Limiting the z travel range on Nikon Ti

[Shalin Mehta]

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Hello listers,
Our lab has damaged two objectives so far by running them into stage
on our inverted Nikon Ti by using the 'Escape' and 'Return' for Z.

Our old Nikon (finite tube length) has a mechanical stop on how close
the objective can come to the stage and all old objectives are in
great shape.

Can we program the limits on Z travel on Nikon Ti? Asking our local
Nikon folks suggests that the answer is No and we should avoid using
escape/return.

If this feature is not in the firmware, this is a request to Nikon
Japan for such a feature.

Thanks
Shalin

[Sylvie Le Guyader]

Hi Shalin

I assume that this happens because one user escapes the objective at the end of the imaging session and leaves the system on for the next user who then presses the reload button.
Indeed I do not understand why Nikon has chosen to lock the focus wheel when the objective has been escaped so that the only way to get in focus again is to reload.

In the meantime I would suggest you do as us: tell users to systematically shut down the software and hardware (leaving only the gas lasers on) between 2 users. This way when the next user turns the system on (it only takes a minute), the objective will be automatically escaped and the focus wheel will be unlocked.

Hope that helps :)

Med vänlig hälsning / Best regards
 
Sylvie
 
@@@@@@@@@@@@@@@@@@@@@@@@
Sylvie Le Guyader
Live Cell Imaging Unit Manager
Dept of Biosciences and Nutrition
Karolinska Institutet
Hälsovägen 7
Novum, G lift, floor 6
14157 Huddinge
Sweden
office: [phone]
LCI room 1: [phone]
LCI room 2: [phone]
mobile: [phone]

> -----Original Message-----
> From: Confocal Microscopy List
> [mailto:[hidden email]] On Behalf Of Shalin Mehta
> Sent: 17 June 2014 16:47
> To: [hidden email]
> Subject: Limiting the z travel range on Nikon Ti
>
> *****
> 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.
> *****
>
> Hello listers,
> Our lab has damaged two objectives so far by running them into stage on our
> inverted Nikon Ti by using the 'Escape' and 'Return' for Z.
>
> Our old Nikon (finite tube length) has a mechanical stop on how close the objective
> can come to the stage and all old objectives are in great shape.
>
> Can we program the limits on Z travel on Nikon Ti? Asking our local Nikon folks
> suggests that the answer is No and we should avoid using escape/return.
>
> If this feature is not in the firmware, this is a request to Nikon Japan for such a
> feature.
>
> Thanks
> Shalin

[Feinstein, Timothy]

*****
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*****

Hi Shalin,

Using the same hardware we have also found the escape button to be quite
risky between users.  Of equal concern is preserving saved XYZ positions.
We have had to replace expensive bits (but not yet an objective, knock on
woodŠ) when the stage automatically tries to return to a previous user¹s
XYZ position that was set with a very different stage insert installed.
As a result we ask all users to manually lower the objectives and delete
their saved XYZ positions when finished.

All the best,


TF

Timothy Feinstein, Ph.D. | Confocal Manager
333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503
Phone: [phone] | Email: [hidden email]







On 6/17/14, 11:20 AM, "Sylvie Le Guyader" <[hidden email]> wrote:

>Hi Shalin
>
>I assume that this happens because one user escapes the objective at the
>end of the imaging session and leaves the system on for the next user who
>then presses the reload button.
>Indeed I do not understand why Nikon has chosen to lock the focus wheel
>when the objective has been escaped so that the only way to get in focus
>again is to reload.
>
>In the meantime I would suggest you do as us: tell users to
>systematically shut down the software and hardware (leaving only the gas
>lasers on) between 2 users. This way when the next user turns the system
>on (it only takes a minute), the objective will be automatically escaped
>and the focus wheel will be unlocked.
>
>Hope that helps :)
>
>Med vänlig hälsning / Best regards
>
>Sylvie
>
>@@@@@@@@@@@@@@@@@@@@@@@@
>Sylvie Le Guyader
>Live Cell Imaging Unit Manager
>Dept of Biosciences and Nutrition
>Karolinska Institutet
>Hälsovägen 7
>Novum, G lift, floor 6
>14157 Huddinge
>Sweden
>office: [phone]
>LCI room 1: [phone]
>LCI room 2: [phone]
>mobile: [phone]
>
>
>> -----Original Message-----
>> From: Confocal Microscopy List
>> [mailto:[hidden email]] On Behalf Of Shalin Mehta
>> Sent: 17 June 2014 16:47
>> To: [hidden email]
>> Subject: Limiting the z travel range on Nikon Ti
>>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>>
>>http://scanmail.trustwave.com/?c=129&d=od6g0zsIvVNfDzegQ8BtCuVmNylcDldtMr
>>Os9h-cGA&u=http%3a%2f%2flists%2eumn%2eedu%2fcgi-bin%2fwa%3fA0%3dconfocalm
>>icroscopy
>> Post images on
>>http://scanmail.trustwave.com/?c=129&d=od6g0zsIvVNfDzegQ8BtCuVmNylcDldtMu
>>atpBXISA&u=http%3a%2f%2fwww%2eimgur%2ecom and include the link in your
>>posting.
>> *****
>>
>> Hello listers,
>> Our lab has damaged two objectives so far by running them into stage on
>>our
>> inverted Nikon Ti by using the 'Escape' and 'Return' for Z.
>>
>> Our old Nikon (finite tube length) has a mechanical stop on how close
>>the objective
>> can come to the stage and all old objectives are in great shape.
>>
>> Can we program the limits on Z travel on Nikon Ti? Asking our local
>>Nikon folks
>> suggests that the answer is No and we should avoid using escape/return.
>>
>> If this feature is not in the firmware, this is a request to Nikon
>>Japan for such a
>> feature.
>>
>> Thanks
>> Shalin

[Sylvie Le Guyader]

*****
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.
*****

Another alternative for the xyz positions is to use the NIS element user log in. This way the xyz positions are saved for each user and do not show up in the other users' account.

I also tell users not to tick in the 'move stage to xy position' as this easily leads to accidentally moving the stage. Instead we found that if you double click in the x or y columns, the stage moves there anyway even if the 'move stage' box is unticked. Single click simply selects the line so that it can be edited. Accidents are less likely to happen if one needs to double click.

Med vänlig hälsning / Best regards
 
Sylvie
 
@@@@@@@@@@@@@@@@@@@@@@@@
Sylvie Le Guyader
Live Cell Imaging Unit Manager
Dept of Biosciences and Nutrition
Karolinska Institutet
Hälsovägen 7
Novum, G lift, floor 6
14157 Huddinge
Sweden
office: [phone]
LCI room 1: [phone]
LCI room 2: [phone]
mobile: [phone]

