Re: CONFOCALMICROSCOPY Digest - 20 Feb 2018 to 21 Feb 2018 (#2018-47)

[Denise Ramirez]

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We've had iLab for 2 years now in my facility and I'm very happy with it. For tracking of actual user-logged time on networked computers which also control the microscopes, we use the usage tracker software. With the exception of some initial hiccups related to Windows versions, Java versions and our local network, the system works beautifully to automatically transmit the logged time for each user to sync with the calendar. If you don't have network access or want to track usage on non-computerized equipment, you can use a standalone tablet for the same purpose (I believe in iLab terms this is a "kiosk") as others suggested. In my case, I don't have a lot of that type of usage, so I just use the old fashioned paper log sheets for that and I manually reconcile the logged time and reserved time in iLab.


Denise M. Ramirez, Ph.D.
Core Manager, Whole Brain Microscopy Facility
Assistant Professor, Department of Neurology and Neurotherapeutics
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Dallas, TX 75390-8813
214-648-0203



-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of CONFOCALMICROSCOPY automatic digest system
Sent: Thursday, February 22, 2018 12:00 AM
To: [hidden email]
Subject: CONFOCALMICROSCOPY Digest - 20 Feb 2018 to 21 Feb 2018 (#2018-47)

There are 7 messages totaling 481 lines in this issue.

Topics of the day:

  1. Advice on Noise Cancelling headphones for lab work (3)
  2. Release of Bio-Formats 5.8.0
  3. iLabs and monitoring real usage of microscopes (2)
  4. Aivia - intelligent image visualization and analysis (commercial post)

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Date:    Wed, 21 Feb 2018 01:04:14 -0600
From:    Kelvin Poon <[hidden email]>
Subject: Re: Advice on Noise Cancelling headphones for lab work

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If your budget allows then Sony WH-1000XM2 is probably the most advanced of its kind on the market. Actually optimizes on the fly and best of all it's wireless. I also echo the suggestion of others of a good custom in-ear-monitor but the costs could be prohibitive. What you can do instead is go to a hearing clinic and actually get custom in ear plugs (without the electronics) that may serve a better job than standard foam plugs. You can get them in silicone or acrylic.

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Date:    Wed, 21 Feb 2018 09:13:18 -0500
From:    MJ Tomaszewski <[hidden email]>
Subject: Re: Advice on Noise Cancelling headphones for lab work

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Just a note that if you are getting these for employees, that in some people, noise cancelling headphones cause a vertigo like experience.

I found this out after buying $300 headphones to drown out a coworker in an open lab space, and I couldn't wear them for more than 5 minutes at a time.

Monica

On Tue, Feb 20, 2018 at 1:40 PM, Xuejun Sun <[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,
>
> I think a better approach for a facility might be to call an acoustic
> control company and have a walk around in the lab. and identify the
> main sources of the noises. They could do wonders. I still have the
> box a company constructed for the 2 fans of the Krypton Argon lasers
> which reduces the ~70db noise to a hum (the lasers are long gone!).
> They also did some things for the chiller for our TEM to make our lab
> space workable again. Noises and the darkness in a facility give me
> headaches. This is the least you could do for your users...
>
> As to noise cancellation headphone, I have been a long Bose user and
> are happy with it (both the Quietconfort 15 and 35). But both came
> without me paying for it, I am sure there are better price/performance
> choices. I cannot tolerate in ear headphones which is just me..
>
> Xuejun
>
> -----Original Message-----
> From: Confocal Microscopy List
> [mailto:[hidden email]]
> On
> Behalf Of Luis Enrique Villegas Hernandez
> Sent: Tuesday, February 20, 2018 7:44 AM
> To: [hidden email]
> Subject: Advice on Noise Cancelling headphones for lab work
>
> *****
> 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 colleages,
>
>
> I have a fairly simple question to ask you about: what is the best
> active noise cancelling headphone on the market for lab-work environment?
>
> We have many fans and few compressors in our facilities, which
> generate constant noise.
>
> We have tried to cancel out the noise by using passive earplugs, but
> they don't totally block the noise, so we wonder if there's a better
> alternative on the active noise cancelling side.
>
> Any suggestions?
>
>
> Thanks in advance,
>
>
>
> Luis Villegas
>
> UiT
>
> Tromso, Norway
>

--
*Monica Tomaszewski, PhD SCYM(ASCP)CM*

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Date:    Wed, 21 Feb 2018 16:36:58 +0100
From:    Ralf Palmisano <[hidden email]>
Subject: Re: Advice on Noise Cancelling headphones for lab work

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Dear all,

I have used different noise cancelling on-ear phones for a while such as:

Bose QC 30: Very good on noise from low to high frequencies. Not very effective in the frequency range of the human voice from 1500 - 3000 Hz.
Comfort on ear for lengthy sessions of wearing is 4 out of 6.

