Switch from 1.4->2.0g: autostretch and % Live View Window size

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Switch from 1.4->2.0g: autostretch and % Live View Window size

Loumarx
I'm trying to make the switch from 1.4 to 2.0g in three of our manual scopes
(with manual acquisition script), but I'm running into two issues not
present in 1.4:

1) MDA produces images with autostretch ALWAYS CHECKED. Even if we turn it
off prior to live view or acquisition it comes back on. How can we keep it
off when desired?

2) % live view window size control is no longer available in options, and
live or acquired images default to 100% -- which can be a pain in some
displays. How can we set a default size?

I tried nightlies 20190616->18.

Thank you
- Luís Marques



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Re: Switch from 1.4->2.0g: autostretch and % Live View Window size

Stuurman, Nico
Hi Luis,

> I'm trying to make the switch from 1.4 to 2.0g in three of our manual scopes
> (with manual acquisition script), but I'm running into two issues not
> present in 1.4:
>
> 1) MDA produces images with autostretch ALWAYS CHECKED. Even if we turn it
> off prior to live view or acquisition it comes back on. How can we keep it
> off when desired?

I can reproduce this and agree that it is very annoying.  I remember
fighting with the new code to make it always remember the last used
settings, but I clearly lost that fight.  Will look into this again soon.

> 2) % live view window size control is no longer available in options, and
> live or acquired images default to 100% -- which can be a pain in some
> displays. How can we set a default size?

Use the Plus and/or Minus zoom buttons in the top of the preview window
to set the desired size.  MM will remember size and position of the
Preview Windows, and you will get it again even after closing the
application.

Best,


Nico

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Re: Switch from 1.4->2.0g: autostretch and % Live View Window size

Loumarx
Nico, ty very much for the replies and your work.

Will check zoom % again tomorrow, but final MDA acquisition always goes to
100%, I think.

I'm going to try to wean users to 2.0g, but I KNOW they're going to freak
over the autostretch :D

Thank you!
- L



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Re: Switch from 1.4->2.0g: autostretch and % Live View Window size

Stuurman, Nico
On 6/19/19 10:12 AM, Loumarx wrote:
> Will check zoom % again tomorrow, but final MDA acquisition always goes to
> 100%, I think.

The behavior may have been a bit inconsistent.  I worked on it a bit,
and it should now be more predictable.  Things are still a bit strange
when you have multiple Acquisition Windows open.  The last window to
"report" its display settings will "win".
> I'm going to try to wean users to 2.0g, but I KNOW they're going to freak
> over the autostretch :D
That is fixed now and should be in tonight's build.  Whenever you change
display settings (including autostretch and zoom level), the next
acquisition will open the same way.  These settings are stored per
profile (so that it will look the same for each user individually).

Thanks for bringing this up!  It bothered me too, but never enough to do
something about it.


Best,

Nico



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Switch from 1.4->2.0g: saving files

Loumarx
[from other post: I can verify that autostretch and zoom are now behaving as
expected :)]

Some users have been having difficulties saving files (nightly 20190623):

1) Files / folders created by "Save files" under MDA have very weird [-1,1]
histogram values, which have to be reset in Fiji>Brightness and Contrast to
the proper image depth (it's a 12bit camera, saving files to a 16bit
container)

2) When users just want simple stack files in a single folder (with a chosen
name, no metadata, etc), they usually do an MDA and then simply Fiji>Save
As>Tiff. This is now semi-broken, as Fiji saves multi-channel but not
composite files (have to be Made Composite, and LUTs are incorrect). Is it
possible to retain proper Fiji>Save As>Tiff functionality?

Thank you
- L



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Re: Switch from 1.4->2.0g: saving files

Stuurman, Nico
On 6/25/19 4:10 AM, Loumarx wrote:

> [from other post: I can verify that autostretch and zoom are now behaving as
> expected :)]
>
> Some users have been having difficulties saving files (nightly 20190623):
>
> 1) Files / folders created by "Save files" under MDA have very weird [-1,1]
> histogram values, which have to be reset in Fiji>Brightness and Contrast to
> the proper image depth (it's a 12bit camera, saving files to a 16bit
> container)
>
> 2) When users just want simple stack files in a single folder (with a chosen
> name, no metadata, etc), they usually do an MDA and then simply Fiji>Save
> As>Tiff. This is now semi-broken, as Fiji saves multi-channel but not
> composite files (have to be Made Composite, and LUTs are incorrect). Is it
> possible to retain proper Fiji>Save As>Tiff functionality?

I guess you mean ImageJ rather than Fiji?  Or do you copy MM into a FIji
installation (or vice versa)?

Regretfully, integration of ImageJ/Micro-Manager data is more elusive
than ever.  Mark and Chris separated out the Micro-Manager data even
further from the ImageJ data structures, and there is no practical way
to make ImageJ>Save As>Tiff work on Micro-Manager data (other than
heavily hacking the ImageJ code). However, there now is a "copy to
ImageJ" command under the gear icon in the viewer.  Do that first, then
save in ImageJ/Fiji.  I think that will help you for both difficulties.

It would eventually be nice to be able to save in different ways, and
even have a mechanism so that the user can decide how to organize the
data on disk, but that will be a substantial amount of work, will be
hard to maintain, and is far beyond what I will be able to contribute.

Best,

Nico




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Re: Switch from 1.4->2.0g: saving files

Loumarx
Stuurman, Nico wrote
> I guess you mean ImageJ rather than Fiji?  Or do you copy MM into a FIji
> installation (or vice versa)?

