Hi Pierre,<br>
<br>
I am CCing the ome-users list to involve more of the OME developers in the discussion.<br>
<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div link="blue" vlink="purple" lang="EN-US"><div><p><span style="font-size: 11pt; color: rgb(31, 73, 125);">About an element LaserCombiner: </span></p>
<p style="margin-left: 72pt; text-indent: -18pt;"><span style="font-size: 11pt; font-family: Symbol; color: rgb(31, 73, 125);"><span>·<span>
</span></span></span><span style="font-size: 11pt; color: rgb(31, 73, 125);">The main problem is that the wavelength and Attenuation of the
light source are defined in the LightSourceRef element. If I have only one
LightSource element (the LaserCombiner), I can't indicate the intensities
of all lasers for a given LogicalChannel. The standard scenario with the laser
combiner is to make a time lapse with a switch between 2 intensities
configurations.</span></p>
<p style="margin-left: 72pt; text-indent: -18pt;"><span style="font-size: 11pt; font-family: Symbol; color: rgb(31, 73, 125);"><span>·<span>
</span></span></span><span style="font-size: 11pt; color: rgb(31, 73, 125);">Our clients also have the possibility to control multiple LEDs
what would define in this case a "LEDCombiner". A LightCombiner
would also be better.</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);"></span></p></div></div></blockquote><div><br>
Good points. I agree with the more general name LightCombiner. My
earlier proposal would have a LightCombiner made up of LightSources via
LightSourceRefs, meaning a given LightCombiner would have fixed
wavelength and attenuation for each component light source. Is that
realistic? Or do you typically adjust the wavelength and attenuation of
each component light source within a defined combiner module?<br>
<br>
If you do adjust them, we would need a mechanism for enumerating the
settings for each component light source for a given LogicalChannel.
The easiest way I can think of to model that at the moment would be to
have a LightCombinerRef element with LightSourceRef children
identifying the component light sources and their settings. The ID of
the LightCombinerRef would reference a LightCombiner (part of your
Instrument), but the LightCombiner itself would not necessarily need to
identify its components, since they are enumerated in each Ref. Or it
could enumerate them there too using LightSourceRefs without any
particular wavelength or attenuation values. Kind of ugly, but it gets the job done.<br>
<br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div link="blue" vlink="purple" lang="EN-US"><div>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">About Tile:</span></p>
<p style="margin-left: 72pt; text-indent: -18pt;"><span style="font-size: 11pt; font-family: Symbol; color: rgb(31, 73, 125);"><span>·<span>
</span></span></span><span style="font-size: 11pt; color: rgb(31, 73, 125);">Each acquired picture of a scanned region have different times
but the T dimension is reserved to indicate a loop on the scan (the region is
scanned several times thus giving information about the evolution of the sample
on a large region over the time).</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);"></span></p></div></div></blockquote><div><br>What we really need is explicit support for tiled Images. It is something that would be good to support anyway, since some third party formats use it, and ideally Bio-Formats would properly represent tiled images within the OME data model. Anyone else on the list want to propose such an extension to the XML schema?<br>
<br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div link="blue" vlink="purple" lang="EN-US"><div>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">A last question: will my pictures still be loaded on OMERO if I
have a number of ChannelComponent different from SizeC (I understand that this
cannot be interpreted but are the additional ChannelComponent ignored or does
it produce an error) ?</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);"></span></p></div></div></blockquote><div><br>
I have no idea; perhaps one of the OMERO developers can comment. I
would suggest trying it yourself, but unless you want to write some
Java code, it would be easiest to wait until import of OME-XML and
