Exports from within acquisition programs vs. Imagej etc

[Avi Jacob]

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Hey all,

Recently I had a conversation with an application specialist from one of
the main manufacturers. I have been having serious issues for quite a while
now with their export system.

He expressed some surprise that I insist on "exporting to tiff" from within
the acquisition program, instead of opening the original microscope file
(e.g. LIF, OIF, CZI, ND2, etc) in any of the many image processing programs
and exporting from there. I have found that well-acquired images do not
need much processing other than scaling (of course all scaling across same
color ch's is the same). So, why not use the built-in export?

Even when doing critical analysis I will usually export RAW tiff files and
analyze those, though when using Imaris or Huygens I *will* use the
original files.

I was wondering what other people do. How do you export?

Cheers,
Avi

--
Avi Jacob, Ph.D.
Head of The Kanbar Light Microscopy Unit
The Mina & Everard Goodman Faculty of Life Sciences
Bar-Ilan University,  Israel

[Arne Seitz]

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Dear Avi,

I prefer opening the original microscope files in any of the many image processing programs.

Exporting images is an additional step which either blocks the microscope or needs an off-line version of the microscope software. Plus you duplicate you data at least if you keep the original data which is currently what we advise or users to do.
The larger the data gets the more time it takes to export and the more disk-space is occupied.
We have users acquiring data over night or even days and I clearly do not want them blocking the microscope with exporting their data.

In addition: any export might screw up the metadata.

So I tend to avoid exporting image data whenever possible.

Just my 2c.

Best
Arne  

-----Original Message-----
From: Confocal Microscopy List <[hidden email]> On Behalf Of Avi Jacob
Sent: Donnerstag, 16. Januar 2020 08:56
To: [hidden email]
Subject: Exports from within acquisition programs vs. Imagej etc

*****
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*****

Hey all,

Recently I had a conversation with an application specialist from one of the main manufacturers. I have been having serious issues for quite a while now with their export system.

He expressed some surprise that I insist on "exporting to tiff" from within the acquisition program, instead of opening the original microscope file (e.g. LIF, OIF, CZI, ND2, etc) in any of the many image processing programs and exporting from there. I have found that well-acquired images do not need much processing other than scaling (of course all scaling across same color ch's is the same). So, why not use the built-in export?

Even when doing critical analysis I will usually export RAW tiff files and analyze those, though when using Imaris or Huygens I *will* use the original files.

I was wondering what other people do. How do you export?

Cheers,
Avi

--
Avi Jacob, Ph.D.
Head of The Kanbar Light Microscopy Unit The Mina & Everard Goodman Faculty of Life Sciences Bar-Ilan University,  Israel

[Benjamin Smith]

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One other advantage to using the manufacturer file types is that all of the
metadata stays with the file, which can be read with Biofromats.  This is
very helpful when writing papers, as it will tell you exactly the laser
lines, objective, etc. that were used to acquire the image, and helps in
troubleshooting when one image set looks different from another.

Additionally, most modern scopes can read the metadata and configure the
scope back to the exact setup that was used to acquire the image.  This is
very helpful when reviewer #3 starts asking for additional data

Finally, a lot of modern file types act as helpful canisters, keeping
multiple image stacks together in one place, etc.  This makes fewer files
to keep track of, and makes it much easier to reconstruct more complex
image structures such as tiled XYZT stacks..

-Ben Smith

On Thu, Jan 16, 2020 at 1:19 AM Seitz Arne <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Dear Avi,
>
> I prefer opening the original microscope files in any of the many image
> processing programs.
>
> Exporting images is an additional step which either blocks the microscope
> or needs an off-line version of the microscope software. Plus you duplicate
> you data at least if you keep the original data which is currently what we
> advise or users to do.
> The larger the data gets the more time it takes to export and the more
> disk-space is occupied.
> We have users acquiring data over night or even days and I clearly do not
> want them blocking the microscope with exporting their data.
>
> In addition: any export might screw up the metadata.
>
> So I tend to avoid exporting image data whenever possible.
>
> Just my 2c.
>
> Best
> Arne
>
> -----Original Message-----
> From: Confocal Microscopy List <[hidden email]> On
> Behalf Of Avi Jacob
> Sent: Donnerstag, 16. Januar 2020 08:56
> To: [hidden email]
> Subject: Exports from within acquisition programs vs. Imagej etc
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hey all,
>
> Recently I had a conversation with an application specialist from one of
> the main manufacturers. I have been having serious issues for quite a while
> now with their export system.
>
> He expressed some surprise that I insist on "exporting to tiff" from
> within the acquisition program, instead of opening the original microscope
> file (e.g. LIF, OIF, CZI, ND2, etc) in any of the many image processing
> programs and exporting from there. I have found that well-acquired images
> do not need much processing other than scaling (of course all scaling
> across same color ch's is the same). So, why not use the built-in export?
>
> Even when doing critical analysis I will usually export RAW tiff files and
> analyze those, though when using Imaris or Huygens I *will* use the
> original files.
>
> I was wondering what other people do. How do you export?
>
> Cheers,
> Avi
>
> --
> Avi Jacob, Ph.D.
> Head of The Kanbar Light Microscopy Unit The Mina & Everard Goodman
> Faculty of Life Sciences Bar-Ilan University,  Israel
>

