Nikon JOBS templates

[kspencer007]

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Dear Nikon JOBS users;
                Would you be able to share some JOBS templates with me? I'm looking for a two-pass JOBS, one that would scan an entire slide at low mag, do General Analysis to find the multiple sections, then return to these sections to do a high mag/Z-stack/large image stitch. I'd like to compare yours to mine for troubleshooting.
                I'm also looking for a template for the Nikon 4-slide holder; I can't seem to get the correct measurements to scan all four slides in their entirety, without clipping sections at the edge of the slides.
                Thanks so much.
Kathy Spencer

The Scripps Research Institute
Core Microscopy
10550 N. Torrey Pines Road
DNC 216
La Jolla, CA 92037

[Michael Abanto]

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We use JOBS daily to scan slides. You can contact me off list and send a bin file/proj description (with what hardware) of your job ('export' it from the jobs window). note that GA or GA3 might need to be sent separately (it wont be included in the job file) @ [hidden email].


If I don't get it soon, you might not get a reply til early January... and JOBS don't always transfer very well from one machine to another, so...


check that when/where you specify the region or point list in GA or GA3, that it is really selected(often this selection is lost per run or exiting the GA active window and you should always check/recheck it's really there - a symptom of this going bad is that you see the binary for the GA segmentation when the job runs, but then the loop over the region never happens and the job ends early) and that you have wisely selected per object v frame (if e.g. you focus on center of frame and not object, there might not be tissue to focus on...).


remember to delete region and point lists at the end of e.g. slide loops, or 'replace' as oppose to 'append' them in GA.


You can't print(...), but there is a debug task and you can return values with expressions and variables with tasks or macros. Also, watch the job run, you can normally see the problem and when it occurs - do you see the binary from the GA segmentation? Also, I debug on small/simple area rather than whole slide, then scale up.


Also check the tasks are connected correctly - selecting one will highlight others that are connected to it.  careful naming can help here too.


When things are really screwed up, I don't know why, but remaking the JOB from scratch without copy pasting can help.


Using IF statement task can help avoid a lot of problems. e.g. IF nuclear count is > 800 then focus. similarly segmenting RGB images in HSI is often practical.


Drawing instead of segmenting in GA can be a useful workaround while/if you are blocked. similarly, you can focus manually. Semi-automation is useful and more robust.


Assuming you haven't hit an xy stage limit, you could make your own 4 slide holder version by entering it as a custom multiwell plate with 4 wells of e.g. 75x25mm  xy dimension - you'll have to measure the spacing with a ruler or get the specs - and then loop over wells. I also often enter a larger slide area than what I have to avoid area and angle problems (check your camera is square to the slide). so rather than entering 25x75mm, I enter 85x 35 and roughly estimate the alignment by eye - this inaccurate alignment doesn't seem to cause problems.


I think Nikon have a git repository and there are some good example JOBS in NIS help.


good luck,


Mike




Michael Abanto, PhD
Head of Microscopy Facility
Department of Biomedicine, Hebelstrasse 20
University Hospital Basel

tel [phone]
http://biomedizin.unibas.ch/services/microscopy-facilities/facility-hebelstrasse/
http://microscopynetwork.unibas.ch
________________________________
From: Confocal Microscopy List <[hidden email]> on behalf of Kathryn Spencer <[hidden email]>
Sent: Tuesday, December 15, 2020 6:37:37 PM
To: [hidden email]
Subject: Nikon JOBS templates

*****
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 Nikon JOBS users;
                Would you be able to share some JOBS templates with me? I'm looking for a two-pass JOBS, one that would scan an entire slide at low mag, do General Analysis to find the multiple sections, then return to these sections to do a high mag/Z-stack/large image stitch. I'd like to compare yours to mine for troubleshooting.
                I'm also looking for a template for the Nikon 4-slide holder; I can't seem to get the correct measurements to scan all four slides in their entirety, without clipping sections at the edge of the slides.
                Thanks so much.
Kathy Spencer

The Scripps Research Institute
Core Microscopy
10550 N. Torrey Pines Road
DNC 216
La Jolla, CA 92037