Actually, the problem reported in 1) happens in both the resident ImageJ in
MM and in a standalone Fiji instalation in another computer.
It's probably something in the way the ome.tif is saved?: ImageJ's
Brightness & Contrast>Set>Unsigned 16-bit range to "Automatic" as default is
unable to correctly display the range. This did not happen before in 1.4.


Stuurman, Nico wrote
> However, there now is a "copy to
> ImageJ" command under the gear icon in the viewer.  Do that first, then
> save in ImageJ/Fiji.  I think that will help you for both difficulties.

Will do that, thank you. Still, depending on user feedback and ease of use,
it's likely I'll be pressured to keep the machines on 1.4... :(

- L




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Re: Switch from 1.4->2.0g: saving files

Loumarx
Can verify that "Send to ImageJ" produces a correct composite multichannel
image that can be readily saved as tiff.

For users counting on MDA "Save images" for straight-to-disk serial
acquisitions, is there anything we can do in MM configuration to make the
final ome.tiff files' 16-bit range be properly recognized by ImageJ, Fiji,
etc?

Thank you
- L



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Re: Switch from 1.4->2.0g: saving files

Loumarx
Regarding this issue, some more information:

- FIJI is unable to properly autodetect histogram ranges in n-channel
ome-tiff images auto saved from MDA. i.e. 12-bit images are set to [0
minimum,-1 maximum] in B&C
- if you set proper 16-bit range from Edit>Appearance, images open with
correct range and usual FIJI autoscale, but wrong LUTs (see below)
- if you enable SCIFIO, images open with correct range and the usual FIJI
autoscale, but wrong LUTs.

Problems:

- SCIFIO enabled breaks Bio-Formats image drag&drop to FIJI - B-F Importer
works.
- No LUT information from the ome-tiffs: FIJI assigns the usual R>G>B>C>M>Y
LUT order to the channels, regardless of what we set in MDA panel.

Is there a way to have the cake and eat it, i.e., auto-save images from MDA
which can be opened in FIJI with correct range and LUT assignment, without
breaking Bio-Formats drag&drop?

(*like we can still do in MM1.4??* :D)


Thank you




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Re: Switch from 1.4->2.0g: saving files

Stuurman, Nico
On 8/13/19 7:48 AM, Loumarx wrote:

> Regarding this issue, some more information:
>
> - FIJI is unable to properly autodetect histogram ranges in n-channel
> ome-tiff images auto saved from MDA. i.e. 12-bit images are set to [0
> minimum,-1 maximum] in B&C
> - if you set proper 16-bit range from Edit>Appearance, images open with
> correct range and usual FIJI autoscale, but wrong LUTs (see below)
> - if you enable SCIFIO, images open with correct range and the usual FIJI
> autoscale, but wrong LUTs.
>
> Problems:
>
> - SCIFIO enabled breaks Bio-Formats image drag&drop to FIJI - B-F Importer
> works.
> - No LUT information from the ome-tiffs: FIJI assigns the usual R>G>B>C>M>Y
> LUT order to the channels, regardless of what we set in MDA panel.
>
> Is there a way to have the cake and eat it, i.e., auto-save images from MDA
> which can be opened in FIJI with correct range and LUT assignment, without
> breaking Bio-Formats drag&drop?

I opened an issue on github
(https://github.com/nicost/micro-manager/issues/60).  Presumably, some
of the niceties tHat Henry Pinkard originally put into the multi-page
TIFF file saving code (it was an amazing feat to make these files
compatible with ome, Imagej, and Micro-Manager) have apparently been
lost in the refactoring leading up to 2.0-gamma. Would be super nice if
someone more knowledgeable then me would look into this...


Best,


Nico



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Re: Switch from 1.4->2.0g: saving files

Stuurman, Nico
In reply to this post by Loumarx
On 8/13/19 7:48 AM, Loumarx wrote:

> Regarding this issue, some more information:
>
> - FIJI is unable to properly autodetect histogram ranges in n-channel
> ome-tiff images auto saved from MDA. i.e. 12-bit images are set to [0
> minimum,-1 maximum] in B&C
> - if you set proper 16-bit range from Edit>Appearance, images open with
> correct range and usual FIJI autoscale, but wrong LUTs (see below)
> - if you enable SCIFIO, images open with correct range and the usual FIJI
> autoscale, but wrong LUTs.
>
> Problems:
>
> - SCIFIO enabled breaks Bio-Formats image drag&drop to FIJI - B-F Importer
> works.
> - No LUT information from the ome-tiffs: FIJI assigns the usual R>G>B>C>M>Y
> LUT order to the channels, regardless of what we set in MDA panel.
>
> Is there a way to have the cake and eat it, i.e., auto-save images from MDA
> which can be opened in FIJI with correct range and LUT assignment, without
> breaking Bio-Formats drag&drop?
>
> (*like we can still do in MM1.4??* :D)
>

This has been addressed (somewhat) :

The latest updates in mm2.0-gamma restore the behavior of files saved in
1.4. The saving code re-gained access to Display settings (albeit in a
somewhat disconnected and feeble way, but it should almost always work),
and will save those in a way that is accessible by ImageJ/Fiji.

There is a caveat (which - I think - also applies to 1.4): ImageJ needs
to have the images saved in a specific order (time - slice - channel).
When you acquire in a different order, and save during acquisition, MM
has no choice but to save the images in the acquisition order (MM does
not rely on the order at all, but can even deal with a random order).
Those files will not open correctly in ImageJ/Fiji.

You have two ways around it. One is to use the floppy disk icon in the
MM viewer to save the data. That will always save the images in the
order preferred by ImageJ. The other is to use the ImageJ menu command
Image > HyperStack > HyperStack to Stack... followed by Image >
HyperStack > Stack to HyperStack... and in the ensuing dialog select the
order used by MM to order the data.



Best,


Nico

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