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Hi Ian,<br>
<br>
Thanks, yes that is typically my first value as well. With a few
types of fluorescent signals this doesn't produce good results (e.g.
FISH labeling or other very sparse punctate labeling) so I'm trying
to come up with something that has some intelligence built-in.
Currently working on a way using Josh's example code to get the min
and max intensity values for a large set of images from
screens/plates but I'm now thinking I'll need the actual histograms
to provide an input to that "intelligence".<br>
<br>
Cheers,<br>
- Damir<br>
<br>
<div class="moz-cite-prefix">On 8/16/2017 2:07, Munro, Ian wrote:<br>
</div>
<blockquote type="cite"
cite="mid:3D4E298F-7AFA-4E51-A4D7-B5AD13CEA09E@imperial.ac.uk">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
I’m afraid I haven’t been following the whole discussion but, in
case it helps…
<div class="">We’ve found that scaling the displayed intensity to
something like the 99th percentile of actual maximum intensity</div>
<div class=""> does a reasonable job of producing an “acceptable”
image without user intevention.</div>
<div class=""><br class="">
</div>
<div class="">Best Wishes</div>
<div class=""><br class="">
</div>
<div class="">Ian</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div>
<blockquote type="cite" class="">
<div class="">On 16 Aug 2017, at 07:47, Damir Sudar <<a
href="mailto:dsudar@lbl.gov" class=""
moz-do-not-send="true">dsudar@lbl.gov</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" style="font-family: Helvetica; font-size:
13px; font-style: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans:
auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;"
class="">
Hi Josh,
<div class=""><br class="">
</div>
<div class="">> <span style="font-size:
12.800000190734863px;" class="">Something like </span><a
href="https://github.com/ome/scripts/pull/103"
rel="noreferrer" target="_blank" style="font-size:
12.800000190734863px;" class=""
moz-do-not-send="true">https://github.com/ome/<wbr
class="">scripts/pull/103</a><span
style="font-size: 12.800000190734863px;" class=""> (also
unmerged)</span></div>
<br style="font-size: 12.800000190734863px;" class="">
<div class="">Yes, that's a great starting point,
thanks!. That's actually an interesting discussion in
there.</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class="">- Damir</div>
</div>
<div class="gmail_extra" style="font-family: Helvetica;
font-size: 13px; font-style: normal; font-variant-caps:
normal; font-weight: normal; letter-spacing: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<br class="">
<div class="gmail_quote">On Tue, Aug 15, 2017 at 8:16
AM, Josh Moore<span class="Apple-converted-space"> </span><span
dir="ltr" class=""><<a
href="mailto:josh@glencoesoftware.com"
target="_blank" class="" moz-do-not-send="true">josh@glencoesoftware.com</a>></span><span
class="Apple-converted-space"> </span>wrote:<br
class="">
<blockquote class="gmail_quote" style="margin: 0px 0px
0px 0.8ex; border-left-width: 1px;
border-left-color: rgb(204, 204, 204);
border-left-style: solid; padding-left: 1ex;">
Hi Damir,<br class="">
<br class="">
On Fri, Aug 11, 2017 at 6:15 PM, Damir Sudar <<a
href="mailto:dsudar@lbl.gov" class=""
moz-do-not-send="true">dsudar@lbl.gov</a>>
wrote:<br class="">
> Hi Josh,<br class="">
><br class="">
> On 8/11/2017 8:32, Josh Moore wrote:<br
class="">
...<br class="">
>>> Now the philosophical question: as in
IDR, we have a very large image<br class="">
>>> dataset that we are quantitatively
analyzing and also want to show<br class="">
>>> visually.<br class="">
>>> This is part of a large project to
asses the effects of a set of<br class="">
>>> perturbing<br class="">
>>> agents (perturbagens) on a panel cell