OME-TIFF are supported within OMERO (in Beta3, due this summer).<br>
<br>
</div>
<span style="font-size: 11pt; color: rgb(31, 73, 125);"></span>-Curtis<br><br><div class="gmail_quote">On Fri, Feb 22, 2008 at 11:48 AM, Pierre Menard <<a href="mailto:menard@till-photonics.com">menard@till-photonics.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div link="blue" vlink="purple" lang="EN-US">
<div>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">Thank you very much for your answer.</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">I just wanted to clear some points:</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">About an element LaserCombiner: </span></p>
<p style="margin-left: 72pt; text-indent: -18pt;"><span style="font-size: 11pt; font-family: Symbol; color: rgb(31, 73, 125);"><span>·<span>
</span></span></span><span style="font-size: 11pt; color: rgb(31, 73, 125);">The main problem is that the wavelength and Attenuation of the
light source are defined in the LightSourceRef element. If I have only one
LightSource element (the LaserCombiner), I can't indicate the intensities
of all lasers for a given LogicalChannel. The standard scenario with the laser
combiner is to make a time lapse with a switch between 2 intensities
configurations.</span></p>
<p style="margin-left: 72pt; text-indent: -18pt;"><span style="font-size: 11pt; font-family: Symbol; color: rgb(31, 73, 125);"><span>·<span>
</span></span></span><span style="font-size: 11pt; color: rgb(31, 73, 125);">Our clients also have the possibility to control multiple LEDs
what would define in this case a "LEDCombiner". A LightCombiner
would also be better.</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">About Tile:</span></p>
<p style="margin-left: 72pt; text-indent: -18pt;"><span style="font-size: 11pt; font-family: Symbol; color: rgb(31, 73, 125);"><span>·<span>
</span></span></span><span style="font-size: 11pt; color: rgb(31, 73, 125);">Each acquired picture of a scanned region have different times
but the T dimension is reserved to indicate a loop on the scan (the region is
scanned several times thus giving information about the evolution of the sample
on a large region over the time).</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">A last question: will my pictures still be loaded on OMERO if I
have a number of ChannelComponent different from SizeC (I understand that this
cannot be interpreted but are the additional ChannelComponent ignored or does
it produce an error) ?</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">Thank you again for your help</span></p><div class="Ih2E3d">
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);" lang="DE">Best Regards</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);" lang="DE"> </span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);" lang="DE">Pierre</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);" lang="DE"> </span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);" lang="DE"> </span></p>
<p><span style="font-size: 10pt; color: rgb(31, 73, 125);" lang="DE">-----------------------------------------</span><span style="font-size: 11pt; color: rgb(31, 73, 125);" lang="DE"></span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);" lang="DE">Pierre MENARD</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);" lang="DE">Software Entwickler</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">TILL Photonics GmbH</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">Lochhamer Shlag 19</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">D - 82166 Gräfelfing</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);"><a href="mailto:menard@till-photonics.com" target="_blank">menard@till-photonics.com</a></span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);" lang="DE"><a href="http://www.till-photonics.com" target="_blank">www.till-photonics.com</a></span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);" lang="DE"> </span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);" lang="DE">CEO: Dr. Rainer Uhl</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);" lang="DE">Amtsgericht München</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);" lang="DE">HRB-No. 104383</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);" lang="DE">Ust.-IdNo. </span><span style="font-size: 11pt; color: rgb(31, 73, 125);">DE 811580073</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">WEEE-Reg.-No DE 39138453</span></p>