> -----Original Message-----
> From: Confocal Microscopy List
> [mailto:[hidden email]] On Behalf Of Feinstein,
> Timothy
> Sent: 17 June 2014 17:40
> To: [hidden email]
> Subject: Re: Limiting the z travel range on Nikon Ti
>
> *****
> 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.
> *****
>
> Hi Shalin,
>
> Using the same hardware we have also found the escape button to be quite risky
> between users.  Of equal concern is preserving saved XYZ positions.
> We have had to replace expensive bits (but not yet an objective, knock on
> woodŠ) when the stage automatically tries to return to a previous user¹s XYZ
> position that was set with a very different stage insert installed.
> As a result we ask all users to manually lower the objectives and delete their saved
> XYZ positions when finished.
>
> All the best,
>
>
> TF
>
> Timothy Feinstein, Ph.D. | Confocal Manager
> 333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503
> Phone: [phone] | Email: [hidden email]
>
>
>
>
>
>
>
> On 6/17/14, 11:20 AM, "Sylvie Le Guyader" <[hidden email]> wrote:
>
> >Hi Shalin
> >
> >I assume that this happens because one user escapes the objective at
> >the end of the imaging session and leaves the system on for the next
> >user who then presses the reload button.
> >Indeed I do not understand why Nikon has chosen to lock the focus wheel
> >when the objective has been escaped so that the only way to get in
> >focus again is to reload.
> >
> >In the meantime I would suggest you do as us: tell users to
> >systematically shut down the software and hardware (leaving only the
> >gas lasers on) between 2 users. This way when the next user turns the
> >system on (it only takes a minute), the objective will be automatically
> >escaped and the focus wheel will be unlocked.
> >
> >Hope that helps :)
> >
> >Med vänlig hälsning / Best regards
> >
> >Sylvie
> >
> >@@@@@@@@@@@@@@@@@@@@@@@@
> >Sylvie Le Guyader
> >Live Cell Imaging Unit Manager
> >Dept of Biosciences and Nutrition
> >Karolinska Institutet
> >Hälsovägen 7
> >Novum, G lift, floor 6
> >14157 Huddinge
> >Sweden
> >office: [phone]
> >LCI room 1: [phone]
> >LCI room 2: [phone]
> >mobile: [phone]
> >
> >
> >> -----Original Message-----
> >> From: Confocal Microscopy List
> >> [mailto:[hidden email]] On Behalf Of Shalin
> Mehta
> >> Sent: 17 June 2014 16:47
> >> To: [hidden email]
> >> Subject: Limiting the z travel range on Nikon Ti
> >>
> >> *****
> >> To join, leave or search the confocal microscopy listserv, go to:
> >>
> >>http://scanmail.trustwave.com/?c=129&d=od6g0zsIvVNfDzegQ8BtCuVmNylcDld
> >>tMr
> >>Os9h-cGA&u=http%3a%2f%2flists%2eumn%2eedu%2fcgi-
> bin%2fwa%3fA0%3dconfoc
> >>alm
> >>icroscopy
> >> Post images on
> >>http://scanmail.trustwave.com/?c=129&d=od6g0zsIvVNfDzegQ8BtCuVmNylcDld
> >>tMu atpBXISA&u=http%3a%2f%2fwww%2eimgur%2ecom and include the link in
> >>your posting.
> >> *****
> >>
> >> Hello listers,
> >> Our lab has damaged two objectives so far by running them into stage
> >>on our  inverted Nikon Ti by using the 'Escape' and 'Return' for Z.
> >>
> >> Our old Nikon (finite tube length) has a mechanical stop on how close
> >>the objective  can come to the stage and all old objectives are in
> >>great shape.
> >>
> >> Can we program the limits on Z travel on Nikon Ti? Asking our local
> >>Nikon folks  suggests that the answer is No and we should avoid using
> >>escape/return.
> >>
> >> If this feature is not in the firmware, this is a request to Nikon
> >>Japan for such a  feature.
> >>
> >> Thanks
> >> Shalin

[Carol Norris]

*****
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.
*****

You can also release the focus lock without moving in z by holding the ‘escape’ button in and then pressing the ‘refocus’ button. I try to impress upon my users that they should never ‘refocus’ from someone else's ‘escaped’ position.

Regards,
Carol
 
Carol E. Norris, Ph.D
Facility Scientist
Flow Cytometry/Confocal Microscopy Facility
Biotechnology/Bioservices Center
University of Connecticut Unit 3149
91 N. Eagleville Rd
Storrs, CT 06269-3149

Phone [phone]
Fax [phone]

On Jun 17, 2014, at 11:46 AM, Sylvie Le Guyader <[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.
> *****
>
> Another alternative for the xyz positions is to use the NIS element user log in. This way the xyz positions are saved for each user and do not show up in the other users' account.
>
> I also tell users not to tick in the 'move stage to xy position' as this easily leads to accidentally moving the stage. Instead we found that if you double click in the x or y columns, the stage moves there anyway even if the 'move stage' box is unticked. Single click simply selects the line so that it can be edited. Accidents are less likely to happen if one needs to double click.
>
> Med vänlig hälsning / Best regards
>  
> Sylvie
>  
> @@@@@@@@@@@@@@@@@@@@@@@@
> Sylvie Le Guyader
> Live Cell Imaging Unit Manager
> Dept of Biosciences and Nutrition
> Karolinska Institutet
> Hälsovägen 7
> Novum, G lift, floor 6
> 14157 Huddinge
> Sweden
> office: [phone]
> LCI room 1: [phone]
> LCI room 2: [phone]
> mobile: [phone]
>
>
>> -----Original Message-----
>> From: Confocal Microscopy List
>> [mailto:[hidden email]] On Behalf Of Feinstein,
>> Timothy
>> Sent: 17 June 2014 17:40
>> To: [hidden email]
>> Subject: Re: Limiting the z travel range on Nikon Ti
>>
>> *****
>> 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.
>> *****
>>
>> Hi Shalin,
>>
>> Using the same hardware we have also found the escape button to be quite risky
>> between users.  Of equal concern is preserving saved XYZ positions.
>> We have had to replace expensive bits (but not yet an objective, knock on
>> woodŠ) when the stage automatically tries to return to a previous user¹s XYZ
>> position that was set with a very different stage insert installed.
>> As a result we ask all users to manually lower the objectives and delete their saved
>> XYZ positions when finished.
>>
>> All the best,
>>
>>
>> TF
>>
>> Timothy Feinstein, Ph.D. | Confocal Manager
>> 333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503
>> Phone: [phone] | Email: [hidden email]
>>
>>
>>
>>
>>
>>
>>
>> On 6/17/14, 11:20 AM, "Sylvie Le Guyader" <[hidden email]> wrote:
>>
>>> Hi Shalin
>>>
>>> I assume that this happens because one user escapes the objective at
>>> the end of the imaging session and leaves the system on for the next
>>> user who then presses the reload button.
>>> Indeed I do not understand why Nikon has chosen to lock the focus wheel
>>> when the objective has been escaped so that the only way to get in
>>> focus again is to reload.
>>>
>>> In the meantime I would suggest you do as us: tell users to
>>> systematically shut down the software and hardware (leaving only the
>>> gas lasers on) between 2 users. This way when the next user turns the
>>> system on (it only takes a minute), the objective will be automatically
>>> escaped and the focus wheel will be unlocked.
>>>
>>> Hope that helps :)
>>>
>>> Med vänlig hälsning / Best regards
>>>
>>> Sylvie
>>>
>>> @@@@@@@@@@@@@@@@@@@@@@@@
>>> Sylvie Le Guyader
>>> Live Cell Imaging Unit Manager
>>> Dept of Biosciences and Nutrition
>>> Karolinska Institutet
>>> Hälsovägen 7
>>> Novum, G lift, floor 6
>>> 14157 Huddinge
>>> Sweden
>>> office: [phone]
>>> LCI room 1: [phone]
>>> LCI room 2: [phone]
>>> mobile: [phone]
>>>
>>>
>>>> -----Original Message-----
>>>> From: Confocal Microscopy List
>>>> [mailto:[hidden email]] On Behalf Of Shalin
>> Mehta
>>>> Sent: 17 June 2014 16:47
>>>> To: [hidden email]
>>>> Subject: Limiting the z travel range on Nikon Ti
>>>>
>>>> *****
>>>> To join, leave or search the confocal microscopy listserv, go to:
>>>>
>>>> http://scanmail.trustwave.com/?c=129&d=od6g0zsIvVNfDzegQ8BtCuVmNylcDld
>>>> tMr
>>>> Os9h-cGA&u=http%3a%2f%2flists%2eumn%2eedu%2fcgi-
>> bin%2fwa%3fA0%3dconfoc
>>>> alm
>>>> icroscopy
>>>> Post images on
>>>> http://scanmail.trustwave.com/?c=129&d=od6g0zsIvVNfDzegQ8BtCuVmNylcDld
>>>> tMu atpBXISA&u=http%3a%2f%2fwww%2eimgur%2ecom and include the link in
>>>> your posting.
>>>> *****
>>>>
>>>> Hello listers,
>>>> Our lab has damaged two objectives so far by running them into stage
>>>> on our  inverted Nikon Ti by using the 'Escape' and 'Return' for Z.
>>>>
>>>> Our old Nikon (finite tube length) has a mechanical stop on how close
>>>> the objective  can come to the stage and all old objectives are in
>>>> great shape.
>>>>
>>>> Can we program the limits on Z travel on Nikon Ti? Asking our local
>>>> Nikon folks  suggests that the answer is No and we should avoid using
>>>> escape/return.
>>>>
>>>> If this feature is not in the firmware, this is a request to Nikon
>>>> Japan for such a  feature.
>>>>
>>>> Thanks
>>>> Shalin

[Craig Brideau]

*****
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.
*****

The Nikon TiControl software lets you communicate directly with the
chassis. Buried in the menus is a setting for creating an upper Z-position
limit. Once you save the setting it is written to the controller on the
chassis. I don't know if Elements can override this or not, but that's the
first thing I would try. (I'm still using EZC1 on my system so I don't know
what Elements would do)