lines, where in our case a large<br class="">
>>> panel<br class="">
>>> of different microenvironment
components and drugs are used as the<br class="">
>>> perturbagens. During import into OMERO
each image gets its rendering<br class="">
>>> settings from the min/max values in the
image itself so all images have<br class="">
>>> different settings and the unsuspecting
viewer may see all kinds of<br class="">
>>> interesting intensity effects that are
mostly fake while real effects may<br class="">
>>> be<br class="">
>>> masked. So I'm looking for a general
way to set the rendering settings<br class="">
>>> across the entire experiment to
something that allows comparing images<br class="">
>>> but<br class="">
>>> doesn't generate loads of black and
over-exposed-looking images. I was<br class="">
>>> thinking that you guys encountered this
same issue with many of the IDR<br class="">
>>> datasets so was hoping for some wise
thoughts.<br class="">
>><br class="">
>> We definitely do but per study, and
typically we can only define that<br class="">
>> after visual inspection since they are
external datasets. You're<br class="">
>> looking to set something *before import*?<br
class="">
><br class="">
><br class="">
> No, after import makes more sense since one
doesn't really know what the<br class="">
> expected min and max values and desired range
setting are going to be, just<br class="">
> as you said. We have been playing with ideas
such as:<br class="">
> - we could look at the min and max values per
channel across a "set" of<br class="">
> wells/plates (tbd what a "set" means) and set
the rendering settings to be<br class="">
> at 2% - 98% (or something) of those values. I'd
need to write a script to<br class="">
> extract such min/max values for a "set" of
plates and then we could test<br class="">
> what those percent values should be for a
pleasing result.<br class="">
<br class="">
Something like<span class="Apple-converted-space"> </span><a
href="https://github.com/ome/scripts/pull/103"
rel="noreferrer" target="_blank" class=""
moz-do-not-send="true">https://github.com/ome/<wbr
class="">scripts/pull/103</a><span
class="Apple-converted-space"> </span>(also
unmerged)<br class="">
<br class="">
<br class="">
> - question to answer then is: what is a "set"
and we're back to different<br class="">
> rendering settings when you do want to compare
images across "sets".<br class="">
> - one option is to let an external
query/visualization tool set the<br class="">
> rendering settings. The OMERO webgateway allows
you to query the min/max<br class="">
> (via a JSON query) and set the rendering
settings via the UR. So that would<br class="">
> rely on an external visualization software do
the "right" thing.<br class="">
> Just to give you an idea of the data we're
dealing with, check out our<br class="">
> AWS-hosted public server at:<br class="">
><span class="Apple-converted-space"> </span><a
href="https://omero.lincsclarion.org/webclient/userdata/?experimenter=52"
rel="noreferrer" target="_blank" class=""
moz-do-not-send="true">https://omero.lincsclarion.<wbr
class="">org/webclient/userdata/?<wbr class="">experimenter=52</a><br
class="">
> The front-end portal with query/visualization
tools is still being built.<br class="">
<br class="">
Looking forward to it!<br class="">
<br class="">
<br class="">
>>> Anyway, this is why I'm so interested
in the render.py utility and thus<br class="">
>>> my hope it will make it to
production-level soon.<br class="">
>><br class="">
>> I don't have a timeline for you on the
production status of render.py,<br class="">
>> but what we *would* like to do for 5.4 is
make it separately<br class="">
>> installable, so that you can upgrade just
render.py as we releases<br class="">
