Thanks, Craig.
Ideally, I would like to automatically fit a two gaussian to each blob, and
integrate it to get the total relative contents of the blobs, which I could
then connect back with the known amount of standards added. For starters I was
able to read in the file using PDL::IO::Image (awesome) and rimage. I tried
using PDL::IO::Pic rim, but that spit out an error for some reason.
I sliced each column of the image and printed out the minimum value of the
image unit (RGB value? sorry, I’m not an expert in manipulating images!). This
spit out something that looked somewhat reasonable when graphed. Thus, I
should be able to grab out the index of the minimum paired with a column to fit
a the gaussian, but it there an easier way to do this?
I’m still a PDL newbie, so even slicing is not trivial for me at this point…
bah!
Demian
below is a copy paste from an IPerl Notebook (I hope it translates!).
In [31]:
use Modern::Perl;
use PDL;
use PDL::IO::Image;
In [32]:
my $pdl1 = rimage('Desktop/TLC_arg.jpg');
print $pdl1->info;
Out[32]:
PDL: Byte D [2625,116,3]
1
In [37]:
foreach my $ic (0 .. 2624){
my $col = min($pdl1->slice("$ic"));
print $col . "\n";
}
> On Apr 23, 2015, at 9:34 AM, Craig DeForest <[email protected]> wrote:
>
> How do you want to quantify them? E.g. are you doing photometry or are you
> doing geometry? PDL can help you either way. The “rim” function will load a
> color image (say a PNG or JPG) into a structured array. After that you can
> manipulate it. Simple geometric extraction or brightness extraction are easy
> after that.
>
>
>
>> On Apr 22, 2015, at 2:14 PM, Demian Riccardi <[email protected]>
>> wrote:
>>
>> Hello,
>>
>> A need has come up for analyzing some thin layer chromatography in one of my
>> chemistry labs (see the attached jpg; I know it isn’t perfect). Is there a
>> way I can pull in this image and automatically quantify the spots? Two of
>> the sets of four are standards and the other two are samples.
>>
>> I was able to load it in with PDL::IO::Image so I know there must be a way!
>>
>> Demian
>>
>> <TLC_arg.jpg>
>> ------------------------------------------------------------------------------
>> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
>> Develop your own process in accordance with the BPMN 2 standard
>> Learn Process modeling best practices with Bonita BPM through live exercises
>> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
>> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF_______________________________________________
>> pdl-general mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/pdl-general
>
------------------------------------------------------------------------------
BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through live exercises
http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
_______________________________________________
pdl-general mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/pdl-general