Craig


On Tue, Jun 17, 2014 at 10:29 AM, Carol Norris <[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.
> *****
>
> You can also release the focus lock without moving in z by holding the
> ‘escape’ button in and then pressing the ‘refocus’ button. I try to impress
> upon my users that they should never ‘refocus’ from someone else's
> ‘escaped’ position.
>
> Regards,
> Carol
>
> Carol E. Norris, Ph.D
> Facility Scientist
> Flow Cytometry/Confocal Microscopy Facility
> Biotechnology/Bioservices Center
> University of Connecticut Unit 3149
> 91 N. Eagleville Rd
> Storrs, CT 06269-3149
>
> Phone [phone]
> Fax [phone]
>
> On Jun 17, 2014, at 11:46 AM, Sylvie Le Guyader <[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.
> > *****
> >
> > Another alternative for the xyz positions is to use the NIS element user
> log in. This way the xyz positions are saved for each user and do not show
> up in the other users' account.
> >
> > I also tell users not to tick in the 'move stage to xy position' as this
> easily leads to accidentally moving the stage. Instead we found that if you
> double click in the x or y columns, the stage moves there anyway even if
> the 'move stage' box is unticked. Single click simply selects the line so
> that it can be edited. Accidents are less likely to happen if one needs to
> double click.
> >
> > Med vänlig hälsning / Best regards
> >
> > Sylvie
> >
> > @@@@@@@@@@@@@@@@@@@@@@@@
> > Sylvie Le Guyader
> > Live Cell Imaging Unit Manager
> > Dept of Biosciences and Nutrition
> > Karolinska Institutet
> > Hälsovägen 7
> > Novum, G lift, floor 6
> > 14157 Huddinge
> > Sweden
> > office: [phone]
> > LCI room 1: [phone]
> > LCI room 2: [phone]
> > mobile: [phone]
> >
> >
> >> -----Original Message-----
> >> From: Confocal Microscopy List
> >> [mailto:[hidden email]] On Behalf Of Feinstein,
> >> Timothy
> >> Sent: 17 June 2014 17:40
> >> To: [hidden email]
> >> Subject: Re: Limiting the z travel range on Nikon Ti
> >>
> >> *****
> >> 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.
> >> *****
> >>
> >> Hi Shalin,
> >>
> >> Using the same hardware we have also found the escape button to be
> quite risky
> >> between users.  Of equal concern is preserving saved XYZ positions.
> >> We have had to replace expensive bits (but not yet an objective, knock
> on
> >> woodŠ) when the stage automatically tries to return to a previous
> user¹s XYZ
> >> position that was set with a very different stage insert installed.
> >> As a result we ask all users to manually lower the objectives and
> delete their saved
> >> XYZ positions when finished.
> >>
> >> All the best,
> >>
> >>
> >> TF
> >>
> >> Timothy Feinstein, Ph.D. | Confocal Manager
> >> 333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503
> >> Phone: [phone] | Email: [hidden email]
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> On 6/17/14, 11:20 AM, "Sylvie Le Guyader" <[hidden email]>
> wrote:
> >>
> >>> Hi Shalin
> >>>
> >>> I assume that this happens because one user escapes the objective at
> >>> the end of the imaging session and leaves the system on for the next
> >>> user who then presses the reload button.
> >>> Indeed I do not understand why Nikon has chosen to lock the focus wheel
> >>> when the objective has been escaped so that the only way to get in
> >>> focus again is to reload.
> >>>
> >>> In the meantime I would suggest you do as us: tell users to
> >>> systematically shut down the software and hardware (leaving only the
> >>> gas lasers on) between 2 users. This way when the next user turns the
> >>> system on (it only takes a minute), the objective will be automatically
> >>> escaped and the focus wheel will be unlocked.
> >>>
> >>> Hope that helps :)
> >>>
> >>> Med vänlig hälsning / Best regards
> >>>
> >>> Sylvie
> >>>
> >>> @@@@@@@@@@@@@@@@@@@@@@@@
> >>> Sylvie Le Guyader
> >>> Live Cell Imaging Unit Manager
> >>> Dept of Biosciences and Nutrition
> >>> Karolinska Institutet
> >>> Hälsovägen 7
> >>> Novum, G lift, floor 6
> >>> 14157 Huddinge
> >>> Sweden
> >>> office: [phone]
> >>> LCI room 1: [phone]
> >>> LCI room 2: [phone]
> >>> mobile: [phone]
> >>>
> >>>
> >>>> -----Original Message-----
> >>>> From: Confocal Microscopy List
> >>>> [mailto:[hidden email]] On Behalf Of Shalin
> >> Mehta
> >>>> Sent: 17 June 2014 16:47
> >>>> To: [hidden email]
> >>>> Subject: Limiting the z travel range on Nikon Ti
> >>>>
> >>>> *****
> >>>> To join, leave or search the confocal microscopy listserv, go to:
> >>>>
> >>>>
> http://scanmail.trustwave.com/?c=129&d=od6g0zsIvVNfDzegQ8BtCuVmNylcDld
> >>>> tMr
> >>>> Os9h-cGA&u=http%3a%2f%2flists%2eumn%2eedu%2fcgi-
> >> bin%2fwa%3fA0%3dconfoc
> >>>> alm
> >>>> icroscopy
> >>>> Post images on
> >>>>
> http://scanmail.trustwave.com/?c=129&d=od6g0zsIvVNfDzegQ8BtCuVmNylcDld
> >>>> tMu atpBXISA&u=http%3a%2f%2fwww%2eimgur%2ecom and include the link in
> >>>> your posting.
> >>>> *****
> >>>>
> >>>> Hello listers,
> >>>> Our lab has damaged two objectives so far by running them into stage
> >>>> on our  inverted Nikon Ti by using the 'Escape' and 'Return' for Z.
> >>>>
> >>>> Our old Nikon (finite tube length) has a mechanical stop on how close
> >>>> the objective  can come to the stage and all old objectives are in
> >>>> great shape.
> >>>>
> >>>> Can we program the limits on Z travel on Nikon Ti? Asking our local
> >>>> Nikon folks  suggests that the answer is No and we should avoid using
> >>>> escape/return.
> >>>>
> >>>> If this feature is not in the firmware, this is a request to Nikon
> >>>> Japan for such a  feature.
> >>>>
> >>>> Thanks
> >>>> Shalin
>

[Christian-103]

I am employed in a very diverse multi-user core facility. 
*****
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.
*****

Listers,

I am employed in a very diverse multi-user core facility.  I primarily operate the Nikon A1 between 5 and 7 hours a day for a wide range of users, from undergraduates to PI's.  In any case, the issue I have is that exporting or minor edits to the raw .nd2 files must occur on the A1 system as our users are mostly completely ignorant and we have no imaging software which is not dedicated to a system.  It's amazing how much time I lose trying to export a two channel z-projection from a three channel .nd2.  Do any of you have any suggest software or tutorials I might build upon to provide to my users?  Nearly everything we do is supplementary information (figures), not quantitative, but then I do not believe the users know the difference between an .nd2 and a .jpg.  

I have used the FIJI build of ImageJ for some users, but getting folks trained up is also time consuming.  I understand I may be out of luck in this venture.  I do thank you for any help you might provide.

Christian

[MORONE Diego RIC]

*****
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.
*****

If you have some common tasks like creating a z-projection, you could set up some simple one-click macros and install them on a shared FIJI workstation. Here's a template to convert all files in a directory (untested, adapt to your needs)

--- code ---
path = getDirectory("ND2 Directory"); //load input directory
filelist = getFilelist(path); //load array of all files inside input directory
for (i=0; i< filelist.length; i++) {
    // process nd2 files only
    if (endsWith(filelist[i], ".nd2")) {
        // open file, requires LOCI tools (aka Bio-Formats)
        run("Bio-Formats Importer", "open=" + path + filelist[i] + "autoscale color_mode=Default view=Hyperstack stack_order=XYCZT");
        getDimensions(width,height, channels, slices, frames);
        // create max intensity z-projection
        run("Z Project...", "start=1 stop="+slices+" projection=[Max Intensity]");
        // assign pseudocolors to channels
        for (c=1; c<= channels; c++) {
            Stack.setChannel(c);
            if (c==1) {
                run("Blue");
            } else if (c==2) {
                run("Green");
            } else if (c==3) {
                run("Red");
            }
         }
         // save as multichannel tiff adding a _MAX suffix
         saveAs("TIFF", path+filelist[i]+"_MAX.tif");
    }
}
--- code ---

If you need a primer on macro programming, this could be useful

http://fiji.sc/Introduction_into_Macro_Programming

Best,
Diego

------------------------------------------
DAI IL TUO 5x1000 ALLA RICERCA HUMANITAS.

