPos: the Z stack position (see sample: ... Z00) 
CPos: the channel (see sample: ... C00)

Image—L0000—S00—U00—V00—J01—E01—X00—Y00—T0000—Z00—C00.ome.tif 
Image—L0000—S00—U01—V01—J22—E01—X01—Y06—T0000—Z10—C01.ome.tif 
Image—L0002—S00—U00—V00—J04—E01—X02—Y02—T0002—Z00—C02.ome.tif ...



On Sep 16, 2010, at 4:12 PM, Melissa Linkert wrote:

> Hi Rubén,
> 
> Thank you for uploading a dataset.  I have filed a ticket and CC'd you;
> in case anyone else is interested, the ticket can be viewed here:
> 
> http://dev.loci.wisc.edu/trac/java/ticket/563
> 
> Regards,
> -Melissa
> 
> On Thu, Sep 16, 2010 at 03:48:22PM +0200, Rubén Muñoz wrote:
>> Hi Melissa, 
>> 
>> Thanks for the info. 
>> I have uploaded a dataset from the matrix screener: experiment--2010_03_30_13_35_06.zip
>> 
>> Although all the images are black or fuzzy, I could do more.
>> 
>> Regards,
>> 
>> Rubén
>> 
>> On Sep 16, 2010, at 3:26 PM, Melissa Linkert wrote:
>> 
>>> Hi Rubén,
>>> 
>>>> - Is there an importer?
>>> 
>>> Not yet.
>>> 
>>>> - How close do you think that these are to multi-file ome.tif?
>>> 
>>> It's difficult to say without seeing an example dataset.
>>> 
>>>> - Would be or worth to make an importer?
>>> 
>>> We can certainly add support for these datasets, but it may take a
>>> while.  Once you are able to upload a dataset, I will investigate and
>>> file a ticket as needed.
>>> 
>>>> I tried to upload the set to dev.loci.wisc.edu but I got an error.
>>> 
>>> You will need to change to the "incoming" directory after connecting.
>>> 
>>> Regards,
>>> -Melissa
>>> 
>>> On Thu, Sep 16, 2010 at 10:20:34AM +0200, Rubén Muñoz wrote:
>>>> Hi Melissa,
>>>> 
>>>> A time ago, I advanced that there's another Leica format. 
>>>> Well it's being generated by our Leica SP5 Matrix Screener.
>>>> 
>>>> The files are OME.TIF but they have no so complete OME-XML headers yet.
>>>> I will be working with this files, to get them close to the ones that bfconvert generates.
>>>> 
>>>> 
>>>> I wanted to ask some questions. 
>>>> - Is there an importer?
>>>> - How close do you think that these are to multi-file ome.tif?
>>>> - Would be or worth to make an importer?
>>>> 
>>>> I tried to upload the set to dev.loci.wisc.edu but I got an error.
>>>> 
>>>> uploading experiment--2010_03_30_13_35_06.zip to /experiment--2010_03_30_13_35_06.zip
>>>> Couldn't get handle: Permission denied
>>>> 
>>>> 
>> 

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