>> fixes without needing to update all of
OMERO.<br class="">
><br class="">
><br class="">
> That sounds like a great approach.<br class="">
<br class="">
We'll keep you posted.<br class="">
<br class="">
<br class="">
>> P.S. from your Jul 12th email while I was
on vacation:<br class="">
>><br class="">
>>> Meanwhile, I had kludged together a
regular OMERO script<br class="">
>>> (HCS_Render_Settings.py) that does a
number of the things that the render.py<br class="">
>>> plugin does but much much less
elegantly and very slowly. I'll use that for<br
class="">
>>> now. That script is on:<span
class="Apple-converted-space"> </span><a
href="https://github.com/dsudar/OMEROscripts"
rel="noreferrer" target="_blank" class=""
moz-do-not-send="true">https://github.com/dsudar/<wbr
class="">OMEROscripts</a><br class="">
>><br class="">
>> There's no inherent reason a script should
be slower that the CLI. Do<br class="">
>> you have specifics?<br class="">
><br class="">
><br class="">
> I think it's mostly that my script is not at
all efficiently implemented<br class="">
> where it does repeated calls to objects to
first get metadata (such as value<br class="">
> ranges) and then again to set values and
probably causes multiple thumbnail<br class="">
> creation calls.<br class="">
<br class="">
Understood. ~J<br class="">
<br class="">
<br class="">
<br class="">
> Cheers,<br class="">
> - Damir<br class="">
><br class="">
>>> On 7/10/2017 6:45, Josh Moore wrote:<br
class="">
>>>><br class="">
>>>><br class="">
>>>>> Next I tried a few of the basic
commands of the render plugin:<br class="">
>>>>> 1 ---<br class="">
>>>><br class="">
>>>> ...<br class="">
>>>>><br class="">
>>>>> File<br class="">
>>>>> "/home/omero_user/OMERO.<wbr
class="">server/lib/python/omero/<wbr class="">plugins/render.py",<br
class="">
>>>>> line 117, in init_from_channel<br
class="">
>>>>> self.min =
channel.getWindowMin()<br class="">
>>>><br class="">
>>>> ...<br class="">
>>>>><br class="">
>>>>> omero.UnloadedEntityException:
Object unloaded:object #0<br class="">
>>>><br class="">
>>>> Vanilla 5.2 is not loading the
necessary metadata for the plugin to<br class="">
>>>> work. Unfortunately, solving this
isn't as simple as copying a new<br class="">
>>>> file into your installation. In
fact, I haven't yet found a smoking<br class="">
>>>> gun between the versions.<br
class="">
>>>><br class="">
>>>><br class="">
>>>>> 2---<br class="">
>>>>> AttributeError: 'ImageI' object
has no attribute '_closeRE'<br class="">
>>>>> ---<br class="">
>>>><br class="">
>>>> Here again, changes from 5.3 are
not available in your version, though<br class="">
>>>> at least these I know where they
come from.<br class="">
>>>><br class="">
>>>><br class="">
>>>>> Rather than trying more of
this, I thought to check with you first<br class="">
>>>>> whether<br class="">
>>>>> I'm missing something
fundamental.<br class="">
>>>><br class="">
>>>> 5.3 :) (or the upcoming 5.4)<br
class="">
>>>><br class="">
>>>> Fundamentally, the plugin is not
production quality and has only been<br class="">
>>>> used in isolated situations. We
certainly intend to get it into the<br class="">
>>>> testing pipeline for 5.4 but that's
not likely to uncover what's going<br class="">
>>>> on with 5.2. If you or anyone on
your side wants to continue digging,<br class="">
>>>> we're happy to evaluate your
changes, but there's a question of how<br class="">
>>>> far you want to go in modifying
your local installation.<br class="">
>>>><br class="">
>>>> Cheers,<br class="">
>>>> ~Josh.<br class="">
>>>><br class="">
>>>><br class="">
>>>><br class="">
>>>>> Thanks,<br class="">
>>>>> - Damir<br class="">
>>>>><br class="">
>>>>> On 6/2/2017 2:35, Simon Li
wrote:<br class="">
>>>>><br class="">
>>>>> The render plugin (not tested