Codice fiscale 10125410158 (Ricerca sanitaria)

http://www.humanitas.it/5x1000
------------------------------------------
________________________________________
From: Confocal Microscopy List [[hidden email]] On Behalf Of Christian [[hidden email]]
Sent: Tuesday, June 17, 2014 20:10
To: [hidden email]
Subject: Dealing with Nikon .nd2 files

I am employed in a very diverse multi-user core facility.
*****
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.
*****

Listers,

I am employed in a very diverse multi-user core facility.  I primarily operate the Nikon A1 between 5 and 7 hours a day for a wide range of users, from undergraduates to PI's.  In any case, the issue I have is that exporting or minor edits to the raw .nd2 files must occur on the A1 system as our users are mostly completely ignorant and we have no imaging software which is not dedicated to a system.  It's amazing how much time I lose trying to export a two channel z-projection from a three channel .nd2.  Do any of you have any suggest software or tutorials I might build upon to provide to my users?  Nearly everything we do is supplementary information (figures), not quantitative, but then I do not believe the users know the difference between an .nd2 and a .jpg.

I have used the FIJI build of ImageJ for some users, but getting folks trained up is also time consuming.  I understand I may be out of luck in this venture.  I do thank you for any help you might provide.

Christian

[Jens]

*****
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.
*****

Hi Christian,

You can save a lot of time by automating steps in ImageJ by writing macros for recurring tasks like "import nd2->split channels->merge two channels>save as tiff".
Let me know if you need sample code or do a quick web search. There are a lot of macro examples on the web.
There is also the batch process option in Fiji under Process->Batch->

Hope that helps!

Jens


On Jun 17, 2014, at 2:10 PM, Christian <[hidden email]> wrote:

> I am employed in a very diverse multi-user core facility.  
> *****
> 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.
> *****
>
> Listers,
>
> I am employed in a very diverse multi-user core facility.  I primarily operate the Nikon A1 between 5 and 7 hours a day for a wide range of users, from undergraduates to PI's.  In any case, the issue I have is that exporting or minor edits to the raw .nd2 files must occur on the A1 system as our users are mostly completely ignorant and we have no imaging software which is not dedicated to a system.  It's amazing how much time I lose trying to export a two channel z-projection from a three channel .nd2.  Do any of you have any suggest software or tutorials I might build upon to provide to my users?  Nearly everything we do is supplementary information (figures), not quantitative, but then I do not believe the users know the difference between an .nd2 and a .jpg.  
>
> I have used the FIJI build of ImageJ for some users, but getting folks trained up is also time consuming.  I understand I may be out of luck in this venture.  I do thank you for any help you might provide.
>
> Christian

[Paul Rigby-2]

Hi All,
The Nikon Ti Control software also allows one to set the limits of travel of the X,Y stage. This is very useful to prevent users from driving the stage into an objective. As far as I know, the NIS software does not override this function.
Hope this helps someone.
Cheers
Paul

Assoc. Prof. Paul Rigby
Centre for Microscopy, Characterisation & Analysis (M510)
The University of Western Australia
35 Stirling Highway
Crawley  WA  6007
Australia

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Craig Brideau
Sent: Wednesday, 18 June 2014 2:01 AM
To: [hidden email]
Subject: Re: Limiting the z travel range on Nikon Ti

*****
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.
*****

The Nikon TiControl software lets you communicate directly with the chassis. Buried in the menus is a setting for creating an upper Z-position limit. Once you save the setting it is written to the controller on the chassis. I don't know if Elements can override this or not, but that's the first thing I would try. (I'm still using EZC1 on my system so I don't know what Elements would do)

Craig


On Tue, Jun 17, 2014 at 10:29 AM, Carol Norris <[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.
> *****
>
> You can also release the focus lock without moving in z by holding the
> ‘escape’ button in and then pressing the ‘refocus’ button. I try to
> impress upon my users that they should never ‘refocus’ from someone
> else's ‘escaped’ position.
>
> Regards,
> Carol
>
> Carol E. Norris, Ph.D
> Facility Scientist
> Flow Cytometry/Confocal Microscopy Facility Biotechnology/Bioservices
> Center University of Connecticut Unit 3149
> 91 N. Eagleville Rd
> Storrs, CT 06269-3149
>
> Phone [phone]
> Fax [phone]
>
> On Jun 17, 2014, at 11:46 AM, Sylvie Le Guyader
> <[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.
> > *****
> >
> > Another alternative for the xyz positions is to use the NIS element
> > user
> log in. This way the xyz positions are saved for each user and do not
> show up in the other users' account.
> >
> > I also tell users not to tick in the 'move stage to xy position' as
> > this
> easily leads to accidentally moving the stage. Instead we found that
> if you double click in the x or y columns, the stage moves there
> anyway even if the 'move stage' box is unticked. Single click simply
> selects the line so that it can be edited. Accidents are less likely
> to happen if one needs to double click.
> >
> > Med vänlig hälsning / Best regards
> >
> > Sylvie
> >
> > @@@@@@@@@@@@@@@@@@@@@@@@
> > Sylvie Le Guyader
> > Live Cell Imaging Unit Manager
> > Dept of Biosciences and Nutrition
> > Karolinska Institutet
> > Hälsovägen 7
> > Novum, G lift, floor 6
> > 14157 Huddinge
> > Sweden
> > office: [phone]
> > LCI room 1: [phone]
> > LCI room 2: [phone]
> > mobile: [phone]
> >
> >
> >> -----Original Message-----
> >> From: Confocal Microscopy List
> >> [mailto:[hidden email]] On Behalf Of Feinstein,
> >> Timothy
> >> Sent: 17 June 2014 17:40
> >> To: [hidden email]
> >> Subject: Re: Limiting the z travel range on Nikon Ti
> >>
> >> *****
> >> 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.
> >> *****
> >>
> >> Hi Shalin,
> >>
> >> Using the same hardware we have also found the escape button to be
> quite risky
> >> between users.  Of equal concern is preserving saved XYZ positions.
> >> We have had to replace expensive bits (but not yet an objective,
> >> knock
> on
> >> woodŠ) when the stage automatically tries to return to a previous
> user¹s XYZ
> >> position that was set with a very different stage insert installed.
> >> As a result we ask all users to manually lower the objectives and
> delete their saved
> >> XYZ positions when finished.
> >>
> >> All the best,
> >>
> >>
> >> TF
> >>
> >> Timothy Feinstein, Ph.D. | Confocal Manager
> >> 333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503
> >> Phone: [phone] | Email: [hidden email]
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> On 6/17/14, 11:20 AM, "Sylvie Le Guyader" <[hidden email]>
> wrote:
> >>
> >>> Hi Shalin
> >>>
> >>> I assume that this happens because one user escapes the objective
> >>> at the end of the imaging session and leaves the system on for the
> >>> next user who then presses the reload button.
> >>> Indeed I do not understand why Nikon has chosen to lock the focus
> >>> wheel when the objective has been escaped so that the only way to
> >>> get in focus again is to reload.
> >>>
> >>> In the meantime I would suggest you do as us: tell users to
> >>> systematically shut down the software and hardware (leaving only
> >>> the gas lasers on) between 2 users. This way when the next user
> >>> turns the system on (it only takes a minute), the objective will
> >>> be automatically escaped and the focus wheel will be unlocked.
> >>>
> >>> Hope that helps :)
> >>>
> >>> Med vänlig hälsning / Best regards
> >>>
> >>> Sylvie
> >>>
> >>> @@@@@@@@@@@@@@@@@@@@@@@@
> >>> Sylvie Le Guyader
> >>> Live Cell Imaging Unit Manager
> >>> Dept of Biosciences and Nutrition
> >>> Karolinska Institutet
> >>> Hälsovägen 7
> >>> Novum, G lift, floor 6
> >>> 14157 Huddinge
> >>> Sweden
> >>> office: [phone]
> >>> LCI room 1: [phone]
> >>> LCI room 2: [phone]
> >>> mobile: [phone]
> >>>
> >>>
> >>>> -----Original Message-----
> >>>> From: Confocal Microscopy List
> >>>> [mailto:[hidden email]] On Behalf Of Shalin
> >> Mehta
> >>>> Sent: 17 June 2014 16:47
> >>>> To: [hidden email]
> >>>> Subject: Limiting the z travel range on Nikon Ti
> >>>>
> >>>> *****
> >>>> To join, leave or search the confocal microscopy listserv, go to:
> >>>>
> >>>>
> http://scanmail.trustwave.com/?c=129&d=od6g0zsIvVNfDzegQ8BtCuVmNylcDld
> >>>> tMr
> >>>> Os9h-cGA&u=http%3a%2f%2flists%2eumn%2eedu%2fcgi-
> >> bin%2fwa%3fA0%3dconfoc
> >>>> alm
> >>>> icroscopy
> >>>> Post images on
> >>>>
> http://scanmail.trustwave.com/?c=129&d=od6g0zsIvVNfDzegQ8BtCuVmNylcDld
> >>>> tMu atpBXISA&u=http%3a%2f%2fwww%2eimgur%2ecom and include the
> >>>> link in your posting.
> >>>> *****
> >>>>
> >>>> Hello listers,
> >>>> Our lab has damaged two objectives so far by running them into
> >>>> stage on our  inverted Nikon Ti by using the 'Escape' and 'Return' for Z.
> >>>>
> >>>> Our old Nikon (finite tube length) has a mechanical stop on how
> >>>> close the objective  can come to the stage and all old objectives
> >>>> are in great shape.
> >>>>
> >>>> Can we program the limits on Z travel on Nikon Ti? Asking our
> >>>> local Nikon folks  suggests that the answer is No and we should
> >>>> avoid using escape/return.
> >>>>
> >>>> If this feature is not in the firmware, this is a request to
> >>>> Nikon Japan for such a  feature.
> >>>>
> >>>> Thanks
> >>>> Shalin
>