<p><span style="font-size: 10pt; color: rgb(31, 73, 125);" lang="DE">-----------------------------------------</span><span style="font-size: 11pt; color: rgb(31, 73, 125);"></span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
</div><div style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
<p><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;">
<a href="mailto:ctrueden.wisc@gmail.com" target="_blank">ctrueden.wisc@gmail.com</a> [mailto:<a href="mailto:ctrueden.wisc@gmail.com" target="_blank">ctrueden.wisc@gmail.com</a>] <b>On Behalf Of </b>Curtis
Rueden<br>
<b>Sent:</b> Freitag, 22. Februar 2008 17:54<br>
<b>To:</b> Pierre Menard<br>
<b>Cc:</b> Andrew Patterson; Kevin Eliceiri; Jason Swedlow<div class="Ih2E3d"><br>
<b>Subject:</b> Re: OME-XML Schema questions</div></span></p>
</div>
<p> </p><div><div></div><div class="Wj3C7c">
<div>
<div>
<p>Hi Pierre,</p>
</div>
<blockquote style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color rgb(204, 204, 204); border-width: medium medium medium 1pt; padding: 0cm 0cm 0cm 6pt; margin-left: 4.8pt; margin-right: 0cm;">
<div>
<div>
<div>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<div>
<p style="text-indent: -18pt;"> <span style="font-family: Symbol;"> </span>Multiple LightSourceRef for a LogicalChannel</p>
<p style="margin-left: 36pt;">Most of our clients use a laser combiner to
acquire TIRF pictures meaning a channel is defined by several light sources
each with a given intensity. Is there a possibility to associate several
LightSourceRef to a single LogicalChannel ?</p>
</div>
</blockquote>
</div>
</div>
</div>
</blockquote>
<div>
<div>
<blockquote style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color rgb(204, 204, 204); border-width: medium medium medium 1pt; padding: 0cm 0cm 0cm 6pt; margin-left: 4.8pt; margin-right: 0cm;">
<div>
<div>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">With a laser combiner, there
are of course several channels (for the light source) but the CCD camera is
only acquiring one picture thus one channel in my Pixel array (SizeC = 1).</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">Or should I define a
LogicalChannel for each laser, each one containing a ChannelComponent pointing
to the same channel dimension of the Pixel array (meaning there can be several
LogicalChannel for the same channel dimension of the Pixel array) ?</span></p>
</div>
</div>
</blockquote>
</div>
<p>There would not be multiple ChannelComponents -- they are
typically used for the opposite of your scenario: one detector (e.g., a color
camera) producing multiple ultimate intensity values (e.g., red, green and
blue). The general rule is that the number of ChannelComponents must equal
SizeC. Since your SizeC is 1, you have a single LogicalChannel with one
ChannelComponent.<br>
<br>
So we are back to the original problem of representing your laser combiner's
component light sources. To do it properly, we should probably add a new kind
of LightSource called LaserCombiner that allows you to list light sources that
define it. Then LogicalChannel continues to need only a single LightSource
reference (to the LaserCombiner), but you can still express exactly which light
sources are involved with the channel.<br>
<br>
I have CCed Kevin Eliceiri, who knows more about optics and microscopy
techniques. Kevin and Andrew, any comments?</p>
</div>
<blockquote style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color rgb(204, 204, 204); border-width: medium medium medium 1pt; padding: 0cm 0cm 0cm 6pt; margin-left: 4.8pt; margin-right: 0cm;">
<div>
<div>
<div>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<div>
<p style="text-indent: -18pt;"><span style="font-family: Symbol;">·</span> <span style="font-family: Symbol;"> </span>Polygon ROI</p>
<p style="margin-left: 36pt;">Our software can perform FRAP on polygons. Will
it be possible in OME-XML to define polygon ROIs (list of points) ?</p>
</div>
</blockquote>
</div>
</div>
</div>
</blockquote>
<div>
<p>It will be possible, but there is no standard yet. We have
had some thorough discussions on the best way to add more complex ROIs