--
Benjamin E. Smith, Ph. D.
Imaging Specialist, Vision Science
University of California, Berkeley
195 Life Sciences Addition
Berkeley, CA  94720-3200
Tel  [phone]
Fax [phone]
e-mail: [hidden email]
https://vision.berkeley.edu/faculty/core-grants-nei/core-grant-microscopic-imaging/

[Steffen Dietzel]

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*****

Same here. I strongly advise our users to always save in the
manufacturer's file format to make sure the meta data are kept. (Having
searched through >20 year old data I know how helpful this can be.) So
exporting to another file format would mean to double the needed disk
space (and time handling the data). This would make sense only if there
would be a significant advantage to have another, second format. I do
not see such an advantage in our applications.

Steffen


Am 16.01.2020 um 10:46 schrieb Benjamin Smith:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> One other advantage to using the manufacturer file types is that all of the
> metadata stays with the file, which can be read with Biofromats.  This is
> very helpful when writing papers, as it will tell you exactly the laser
> lines, objective, etc. that were used to acquire the image, and helps in
> troubleshooting when one image set looks different from another.
>
> Additionally, most modern scopes can read the metadata and configure the
> scope back to the exact setup that was used to acquire the image.  This is
> very helpful when reviewer #3 starts asking for additional data
>
> Finally, a lot of modern file types act as helpful canisters, keeping
> multiple image stacks together in one place, etc.  This makes fewer files
> to keep track of, and makes it much easier to reconstruct more complex
> image structures such as tiled XYZT stacks..
>
> -Ben Smith
>
> On Thu, Jan 16, 2020 at 1:19 AM Seitz Arne <[hidden email]> wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> Post images on http://www.imgur.com and include the link in your posting.
>> *****
>>
>> Dear Avi,
>>
>> I prefer opening the original microscope files in any of the many image
>> processing programs.
>>
>> Exporting images is an additional step which either blocks the microscope
>> or needs an off-line version of the microscope software. Plus you duplicate
>> you data at least if you keep the original data which is currently what we
>> advise or users to do.
>> The larger the data gets the more time it takes to export and the more
>> disk-space is occupied.
>> We have users acquiring data over night or even days and I clearly do not
>> want them blocking the microscope with exporting their data.
>>
>> In addition: any export might screw up the metadata.
>>
>> So I tend to avoid exporting image data whenever possible.
>>
>> Just my 2c.
>>
>> Best
>> Arne
>>
>> -----Original Message-----
>> From: Confocal Microscopy List <[hidden email]> On
>> Behalf Of Avi Jacob
>> Sent: Donnerstag, 16. Januar 2020 08:56
>> To: [hidden email]
>> Subject: Exports from within acquisition programs vs. Imagej etc
>>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> Post images on http://www.imgur.com and include the link in your posting.
>> *****
>>
>> Hey all,
>>
>> Recently I had a conversation with an application specialist from one of
>> the main manufacturers. I have been having serious issues for quite a while
>> now with their export system.
>>
>> He expressed some surprise that I insist on "exporting to tiff" from
>> within the acquisition program, instead of opening the original microscope
>> file (e.g. LIF, OIF, CZI, ND2, etc) in any of the many image processing
>> programs and exporting from there. I have found that well-acquired images
>> do not need much processing other than scaling (of course all scaling
>> across same color ch's is the same). So, why not use the built-in export?
>>
>> Even when doing critical analysis I will usually export RAW tiff files and
>> analyze those, though when using Imaris or Huygens I *will* use the
>> original files.
>>
>> I was wondering what other people do. How do you export?
>>
>> Cheers,
>> Avi
>>
>> --
>> Avi Jacob, Ph.D.
>> Head of The Kanbar Light Microscopy Unit The Mina & Everard Goodman
>> Faculty of Life Sciences Bar-Ilan University,  Israel
>>
>

--
------------------------------------------------------------
Steffen Dietzel, PD Dr. rer. nat
Ludwig-Maximilians-Universität München
Biomedical Center (BMC)
Head of the Core Facility Bioimaging

Großhaderner Straße 9
D-82152 Planegg-Martinsried
Germany

http://www.bioimaging.bmc.med.uni-muenchen.de