[Glen MacDonald-2]

*****
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 problem with setting focus limits occurs when users bring in specimens mounted in special holders.  Sometimes a sample sits particularly far from the lens, then a collision occurs if the limit is not reset to a “normal” level afterwards.   We’ve even had this problem using glass bottomed 96-well plates where the skirt around the bottom of the plate may extend a large amount with some manufacturers.  

Glen MacDonald
        Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
        Cellular Morphology Core
Center on Human Development and Disability
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
[phone]
[hidden email]







On Jun 18, 2014, at 2:44 AM, Paul Rigby <[hidden email]> wrote:

> Hi All,
> The Nikon Ti Control software also allows one to set the limits of travel of the X,Y stage. This is very useful to prevent users from driving the stage into an objective. As far as I know, the NIS software does not override this function.
> Hope this helps someone.
> Cheers
> Paul
>
> Assoc. Prof. Paul Rigby
> Centre for Microscopy, Characterisation & Analysis (M510)
> The University of Western Australia
> 35 Stirling Highway
> Crawley  WA  6007
> Australia
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Craig Brideau
> Sent: Wednesday, 18 June 2014 2:01 AM
> To: [hidden email]
> Subject: Re: Limiting the z travel range on Nikon Ti
>
> *****
> 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.
> *****
>
> The Nikon TiControl software lets you communicate directly with the chassis. Buried in the menus is a setting for creating an upper Z-position limit. Once you save the setting it is written to the controller on the chassis. I don't know if Elements can override this or not, but that's the first thing I would try. (I'm still using EZC1 on my system so I don't know what Elements would do)
>
> Craig
>
>
> On Tue, Jun 17, 2014 at 10:29 AM, Carol Norris <[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.
>> *****
>>
>> You can also release the focus lock without moving in z by holding the
>> ‘escape’ button in and then pressing the ‘refocus’ button. I try to
>> impress upon my users that they should never ‘refocus’ from someone
>> else's ‘escaped’ position.
>>
>> Regards,
>> Carol
>>
>> Carol E. Norris, Ph.D
>> Facility Scientist
>> Flow Cytometry/Confocal Microscopy Facility Biotechnology/Bioservices
>> Center University of Connecticut Unit 3149
>> 91 N. Eagleville Rd
>> Storrs, CT 06269-3149
>>
>> Phone [phone]
>> Fax [phone]
>>
>> On Jun 17, 2014, at 11:46 AM, Sylvie Le Guyader
>> <[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.
>>> *****
>>>
>>> Another alternative for the xyz positions is to use the NIS element
>>> user
>> log in. This way the xyz positions are saved for each user and do not
>> show up in the other users' account.
>>>
>>> I also tell users not to tick in the 'move stage to xy position' as
>>> this
>> easily leads to accidentally moving the stage. Instead we found that
>> if you double click in the x or y columns, the stage moves there
>> anyway even if the 'move stage' box is unticked. Single click simply
>> selects the line so that it can be edited. Accidents are less likely
>> to happen if one needs to double click.
>>>
>>> Med vänlig hälsning / Best regards
>>>
>>> Sylvie
>>>
>>> @@@@@@@@@@@@@@@@@@@@@@@@
>>> Sylvie Le Guyader
>>> Live Cell Imaging Unit Manager
>>> Dept of Biosciences and Nutrition
>>> Karolinska Institutet
>>> Hälsovägen 7
>>> Novum, G lift, floor 6
>>> 14157 Huddinge
>>> Sweden
>>> office: [phone]
>>> LCI room 1: [phone]
>>> LCI room 2: [phone]
>>> mobile: [phone]
>>>
>>>
>>>> -----Original Message-----
>>>> From: Confocal Microscopy List
>>>> [mailto:[hidden email]] On Behalf Of Feinstein,
>>>> Timothy
>>>> Sent: 17 June 2014 17:40
>>>> To: [hidden email]
>>>> Subject: Re: Limiting the z travel range on Nikon Ti
>>>>
>>>> *****
>>>> 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.
>>>> *****
>>>>
>>>> Hi Shalin,
>>>>
>>>> Using the same hardware we have also found the escape button to be
>> quite risky
>>>> between users.  Of equal concern is preserving saved XYZ positions.
>>>> We have had to replace expensive bits (but not yet an objective,
>>>> knock
>> on
>>>> woodŠ) when the stage automatically tries to return to a previous
>> user¹s XYZ
>>>> position that was set with a very different stage insert installed.
>>>> As a result we ask all users to manually lower the objectives and
>> delete their saved
>>>> XYZ positions when finished.
>>>>
>>>> All the best,
>>>>
>>>>
>>>> TF
>>>>
>>>> Timothy Feinstein, Ph.D. | Confocal Manager
>>>> 333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503
>>>> Phone: [phone] | Email: [hidden email]
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 6/17/14, 11:20 AM, "Sylvie Le Guyader" <[hidden email]>
>> wrote:
>>>>
>>>>> Hi Shalin
>>>>>
>>>>> I assume that this happens because one user escapes the objective
>>>>> at the end of the imaging session and leaves the system on for the
>>>>> next user who then presses the reload button.
>>>>> Indeed I do not understand why Nikon has chosen to lock the focus
>>>>> wheel when the objective has been escaped so that the only way to
>>>>> get in focus again is to reload.
>>>>>
>>>>> In the meantime I would suggest you do as us: tell users to
>>>>> systematically shut down the software and hardware (leaving only
>>>>> the gas lasers on) between 2 users. This way when the next user
>>>>> turns the system on (it only takes a minute), the objective will
>>>>> be automatically escaped and the focus wheel will be unlocked.
>>>>>
>>>>> Hope that helps :)
>>>>>
>>>>> Med vänlig hälsning / Best regards
>>>>>
>>>>> Sylvie
>>>>>
>>>>> @@@@@@@@@@@@@@@@@@@@@@@@
>>>>> Sylvie Le Guyader
>>>>> Live Cell Imaging Unit Manager
>>>>> Dept of Biosciences and Nutrition
>>>>> Karolinska Institutet
>>>>> Hälsovägen 7
>>>>> Novum, G lift, floor 6
>>>>> 14157 Huddinge
>>>>> Sweden
>>>>> office: [phone]
>>>>> LCI room 1: [phone]
>>>>> LCI room 2: [phone]
>>>>> mobile: [phone]
>>>>>
>>>>>
>>>>>> -----Original Message-----
>>>>>> From: Confocal Microscopy List
>>>>>> [mailto:[hidden email]] On Behalf Of Shalin
>>>> Mehta
>>>>>> Sent: 17 June 2014 16:47
>>>>>> To: [hidden email]
>>>>>> Subject: Limiting the z travel range on Nikon Ti
>>>>>>
>>>>>> *****
>>>>>> To join, leave or search the confocal microscopy listserv, go to:
>>>>>>
>>>>>>
>> http://scanmail.trustwave.com/?c=129&d=od6g0zsIvVNfDzegQ8BtCuVmNylcDld
>>>>>> tMr
>>>>>> Os9h-cGA&u=http%3a%2f%2flists%2eumn%2eedu%2fcgi-
>>>> bin%2fwa%3fA0%3dconfoc
>>>>>> alm
>>>>>> icroscopy
>>>>>> Post images on
>>>>>>
>> http://scanmail.trustwave.com/?c=129&d=od6g0zsIvVNfDzegQ8BtCuVmNylcDld
>>>>>> tMu atpBXISA&u=http%3a%2f%2fwww%2eimgur%2ecom and include the
>>>>>> link in your posting.
>>>>>> *****
>>>>>>
>>>>>> Hello listers,
>>>>>> Our lab has damaged two objectives so far by running them into
>>>>>> stage on our  inverted Nikon Ti by using the 'Escape' and 'Return' for Z.
>>>>>>
>>>>>> Our old Nikon (finite tube length) has a mechanical stop on how
>>>>>> close the objective  can come to the stage and all old objectives
>>>>>> are in great shape.
>>>>>>
>>>>>> Can we program the limits on Z travel on Nikon Ti? Asking our
>>>>>> local Nikon folks  suggests that the answer is No and we should
>>>>>> avoid using escape/return.
>>>>>>
>>>>>> If this feature is not in the firmware, this is a request to
>>>>>> Nikon Japan for such a  feature.
>>>>>>
>>>>>> Thanks
>>>>>> Shalin
>>