(non-rectangular, multidimensional, potentially disjoint, etc.) to the schema, but
do not yet have a solution. It is something we want to add soon, as both OMERO
and VisBio now both have similar manual annotation tools that could make use of
it.</p>
</div>
<blockquote style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color rgb(204, 204, 204); border-width: medium medium medium 1pt; padding: 0cm 0cm 0cm 6pt; margin-left: 4.8pt; margin-right: 0cm;">
<div>
<div>
<div>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<div>
<p style="text-indent: -18pt;"><span style="font-family: Symbol;">·</span> <span style="font-family: Symbol;"> </span>Tiled pictures</p>
<p>Is it possible in the OME schema to have several pictures in a single ZCT
plane. It is common for our clients to scan a XY region, thus acquiring several
pictures with the same Z, the same C and the same T information. These pictures
are then stitched in a single picture but we would like to conserve the
original pictures. The only way we found in OME is to define a Pixels element
for each XY position but we then lose the logic of the data.</p>
</div>
</blockquote>
</div>
</div>
</div>
</blockquote>
</div>
<p style="margin-bottom: 12pt;">As of the 2007-06 schema
version, you can specify a custom stage position for each plane in the pixels
set. When you say the pictures have "the same T information," is that
really true, since it takes a non-zero amount of time to scan the region? If
not, one way is to have a separate time point for each XY position. But then it
would be up to the client to reconstruct the images properly. Andrew, do you
know a better way?<br>
<br>
Another possibility could be to store each composite image plane as a single
image plane in the OME-TIFF file, but use TIFF's tiling capability to store
each piece of the image plane as its own tile. (Are the tiles all the same
size?) But then you are not annotating in the metadata why the image planes are
tiled like that, unless you introduce a custom semantic type for it somewhere.<br>
<br>
-Curtis</p>
<div>
<p>On Tue, Feb 19, 2008 at 4:56 PM, Jason Swedlow <<a href="mailto:jason@lifesci.dundee.ac.uk" target="_blank">jason@lifesci.dundee.ac.uk</a>>
wrote:</p>
<div>
<p>Hi Pierre-</p>
<div>
<p> </p>
</div>
<div>
<p>Thanks for your email.</p>
</div>
<div>
<p> </p>
</div>
<div>
<p>I am cc'ing your email to Andrew Patterson, who covers
OME-XML and Curtis Rueden, who covers OME-TIFF.</p>
</div>
<div>
<p> </p>
</div>
<div>
<p>I am pretty sure that most of what you want is already in
there, but they are the experts and can confirm. See for example:</p>
</div>
<div>
<p> </p>
</div>
<div>
<div>
<p><span style="font-size: 9pt;"><a href="http://www.openmicroscopy.org/Schemas/OME/2007-06/ome.xsd" target="_blank">http://www.openmicroscopy.org/Schemas/OME/2007-06/ome.xsd</a></span></p>
</div>
<div>
<p> </p>
</div>
<div>
<p><span>Documentation
is available:</span></p>
</div>
<div>
<p> </p>
</div>
<div>
<div>
<p><span style="font-size: 9pt;"><a href="http://www.openmicroscopy.org/Schemas/" target="_blank">http://www.openmicroscopy.org/Schemas/</a></span><span></span></p>
</div>
<div>
<p><span> </span></p>
</div>
<div>
<p><span>I am
confused on the first issue-- I can see the use of a laser combiner, but is a
single channel coming from multiple lasers? Maybe I missed your point.
</span></p>
</div>
<div>
<p><span> </span></p>
</div>
<div>
<p><span>Cheers,</span></p>
</div>
<div>
<p><span> </span></p>
</div>
<div>
<p><span>Jason</span></p>
</div>
</div>
<div>
<p> </p>
</div>
<div>
<p> </p>
</div>
<div>
<div>
<p>On 19 Feb 2008, at 15:09, Pierre Menard wrote:</p>
</div>
<p><br>
<br>
</p>
<div>
<p>Hi,</p>
<p> </p>
<p>We are currently developing a new software to control our microscopy
environment and we decided to use OME-XML and OME-TIFF as default metadata
format. We still have problem to integrate some of our data. Could you please
inform us if a changes are planned for the following points or if a solution
already exists ?</p>
<p> </p>
<p style="text-indent: -18pt;"><span style="font-family: Symbol;">·</span> <span style="font-family: Symbol;"> </span>Multiple LightSourceRef for a LogicalChannel</p>
<p style="margin-left: 36pt;">Most of our clients use a laser combiner to
acquire TIRF pictures meaning a channel is defined by several light sources
