[ome-users] Fwd: a couple of questions on LOCI

Tue Dec 4 23:20:02 GMT 2012

---------- Forwarded message ----------
From: Bergson, Clare <CBERGSON at georgiahealth.edu>
Date: Tue, Dec 4, 2012 at 2:44 PM
Subject: Fwd: a couple of questions on LOCI
To: Curtis Rueden <ctrueden at wisc.edu>

 hi Curtis, please find attached the apl files in question. Thanks so much
for helping me with this.  do you want me to send one of the tif files. it
is ~1GB... i could transfer it to dropbox...thanks! clare

Begin forwarded message:

 *From: *"Bergson, Clare" <CBERGSON at georgiahealth.edu>
 *Subject: **Re: a couple of questions on LOCI*
 *Date: *November 29, 2012 11:34:57 AM EST
 *To: *Philip Smith <PJS704 at bham.ac.uk>

 hi Philip, super and thanks for being so generous with your time. Please
find my apl, ldb, and mtb files attached. All are under 200 kb. I don't
know why there are so many ldb files??? but i do remember backing up the
data a few times just to make sure....ha ha...hope it can be opened! :-)
The data might still be on one of the hard drives of the Olympus....Also,
Guilio kindly offered to back it up onto his portable drive, so perhaps he
has it.  Anyway, THANK YOU!!!!! clare

On Nov 29, 2012, at 4:36 AM, Philip Smith wrote:

> Hi Clare,
>
> What size are your .apl files? The ones I have are only a couple of
hundred kilobytes, which definitely isn't big enough to hold images... Do
you remember what folder you took all of your files from? If I can end up
with the same thing as you on my computer then I'll be able to work through
it all with you.
>
> The other thing to try is to reveal all the hidden files- I think I
encountered this problem at one point.
> To show hidden files, just click on the Organize button in any folder,
and then select “Folder and Search Options” from the menu. Click the View
tab, and then you should select “Show hidden files and folders” in the
list. Just select that, and click OK. That should reveal all the .tif files
if the Olympus computer had them all set to 'hidden'.
>
> Let me know if that helps at all, if not I'll try something else!
>
> Best,
> Phil
>
----------------------------------------------------------------------------------------------
>
> Philip Smith
> PSIBS Doctoral Training Centre
> School of Chemistry
> University of Birmingham
> Birmingham
> B15 2TT
>
> ________________________________________
> From: Bergson, Clare [CBERGSON at georgiahealth.edu]
> Sent: Wednesday, November 28, 2012 11:14 PM
> To: Philip Smith
> Subject: Re: a couple of questions on LOCI
>
> Hi Phil, what's involved in unpacking the .apl databases into sets of tif
files? thanks, clare
> On Nov 27, 2012, at 5:15 AM, Philip Smith wrote:
>
>> Hi Clare,
>>
>> Sorry it's taken me a while to reply! Are you managing to access your
images successfully, or are you having problems with those as well as the
.apl, .mtb and .tnb files? I only open my images with ImageJ you see, but I
will have a go at getting into these other ones!
>>
>> Best,
>>
>> Phil
>>
>>
----------------------------------------------------------------------------------------------
>>
>> Philip Smith
>> PSIBS Doctoral Training Centre
>> School of Chemistry
>> University of Birmingham
>> Birmingham
>> B15 2TT
>> ________________________________
>> From: William Pitkeathly [WTP628 at bham.ac.uk]
>> Sent: Friday, November 16, 2012 7:00 PM
>> To: Bergson, Clare
>> Cc: pjs704 at bham.ac.uk
>> Subject: RE: a couple of questions on LOCI
>>
>> Hi Clare,
>>
>> Sorry for the delayed reply.
>>
>>> One question is of the saved  .apl, .mtb, or .tnb files, which one do i
ask it to import?
>>
>> These files are the ones which Olympus generates I think.. Im not 100%
sure which are which but you can usually work out which ones contain the
images as they are the largest in size. So try opening those with LOCI to
get the images out. I think the other files are to do with the experimental
settings. I am not too familiar with the Olympus setup (I just use the
nikon), so phil (CCd)  might have a batter idea.
>>
>>> What boxes do I check to open the database?
>>
>> try checking "Open files individually", this usually gives you a list of
images with check boxes so you can choose which ones you want to load.
>>
>> I think this might do the trick, if Phil could you tell Clare how to do
this.
>>
>> Regards,
>>
>> Eric
>>
>>
>>
>>
>>
>> ________________________________
>> From: Bergson, Clare [CBERGSON at georgiahealth.edu]
>> Sent: Thursday, November 15, 2012 2:28 PM
>> To: William Pitkeathly
>> Subject: a couple of questions on LOCI
>>
>> hi Eric, hope your day is going well....LOCI is running as a plugin on
Image J on my computer.  One question is of the saved  .apl, .mtb, or .tnb
files, which one do i ask it to import? Another question is on the '[cid:
2E90963B-0A1E-4597-ACC0-BA68E7B3B389 at georgiahealth.edu]BioFormats Import
Options' screen (see attached).  What boxes do i check to open the
database? Finally, is there a way to go from opening the database to
opening a particular image series (experiment)? If so, how? Thanks so much
for your help, and please say 'hi' to everyone there for me....clare
>> On Nov 6, 2012, at 9:07 AM, William Pitkeathly wrote:
>>
>> Hi Clare,
>>
>> In order to open the files you first need to install the LOCI tools
plugin for imageJ. This can be downloaded from
http://loci.wisc.edu/bio-formats/imagej
>> Basically you just download it and then place it in your plugins file
for imageJ then restart imageJ. Then you should be able to open the Olympus
files as if they were any other image.
>>
>> If you want to align the 2 channels for further analysis then let me
know and ill send you the latest version to Auto-Align ASAP. I made some
changes to it when you visited and havent tested it as a standalone plugin
yet.
>>
>> Any other questions then just drop me an email.
>>
>> Kind Regards,
>>
>> Eric
>>
>>
>>
>>
>> ________________________________________
>> From: Bergson, Clare [CBERGSON at georgiahealth.edu<
mailto:CBERGSON at georgiahealth.edu <CBERGSON at georgiahealth.edu>>]
>> Sent: Monday, November 05, 2012 8:48 PM
>> To: wtp628 at bham.ac.uk<mailto:wtp628 at bham.ac.uk <wtp628 at bham.ac.uk>>
>> Subject: opening olympus TIRF files in Image J?
>>
>> hi Eric, I hope this email finds you well. blast from the recent past!
Finally, i'm ready to start analyzing the TIRF data collected at the end of
September with Guilio. It would be great if you could let me know how to
open the Olympus database files in Image J....did once as soon as i got
back but to no avail....Thanks so much, Clare
>>
>
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