[ome-devel] INCell images/importer

[Bernd Jagla]

Ilya, and all,

 

First of all thanks a lot for all the kind help so far. Even though the
progress is very slow (due to my lack of time) I believe I made some
substantial progress thanks to your kind help.

 

I just wanted to clarify a few things when implementing the INCell importer:

The way GE/Amersham handles the information from their INCell 3000 is to
store information about a screen in a file called "run"-file. This file
would contain information about the number of plates, which lasers where
used, what the plates where named and basically anything that is true for
all images from that screen. Images are stored in sub-directories; each
plate having its own sub-directory. Then there can be several other
sub-directories with addition information that is not that important. At
some point I would also like to be able to read in the information from the
automated and semi-automated analyses that can be done with the INCell
software, which are stored in some of those subdirectories (but this we will
do later. ;-).

 

I would store the information from the "run"-files on the dataset level and
come up with additional attributes on the dataset level to store that
information.

 

*      How do I access those attributes? I would do it from the importGroup
function (that I have to write) using the newAttribute function ( I will
look through a few examples to find a clue on how to do that, so far I have
only seen attributes for images.).

*      How should I distinguish between different plates? Would this be a
dataset underneath a dataset or a parallel dataset? I could probably also
create different new datasets from the run-file and link later the images to
those dataset. How would I do this the best way? 

*      Since all the information about a dataset is in a run-file, I would
like to remove all other files from the list and therefore allow only one
file (the run-file) to be in the list at the beginning. Would this be OK?
This would mean that the "run"-files have to be processed first.

 

In the getGroups function I would then add all the images (frm-files) to the
list. 

 

*      Should I modify the attributes of the dataset already in the
getGroups function? This would make my life easier when importing the frm
images, because I can then remove even the run-file from the file list (no
need for an importGroups function) and do the rest of the work in the frm
importer.

 

The run-file "knows" about the images and where they are stored (also which
colors where used, which is very important for converting them into any
other format) and thanks to Ilya we now know also the path so we can add the
additional images.

 

*      How do I add image files (frm files) to the file list? I use upload
(as Ilya said) but then I don't know how to register the connection in the
"regular" way and I don't see the new file being processed (I guess this has
something to do with the registration).

 

 

Well I guess that's enough for now.

 

Thanks for your input.

 

Bernd

 

 

 

Bernd Jagla, PhD
Associate Research Scientist
Columbia University
1150 St. Nicholas Avenue
Russ Berrie Medical Pavilion, Room 520
New York, NY 10032
Tel: 212 - 851 5560 x16
Fax: 212 - 851 5570
e-mail: baj2107 at columbia.edu
  

 

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