Sennheiser PCX 550: Very good on noise from low to high frequencies.
Less effective in the frequency range of the human voice from 1500 -
3000 Hz than the Bose QC 30. Comfort on ear for lengthy sessions of wearing is 6 out of 6.

Bowers & Wilkins PX Wireless: Very good on noise from low to high frequencies. If you use the app with it you can nicely adjust the opening / closing of the frequency range of the human voice, sort of like an inverted equalizer. Comfort on ear for lengthy sessions of wearing is 5 out of 6. They look very posh, that might disencourage some people from using them in a professionel environment.

All of them cost around 400 €. My favourite at present is the B&W one.

Best Ralf


Am 20.02.2018 um 15:44 schrieb Luis Enrique Villegas Hernandez:

> *****
> 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 colleages,
>
>
> I have a fairly simple question to ask you about: what is the best active noise cancelling headphone on the market for lab-work environment?
>
> We have many fans and few compressors in our facilities, which generate constant noise.
>
> We have tried to cancel out the noise by using passive earplugs, but they don't totally block the noise, so we wonder if there's a better alternative on the active noise cancelling side.
>
> Any suggestions?
>
>
> Thanks in advance,
>
>
>
> Luis Villegas
>
> UiT
>
> Tromso, Norway

--
Ralf Palmisano
Head - Optical Imaging Centre Erlangen

Hartmannstr. 14
91052 Erlangen, Germany
[phone] (Office)
[phone] (Secretary Ms. Lang)
[phone] (Fax)

www.oice.uni-erlangen.de

------------------------------

Date:    Wed, 21 Feb 2018 17:03:56 +0000
From:    "David Gault (Staff)" <[hidden email]>
Subject: Release of Bio-Formats 5.8.0

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Dear all,

Today we are releasing Bio-Formats 5.8.0 which includes the following changes:

New file formats:

  *   Ionpath MIBI
     *   added a new reader to support the reading of Ionpath Multiplexed Ion Beam Imaging (MIBI) files (thanks to Rachel Finck)
  *   PerkinElmer Vectra QPTIFF
     *   added support for PerkinElmer Vectra QPTIFF files (The QPTIFF Bio-Formats reader is provided through a collaboration between PerkinElmer, Inc and Glencoe Software Inc.)

File format fixes and improvements:

  *   cellSens VSI
     *   added support for lossless JPEG compression
  *   Imspector OBF
     *   improved the parsing of OBF files with embedded OME-XML metadata (thanks to Bjoern Thiel)
  *   Leica LIF
     *   companion metadata files are now attached if present
  *   Micro-Manager
     *   fixed a bug related to the parsing of the metadata closing block
  *   NRRD (Nearly Raw Raster Data)
     *   added support for GZIP pixel stream contained within a .nrrd file
  *   Olympus OIR
     *   added support for multi-file datasets
  *   OME-TIFF
     *   when files are ungrouped the dimensions are corrected by checking the indexes for each associated TiffData
  *   PerkinElmer Operetta
     *   added support for additional metadata fields such as Instrument, Wavelength and Exposure time
  *   TIFF
     *   fixed a bug when printing IFD values of type OnDemandLongArray
     *   fixed a bug when writing tile sizes for multi-series images
  *   Zeiss CZI
     *   when Z positions are not enumerated then values are calculated from a Z step
     *   metadata for DisplaySetting will now be preserved in the original metadata table

Bug fixes and improvements:

  *   removed unused ScreenReader in preparation for migrating it to be an external reader
  *   fixed a bug with the generation of thumbnails in Bio-Formats plugins
  *   updated the Maven POM to unify component version property names
  *   tile size is now reported in the core metadata when using the showinf tool
  *   added setFilePatternIds to ImporterOptions for use with Bio-Formats plugins
  *   improved the precision of format identification for MRC, I2I, and Zeiss LSM

Documentation improvements:

  *   fixed and updated a number of external documentation links
  *   added links to public NRRD samples<https://downloads.openmicroscopy.org/images/NRRD/>

Full details can be found at https://docs.openmicroscopy.org/bio-formats/5.8.0/about/whats-new.html

The software is available at:
https://www.openmicroscopy.org/bio-formats/downloads/
and will shortly be available from the Java-8 update site for Fiji users.