[Craig Brideau]

*****
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.
*****

I actually had to create some stage adapters that hold different types of
sample holders at the same height to address this issue. I have a 96 well
plate stage that puts the bottoms at the same relative location as the
standard holder puts dishes and slides. I had to 3d print the stage insert
but it works fairly well.

Craig


On Wed, Jun 18, 2014 at 9:22 AM, Glen MacDonald <[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.
> *****
>
> One problem with setting focus limits occurs when users bring in specimens
> mounted in special holders.  Sometimes a sample sits particularly far from
> the lens, then a collision occurs if the limit is not reset to a “normal”
> level afterwards.   We’ve even had this problem using glass bottomed
> 96-well plates where the skirt around the bottom of the plate may extend a
> large amount with some manufacturers.
>
> Glen MacDonald
>         Core for Communication Research
> Virginia Merrill Bloedel Hearing Research Center
>         Cellular Morphology Core
> Center on Human Development and Disability
> Box 357923
> University of Washington
> Seattle, WA 98195-7923  USA
> [phone]
> [hidden email]
>
>
>
>
>
>
>
> On Jun 18, 2014, at 2:44 AM, Paul Rigby <[hidden email]> wrote:
>
> > Hi All,
> > The Nikon Ti Control software also allows one to set the limits of
> travel of the X,Y stage. This is very useful to prevent users from driving
> the stage into an objective. As far as I know, the NIS software does not
> override this function.
> > Hope this helps someone.
> > Cheers
> > Paul
> >
> > Assoc. Prof. Paul Rigby
> > Centre for Microscopy, Characterisation & Analysis (M510)
> > The University of Western Australia
> > 35 Stirling Highway
> > Crawley  WA  6007
> > Australia
> >
> > -----Original Message-----
> > From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of Craig Brideau
> > Sent: Wednesday, 18 June 2014 2:01 AM
> > To: [hidden email]
> > Subject: Re: Limiting the z travel range on Nikon Ti
> >
> > *****
> > 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.
> > *****
> >
> > The Nikon TiControl software lets you communicate directly with the
> chassis. Buried in the menus is a setting for creating an upper Z-position
> limit. Once you save the setting it is written to the controller on the
> chassis. I don't know if Elements can override this or not, but that's the
> first thing I would try. (I'm still using EZC1 on my system so I don't know
> what Elements would do)
> >
> > Craig
> >
> >
> > On Tue, Jun 17, 2014 at 10:29 AM, Carol Norris <[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.
> >> *****
> >>
> >> You can also release the focus lock without moving in z by holding the
> >> ‘escape’ button in and then pressing the ‘refocus’ button. I try to
> >> impress upon my users that they should never ‘refocus’ from someone
> >> else's ‘escaped’ position.
> >>
> >> Regards,
> >> Carol
> >>
> >> Carol E. Norris, Ph.D
> >> Facility Scientist
> >> Flow Cytometry/Confocal Microscopy Facility Biotechnology/Bioservices
> >> Center University of Connecticut Unit 3149
> >> 91 N. Eagleville Rd
> >> Storrs, CT 06269-3149
> >>
> >> Phone [phone]
> >> Fax [phone]
> >>
> >> On Jun 17, 2014, at 11:46 AM, Sylvie Le Guyader
> >> <[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.
> >>> *****
> >>>
> >>> Another alternative for the xyz positions is to use the NIS element
> >>> user
> >> log in. This way the xyz positions are saved for each user and do not
> >> show up in the other users' account.
> >>>
> >>> I also tell users not to tick in the 'move stage to xy position' as
> >>> this
> >> easily leads to accidentally moving the stage. Instead we found that
> >> if you double click in the x or y columns, the stage moves there
> >> anyway even if the 'move stage' box is unticked. Single click simply
> >> selects the line so that it can be edited. Accidents are less likely
> >> to happen if one needs to double click.
> >>>
> >>> Med vänlig hälsning / Best regards
> >>>
> >>> Sylvie
> >>>
> >>> @@@@@@@@@@@@@@@@@@@@@@@@
> >>> Sylvie Le Guyader
> >>> Live Cell Imaging Unit Manager
> >>> Dept of Biosciences and Nutrition
> >>> Karolinska Institutet
> >>> Hälsovägen 7
> >>> Novum, G lift, floor 6
> >>> 14157 Huddinge
> >>> Sweden
> >>> office: [phone]
> >>> LCI room 1: [phone]
> >>> LCI room 2: [phone]
> >>> mobile: [phone]
> >>>
> >>>
> >>>> -----Original Message-----
> >>>> From: Confocal Microscopy List
> >>>> [mailto:[hidden email]] On Behalf Of Feinstein,
> >>>> Timothy
> >>>> Sent: 17 June 2014 17:40
> >>>> To: [hidden email]
> >>>> Subject: Re: Limiting the z travel range on Nikon Ti
> >>>>
> >>>> *****
> >>>> 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.
> >>>> *****
> >>>>
> >>>> Hi Shalin,
> >>>>
> >>>> Using the same hardware we have also found the escape button to be
> >> quite risky
> >>>> between users.  Of equal concern is preserving saved XYZ positions.
> >>>> We have had to replace expensive bits (but not yet an objective,
> >>>> knock
> >> on
> >>>> woodŠ) when the stage automatically tries to return to a previous
> >> user¹s XYZ
> >>>> position that was set with a very different stage insert installed.
> >>>> As a result we ask all users to manually lower the objectives and
> >> delete their saved
> >>>> XYZ positions when finished.
> >>>>
> >>>> All the best,
> >>>>
> >>>>
> >>>> TF
> >>>>
> >>>> Timothy Feinstein, Ph.D. | Confocal Manager
> >>>> 333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503
> >>>> Phone: [phone] | Email: [hidden email]
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> On 6/17/14, 11:20 AM, "Sylvie Le Guyader" <[hidden email]>
> >> wrote:
> >>>>
> >>>>> Hi Shalin
> >>>>>
> >>>>> I assume that this happens because one user escapes the objective
> >>>>> at the end of the imaging session and leaves the system on for the
> >>>>> next user who then presses the reload button.
> >>>>> Indeed I do not understand why Nikon has chosen to lock the focus
> >>>>> wheel when the objective has been escaped so that the only way to
> >>>>> get in focus again is to reload.
> >>>>>
> >>>>> In the meantime I would suggest you do as us: tell users to
> >>>>> systematically shut down the software and hardware (leaving only
> >>>>> the gas lasers on) between 2 users. This way when the next user
> >>>>> turns the system on (it only takes a minute), the objective will
> >>>>> be automatically escaped and the focus wheel will be unlocked.
> >>>>>
> >>>>> Hope that helps :)
> >>>>>
> >>>>> Med vänlig hälsning / Best regards
> >>>>>
> >>>>> Sylvie
> >>>>>
> >>>>> @@@@@@@@@@@@@@@@@@@@@@@@
> >>>>> Sylvie Le Guyader
> >>>>> Live Cell Imaging Unit Manager
> >>>>> Dept of Biosciences and Nutrition
> >>>>> Karolinska Institutet
> >>>>> Hälsovägen 7
> >>>>> Novum, G lift, floor 6
> >>>>> 14157 Huddinge
> >>>>> Sweden
> >>>>> office: [phone]
> >>>>> LCI room 1: [phone]
> >>>>> LCI room 2: [phone]
> >>>>> mobile: [phone]
> >>>>>
> >>>>>
> >>>>>> -----Original Message-----
> >>>>>> From: Confocal Microscopy List
> >>>>>> [mailto:[hidden email]] On Behalf Of Shalin
> >>>> Mehta
> >>>>>> Sent: 17 June 2014 16:47
> >>>>>> To: [hidden email]
> >>>>>> Subject: Limiting the z travel range on Nikon Ti
> >>>>>>
> >>>>>> *****
> >>>>>> To join, leave or search the confocal microscopy listserv, go to:
> >>>>>>
> >>>>>>
> >> http://scanmail.trustwave.com/?c=129&d=od6g0zsIvVNfDzegQ8BtCuVmNylcDld
> >>>>>> tMr
> >>>>>> Os9h-cGA&u=http%3a%2f%2flists%2eumn%2eedu%2fcgi-
> >>>> bin%2fwa%3fA0%3dconfoc
> >>>>>> alm
> >>>>>> icroscopy
> >>>>>> Post images on
> >>>>>>
> >> http://scanmail.trustwave.com/?c=129&d=od6g0zsIvVNfDzegQ8BtCuVmNylcDld
> >>>>>> tMu atpBXISA&u=http%3a%2f%2fwww%2eimgur%2ecom and include the
> >>>>>> link in your posting.
> >>>>>> *****
> >>>>>>
> >>>>>> Hello listers,
> >>>>>> Our lab has damaged two objectives so far by running them into
> >>>>>> stage on our  inverted Nikon Ti by using the 'Escape' and 'Return'
> for Z.
> >>>>>>
> >>>>>> Our old Nikon (finite tube length) has a mechanical stop on how
> >>>>>> close the objective  can come to the stage and all old objectives
> >>>>>> are in great shape.
> >>>>>>
> >>>>>> Can we program the limits on Z travel on Nikon Ti? Asking our
> >>>>>> local Nikon folks  suggests that the answer is No and we should
> >>>>>> avoid using escape/return.
> >>>>>>
> >>>>>> If this feature is not in the firmware, this is a request to
> >>>>>> Nikon Japan for such a  feature.
> >>>>>>
> >>>>>> Thanks
> >>>>>> Shalin
> >>
>