on 5.3):<br class="">
>>>>><br class="">
>>>>><br class="">
>>>>><span
class="Apple-converted-space"> </span><a
href="https://github.com/openmicroscopy/openmicroscopy/blob/metadata53/components/tools/OmeroPy/src/omero/plugins/render.py"
rel="noreferrer" target="_blank" class=""
moz-do-not-send="true">https://github.com/<wbr
class="">openmicroscopy/openmicroscopy/<wbr
class="">blob/metadata53/components/<wbr
class="">tools/OmeroPy/src/omero/<wbr class="">plugins/render.py</a><br
class="">
>>>>> Try dropping this into
OMERO.server/lib/python/omero/<wbr class="">plugins/<br
class="">
>>>>><br class="">
>>>>> Example YAML render settings
file:<br class="">
>>>>><br class="">
>>>>><br class="">
>>>>><span
class="Apple-converted-space"> </span><a
href="https://github.com/IDR/idr-metadata/blob/master/idr0015-UNKNOWN-taraoceans/screenA/idr0015-screenA-renderdef.yml"
rel="noreferrer" target="_blank" class=""
moz-do-not-send="true">https://github.com/IDR/idr-<wbr
class="">metadata/blob/master/idr0015-<wbr
class="">UNKNOWN-taraoceans/screenA/<wbr
class="">idr0015-screenA-renderdef.yml</a><br
class="">
>>>>><br class="">
>>>>> omero render edit --help<br
class="">
>>>>> omero render edit --copy
Plate:1 renderdef.yml<br class="">
>>>>> omero render copy Image:SrcID
Plate:TargetID<br class="">
><br class="">
<span class="HOEnZb"><font class="" color="#888888">><br
class="">
> --<br class="">
> Damir Sudar - Affiliate Scientist<br
class="">
> Lawrence Berkeley Natl Laboratory / MBIB<br
class="">
> One Cyclotron Road, MS 977, Berkeley, CA
94720, USA<br class="">
> T:<span class="Apple-converted-space"> </span><a
href="tel:510%2F486-5346" value="+15104865346"
class="" moz-do-not-send="true">510/486-5346</a><span
class="Apple-converted-space"> </span>- F:<span
class="Apple-converted-space"> </span><a
href="tel:510%2F486-5586" value="+15104865586"
class="" moz-do-not-send="true">510/486-5586</a><span
class="Apple-converted-space"> </span>- E:<span
class="Apple-converted-space"> </span><a
href="mailto:DSudar@lbl.gov" class=""
moz-do-not-send="true">DSudar@lbl.gov</a><br
class="">
><span class="Apple-converted-space"> </span><a
href="http://biosciences.lbl.gov/profiles/damir-sudar-2/"
rel="noreferrer" target="_blank" class=""
moz-do-not-send="true">http://biosciences.lbl.gov/<wbr
class="">profiles/damir-sudar-2/</a><br
class="">
><br class="">
> Visiting Scientist, Oregon Health &
Science University<br class="">
><br class="">
</font></span></blockquote>
</div>
<br class="">
<br class="" clear="all">
<div class=""><br class="">
</div>
--<span class="Apple-converted-space"> </span><br
class="">
<div class="gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">Damir Sudar -
Affiliate Staff Scientist<br
class="">
Lawrence Berkeley National
Laboratory<br class="">
One Cyclotron Road, MS 977,
Berkeley, CA 94720, USA<br class="">
T: 510/486-5346 - F: 510/486-5586 -
E:<span
class="Apple-converted-space"> </span><a
href="mailto:DSudar@lbl.gov"
target="_blank" class=""
moz-do-not-send="true">DSudar@lbl.gov</a><br
class="">
<br class="">
</div>
</div>
<div class="">Visiting Scientist, Oregon
Health and Science University</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
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<br>
<pre class="moz-signature" cols="72">--
Damir Sudar - Affiliate Scientist
Lawrence Berkeley Natl Laboratory / MBIB
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: <a class="moz-txt-link-abbreviated" href="mailto:DSudar@lbl.gov">DSudar@lbl.gov</a>
<a class="moz-txt-link-freetext" href="http://biosciences.lbl.gov/profiles/damir-sudar-2/">http://biosciences.lbl.gov/profiles/damir-sudar-2/</a>
Visiting Scientist, Oregon Health & Science University</pre>
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