each with a given intensity. Is there a possibility to associate several
LightSourceRef to a single LogicalChannel ?</p>
<p> </p>
<p style="text-indent: -18pt;"><span style="font-family: Symbol;">·</span> <span style="font-family: Symbol;"> </span>Polygon ROI</p>
<p style="margin-left: 36pt;">Our software can perform FRAP on polygons. Will
it be possible in OME-XML to define polygon ROIs (list of points) ?</p>
<p style="margin-left: 36pt;"> </p>
<p style="text-indent: -18pt;"><span style="font-family: Symbol;">·</span> <span style="font-family: Symbol;"> </span>Tiled pictures</p>
<p>Is it possible in the OME schema to have several pictures in a single ZCT
plane. It is common for our clients to scan a XY region, thus acquiring several
pictures with the same Z, the same C and the same T information. These pictures
are then stitched in a single picture but we would like to conserve the
original pictures. The only way we found in OME is to define a Pixels element
for each XY position but we then lose the logic of the data.</p>
<p> </p>
<p>Thank you for your help</p>
<p> </p>
<p>Best Regards</p>
<p> </p>
<p> </p>
<p><span style="font-size: 10pt;" lang="DE">-----------------------------------------</span></p>
<p><span lang="DE">Pierre MENARD</span></p>
<p><span lang="DE">Software Entwickler</span></p>
<p><span lang="DE">TILL Photonics GmbH</span></p>
<p><span lang="DE">Lochhamer Shlag 19</span></p>
<p><span lang="DE">D - 82166 Gräfelfing</span></p>
<p><span lang="DE"><a href="mailto:menard@till-photonics.com" target="_blank">menard@till-photonics.com</a></span></p>
<p><span lang="DE"><a href="http://www.till-photonics.com" target="_blank">www.till-photonics.com</a></span></p>
<p><span lang="DE"> </span></p>
<p><span lang="DE">CEO: Dr. Rainer Uhl</span></p>
<p><span lang="DE">Amtsgericht München</span></p>
<p><span lang="DE">HRB-No. 104383</span></p>
<p><span lang="DE">Ust.-IdNo. </span>DE 811580073</p>
<p>WEEE-Reg.-No DE 39138453</p>
<p><span style="font-size: 10pt;" lang="DE">-----------------------------------------</span></p>
<p> </p>
</div>
</div>
<p> </p>
<div>
<p><span style="font-size: 9pt; color: black;"> </span></p>
<div>
<p><span style="font-size: 9pt; color: black;"> </span></p>
</div>
<div>
<p><span style="font-size: 9pt; color: black;">**************************</span></p>
</div>
<div>
<p><span style="font-size: 9pt; color: black;">Wellcome Trust Centre for Gene Regulation & Expression</span><span style="font-size: 9pt; color: black;"></span></p>
</div>
<div>
<p><span style="font-size: 9pt; color: black;">College of Life Sciences</span><span style="font-size: 9pt; color: black;"></span></p>
</div>
<div>
<p><span style="font-size: 9pt; color: black;">MSI/WTB/JBC Complex</span><span style="font-size: 9pt; color: black;"></span></p>
</div>
<div>
<p><span style="font-size: 9pt; color: black;">University of Dundee</span></p>
</div>
<div>
<p><span style="font-size: 9pt; color: black;">Dow Street</span></p>
</div>
<div>
<p><span style="font-size: 9pt; color: black;">Dundee DD1 5EH</span></p>
</div>
<div>
<p><span style="font-size: 9pt; color: black;">United Kingdom</span></p>
</div>
<div>
<p><span style="font-size: 9pt; color: black;"> </span></p>
</div>
<div>
<p><span style="font-size: 9pt; color: black;">phone (01382) 385819</span></p>
</div>
<div>
<p><span style="font-size: 9pt; color: black;">Intl phone: 44 1382 385819 </span></p>
</div>
<div>
<p><span style="font-size: 9pt; color: black;">FAX (01382) 388072 </span></p>
</div>
<div>
<p><span style="font-size: 9pt; color: black;">email: <a href="mailto:jason@lifesci.dundee.ac.uk" target="_blank">jason@lifesci.dundee.ac.uk</a></span></p>
</div>
<div>
<p><span style="font-size: 9pt; color: black;"> </span></p>
</div>
<div>
<p><span style="font-size: 9pt; color: black;">Lab Page: <a href="http://www.dundee.ac.uk/lifesciences/swedlow/" target="_blank">http://www.dundee.ac.uk/lifesciences/swedlow/</a></span></p>
</div>
<div>
<p><span style="font-size: 9pt; color: black;">Open Microscopy Environment: <a href="http://openmicroscopy.org" target="_blank">http://openmicroscopy.org</a></span></p>
</div>
<div>
<p><span style="font-size: 9pt; color: black;">**************************</span></p>
</div>
<p> </p>
</div>
<p> </p>
</div>
</div>
</div>
<p> </p>
</div></div></div>
</div>
</blockquote></div><br>