[mcammer]

*****
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.
*****

We tell all users to bring the focus to the farthest position away from the sample at the end of their working session and to manually bring the focus up to the sample at the beginning of the next session.  The reason is because, as Glen points out below, people from different labs bring all sorts of different samples and assuming a normal focal position invites crashes.  This is the same on all brands of microscopes including a Nikon Ti with PFS.

===========================================================================
Michael Cammer, Microscopy Core & Dustin Lab , Skirball Institute, NYU Langone Medical Center
Cell:  914-309-3270   Lab: 212-263-3208
http://ocs.med.nyu.edu/microscopy & http://www.med.nyu.edu/skirball-lab/dustinlab/

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Glen MacDonald
Sent: Wednesday, June 18, 2014 11:22 AM
To: [hidden email]
Subject: Re: Limiting the z travel range on Nikon Ti


One problem with setting focus limits occurs when users bring in specimens mounted in special holders.  Sometimes a sample sits particularly far from the lens, then a collision occurs if the limit is not reset to a "normal" level afterwards.   We've even had this problem using glass bottomed 96-well plates where the skirt around the bottom of the plate may extend a large amount with some manufacturers.  

Glen MacDonald
        Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
        Cellular Morphology Core
Center on Human Development and Disability Box 357923 University of Washington Seattle, WA 98195-7923  USA
[phone]
[hidden email]


 

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=================================

[Christian-103]

*****
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.
*****

Thank you all for the advice.  I will try this macro out, and will admit I have no experience with writing macros.  I have two more questions, is FIJI able to pull the header information off the .nd2 to set scale bars and is there a FIJI discussion group/list serv?

Thanks again, this input will save me many hours of labor.

Christian




________________________________
 From: MORONE Diego RIC <[hidden email]>
To: [hidden email]
Sent: Tuesday, June 17, 2014 4:25 PM
Subject: FW: Dealing with Nikon .nd2 files
 

*****
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.
*****

If you have some common tasks like creating a z-projection, you could set up some simple one-click macros and install them on a shared FIJI workstation. Here's a template to convert all files in a directory (untested, adapt to your needs)

--- code ---
path = getDirectory("ND2 Directory"); //load input directory
filelist = getFilelist(path); //load array of all files inside input directory
for (i=0; i< filelist.length; i++) {
    // process nd2 files only
    if (endsWith(filelist[i], ".nd2")) {
        // open file, requires LOCI tools (aka Bio-Formats)
        run("Bio-Formats Importer", "open=" + path + filelist[i] + "autoscale color_mode=Default view=Hyperstack stack_order=XYCZT");
        getDimensions(width,height, channels, slices, frames);
        // create max intensity z-projection
        run("Z Project...", "start=1 stop="+slices+" projection=[Max Intensity]");
        // assign pseudocolors to channels
        for (c=1; c<= channels; c++) {
            Stack.setChannel(c);
            if (c==1) {
                run("Blue");
            } else if (c==2) {
                run("Green");
            } else if (c==3) {
                run("Red");
            }
         }
         // save as multichannel tiff adding a _MAX suffix
         saveAs("TIFF", path+filelist[i]+"_MAX.tif");
    }
}
--- code ---

If you need a primer on macro programming, this could be useful

http://fiji.sc/Introduction_into_Macro_Programming

Best,
Diego

------------------------------------------
DAI IL TUO 5x1000 ALLA RICERCA HUMANITAS.

Codice fiscale 10125410158 (Ricerca sanitaria)

http://www.humanitas.it/5x1000
------------------------------------------
________________________________________
From: Confocal Microscopy List [[hidden email]] On Behalf Of Christian [[hidden email]]
Sent: Tuesday, June 17, 2014 20:10



To: [hidden email]
Subject: Dealing with Nikon .nd2 files

I am employed in a very diverse multi-user core facility.
*****
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.
*****

Listers,

I am employed in a very diverse multi-user core facility.  I primarily operate the Nikon A1 between 5 and 7 hours a day for a wide range of users, from undergraduates to PI's.  In any case, the issue I have is that exporting or minor edits to the raw .nd2 files must occur on the A1 system as our users are mostly completely ignorant and we have no imaging software which is not dedicated to a system.  It's amazing how much time I lose trying to export a two channel z-projection from a three channel .nd2.  Do any of you have any suggest software or tutorials I might build upon to provide to my users?  Nearly everything we do is supplementary information (figures), not quantitative, but then I do not believe the users know the difference between an .nd2 and a .jpg.

I have used the FIJI build of ImageJ for some users, but getting folks trained up is also time consuming.  I understand I may be out of luck in this venture.  I do thank you for any help you might provide.

Christian

[MORONE Diego RIC]

*****
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.
*****

Hi Christian,

the plugin that opens .nd2 files (LOCI Bio-formats importer) is able to read the header information. There's a very active community at imagej listserv

http://list.nih.gov/cgi-bin/wa.exe?LIST=IMAGEJ

In Fiji you could also try Process>Batch>Convert..., with "Read images using Bio-formats" option enabled.

Best,
Diego



................................
Diego Morone
Staff Scientist
Humanitas Clinical and Research Center
Rozzano - Milano, Italy
www.humanitas.it/hur/cms/english/




------------------------------------------
DAI IL TUO 5x1000 ALLA RICERCA HUMANITAS.

Codice fiscale 10125410158 (Ricerca sanitaria)

http://www.humanitas.it/5x1000
------------------------------------------
-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Christian
Sent: giovedì 19 giugno 2014 00:04
To: [hidden email]
Subject: Re: Dealing with Nikon .nd2 files

*****
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.
*****

Thank you all for the advice.  I will try this macro out, and will admit I have no experience with writing macros.  I have two more questions, is FIJI able to pull the header information off the .nd2 to set scale bars and is there a FIJI discussion group/list serv?

Thanks again, this input will save me many hours of labor.

Christian




________________________________
 From: MORONE Diego RIC <[hidden email]>
To: [hidden email]
Sent: Tuesday, June 17, 2014 4:25 PM
Subject: FW: Dealing with Nikon .nd2 files


*****
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.
*****

If you have some common tasks like creating a z-projection, you could set up some simple one-click macros and install them on a shared FIJI workstation. Here's a template to convert all files in a directory (untested, adapt to your needs)

--- code ---
path = getDirectory("ND2 Directory"); //load input directory
filelist = getFilelist(path); //load array of all files inside input directory
for (i=0; i< filelist.length; i++) {
    // process nd2 files only
    if (endsWith(filelist[i], ".nd2")) {
        // open file, requires LOCI tools (aka Bio-Formats)
        run("Bio-Formats Importer", "open=" + path + filelist[i] + "autoscale color_mode=Default view=Hyperstack stack_order=XYCZT");
        getDimensions(width,height, channels, slices, frames);
        // create max intensity z-projection
        run("Z Project...", "start=1 stop="+slices+" projection=[Max Intensity]");
        // assign pseudocolors to channels
        for (c=1; c<= channels; c++) {
            Stack.setChannel(c);
            if (c==1) {
                run("Blue");
            } else if (c==2) {
                run("Green");
            } else if (c==3) {
                run("Red");
            }
         }
         // save as multichannel tiff adding a _MAX suffix
         saveAs("TIFF", path+filelist[i]+"_MAX.tif");
    }
}
--- code ---

If you need a primer on macro programming, this could be useful

http://fiji.sc/Introduction_into_Macro_Programming

Best,
Diego

------------------------------------------
DAI IL TUO 5x1000 ALLA RICERCA HUMANITAS.

Codice fiscale 10125410158 (Ricerca sanitaria)

http://www.humanitas.it/5x1000
------------------------------------------
________________________________________
From: Confocal Microscopy List [[hidden email]] On Behalf Of Christian [[hidden email]]
Sent: Tuesday, June 17, 2014 20:10



To: [hidden email]
Subject: Dealing with Nikon .nd2 files

I am employed in a very diverse multi-user core facility.
*****
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.
*****

Listers,

I am employed in a very diverse multi-user core facility.  I primarily operate the Nikon A1 between 5 and 7 hours a day for a wide range of users, from undergraduates to PI's.  In any case, the issue I have is that exporting or minor edits to the raw .nd2 files must occur on the A1 system as our users are mostly completely ignorant and we have no imaging software which is not dedicated to a system.  It's amazing how much time I lose trying to export a two channel z-projection from a three channel .nd2.  Do any of you have any suggest software or tutorials I might build upon to provide to my users?  Nearly everything we do is supplementary information (figures), not quantitative, but then I do not believe the users know the difference between an .nd2 and a .jpg.

I have used the FIJI build of ImageJ for some users, but getting folks trained up is also time consuming.  I understand I may be out of luck in this venture.  I do thank you for any help you might provide.

Christian

[phil laissue-2]

*****
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.
*****

Hi Christian,

you could ask them to use the viewer:
http://www.nikoninstruments.com/en_GB/Products/Software/NIS-Elements-Viewer
Limited as it is, it seems to be more intuitive to none-too-experienced
users (more so than ImageJ).
Write one how-to guide (also for saving them as tif or jpeg) and put it on
a website, or send per email.
True, most won't see a difference between jpg and tiff/nd2, but compression
artefacts like to show most in print, so it's always worth while keeping
the original file with metadata. Jpegs are only for lab journals.
Opening nd2 using bioformats doesn't work on all machines, so a workaround
is saving in ics format.
But really, make sure you can have the users do as much as possible
themselves, so you don't spend loads of time converting files...

Cheers,

Philippe

_________________________________________
Philippe Laissue, PhD, Director of Bioimaging Unit
School of Biological Sciences, Room 4.17
University of Essex, Colchester CO4 3SQ, UK
(0044) 01206 872246 / (0044) 07842 676 456
[hidden email]
privatewww.essex.ac.uk/~plaissue


On 19 June 2014 15:29, MORONE Diego RIC <[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.
> *****
>
> Hi Christian,
>
> the plugin that opens .nd2 files (LOCI Bio-formats importer) is able to
> read the header information. There's a very active community at imagej
> listserv
>
> http://list.nih.gov/cgi-bin/wa.exe?LIST=IMAGEJ
>
> In Fiji you could also try Process>Batch>Convert..., with "Read images
> using Bio-formats" option enabled.
>
> Best,
> Diego
>
>
>
> ................................
> Diego Morone
> Staff Scientist
> Humanitas Clinical and Research Center
> Rozzano - Milano, Italy
> www.humanitas.it/hur/cms/english/
>
>
>
>
> ------------------------------------------
> DAI IL TUO 5x1000 ALLA RICERCA HUMANITAS.
>
> Codice fiscale 10125410158 (Ricerca sanitaria)
>
> http://www.humanitas.it/5x1000
> ------------------------------------------
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of Christian
> Sent: giovedì 19 giugno 2014 00:04
> To: [hidden email]
> Subject: Re: Dealing with Nikon .nd2 files
>
> *****
> 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.
> *****
>
> Thank you all for the advice.  I will try this macro out, and will admit I
> have no experience with writing macros.  I have two more questions, is FIJI
> able to pull the header information off the .nd2 to set scale bars and is
> there a FIJI discussion group/list serv?
>
> Thanks again, this input will save me many hours of labor.
>
> Christian
>
>
>
>
> ________________________________
>  From: MORONE Diego RIC <[hidden email]>
> To: [hidden email]
> Sent: Tuesday, June 17, 2014 4:25 PM
> Subject: FW: Dealing with Nikon .nd2 files
>
>
> *****
> 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.
> *****
>
> If you have some common tasks like creating a z-projection, you could set
> up some simple one-click macros and install them on a shared FIJI
> workstation. Here's a template to convert all files in a directory
> (untested, adapt to your needs)
>
> --- code ---
> path = getDirectory("ND2 Directory"); //load input directory
> filelist = getFilelist(path); //load array of all files inside input
> directory
> for (i=0; i< filelist.length; i++) {
>     // process nd2 files only
>     if (endsWith(filelist[i], ".nd2")) {
>         // open file, requires LOCI tools (aka Bio-Formats)
>         run("Bio-Formats Importer", "open=" + path + filelist[i] +
> "autoscale color_mode=Default view=Hyperstack stack_order=XYCZT");
>         getDimensions(width,height, channels, slices, frames);
>         // create max intensity z-projection
>         run("Z Project...", "start=1 stop="+slices+" projection=[Max
> Intensity]");
>         // assign pseudocolors to channels
>         for (c=1; c<= channels; c++) {
>             Stack.setChannel(c);
>             if (c==1) {
>                 run("Blue");
>             } else if (c==2) {
>                 run("Green");
>             } else if (c==3) {
>                 run("Red");
>             }
>          }
>          // save as multichannel tiff adding a _MAX suffix
>          saveAs("TIFF", path+filelist[i]+"_MAX.tif");
>     }
> }
> --- code ---
>
> If you need a primer on macro programming, this could be useful
>
> http://fiji.sc/Introduction_into_Macro_Programming
>
> Best,
> Diego
>
> ------------------------------------------
> DAI IL TUO 5x1000 ALLA RICERCA HUMANITAS.
>
> Codice fiscale 10125410158 (Ricerca sanitaria)
>
> http://www.humanitas.it/5x1000
> ------------------------------------------
> ________________________________________
> From: Confocal Microscopy List [[hidden email]] On
> Behalf Of Christian [[hidden email]]
> Sent: Tuesday, June 17, 2014 20:10
>
>
>
> To: [hidden email]
> Subject: Dealing with Nikon .nd2 files
>
> I am employed in a very diverse multi-user core facility.
> *****
> 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.
> *****
>
> Listers,
>
> I am employed in a very diverse multi-user core facility.  I primarily
> operate the Nikon A1 between 5 and 7 hours a day for a wide range of users,
> from undergraduates to PI's.  In any case, the issue I have is that
> exporting or minor edits to the raw .nd2 files must occur on the A1 system
> as our users are mostly completely ignorant and we have no imaging software
> which is not dedicated to a system.  It's amazing how much time I lose
> trying to export a two channel z-projection from a three channel .nd2.  Do
> any of you have any suggest software or tutorials I might build upon to
> provide to my users?  Nearly everything we do is supplementary information
> (figures), not quantitative, but then I do not believe the users know the
> difference between an .nd2 and a .jpg.
>
> I have used the FIJI build of ImageJ for some users, but getting folks
> trained up is also time consuming.  I understand I may be out of luck in
> this venture.  I do thank you for any help you might provide.
>
> Christian
>