Any problems or comments, please use the OME Forums or mailing lists:

http://www.openmicroscopy.org/support


Regards,

The OME Team

The University of Dundee is a registered Scottish Charity, No: SC015096

------------------------------

Date:    Wed, 21 Feb 2018 18:32:00 -0600
From:    Stanislav Vitha <[hidden email]>
Subject: iLabs and monitoring real usage of microscopes

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Deal All,
I have a question for those who have the iLabs scheduling/billing platform in their imaging facilities - how do you keep track of the real use of a microscope?
We are in process of setting up iLabs for our Center  and would prefer not to rely on the users to correctly enter the start and end time of their imaging session when they check in and check out of the reservation system.
We would rather prefer to start counting when users log into the imaging computer and stop counting time when users log out from the imaging computer.
Any advice much appreciated!

Sincerely,

Stan Vitha
Microscopy and Imaging Center
Texas A&M Unibersity

------------------------------

Date:    Wed, 21 Feb 2018 19:54:39 -0600
From:    Luciano Lucas <[hidden email]>
Subject: Aivia - intelligent image visualization and analysis (commercial post)

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Dear All,

  In one week I will be giving a talk about image visualization and analysis while using Aivia (v7). I would like to invite you to attend the live webcast which will take place at 10.30am EST (USA).

Here are the key details for the event:
Date: 1st of March 2018
Time: 10 AM (EST, USA) / 5 PM (GMT, Europe)
Where: Live webcast of event at the Microscopy Imaging Core Facility at Wake Forest University, North Carolina, USA.

To register (free): https://www.drvtechnologies.com/webinar

Title: Tracking life science's processes - Aivia 7
Presenter: Luciano A. G. Lucas, PhD


Key features for Aivia 7 (will be demoed in the webcast):
1. 3D object tracking and lineage tracing 2. New track editor (for 2D and 3D tracks/lineages) 3. Fast surfaces 4. Lossless aivia.tiff compression

To learn more about Aivia 7: https://www.drvtechnologies.com/aivia7

Aivia includes:
1) Machine learning object classification (2 and 3D objects)
2) Use of deep learning for specific applications (e.g. 3D EM image segmentation)
3) Handling of large nD data sets (e.g. 100 of GBs per time point)
      a - Volume rendering
      b - Surface rendering (used to represent the results of segmentation)
4) A wide range of 2 and 3D image analysis pipelines/workflows (including 3D neuron and spine analysis)
     a - several of these supervised or semi-supervised learning
5) Virtual reality image (and results) exploration

  We presented our solution for rendering large data sets at ASCB-EMBO2017: https://www.drvtechnologies.com/single-post/2018/01/26/ASCB-EMBO-2017-Poster-Efficient-microscopy-image-visualization-and-cell-tracking-analysis-of-multi-gigabyte-datasets

  About DRVISION: Aivia is made by DRVISION Technologies (based in Bellevue - greater Seattle area). DRVISION is an algorithm and software development house specialized in machine vision and (machine) learning approaches. Over the last 18 years it has developed and deployed (inside the products of other companies) dozens of machine learning solutions for a wide range of applications, from wafer inspection and civil engineering quality control all the way to 2D / 3D microscopy image analysis. DRVISION has been granted 50 patents, most of which are for novel machine learning solutions.

  My email is [hidden email]. You are welcome to contact me for any details or to test Aivia.

  With best wishes
  Luciano

____________________
Luciano A G Lucas, PhD
Executive Vice President
DRVISION Technologies
[phone]




------------------------------

Date:    Wed, 21 Feb 2018 22:55:04 -0500
From:    Timothy Chaya <[hidden email]>
Subject: Re: iLabs and monitoring real usage of microscopes

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Hello Stan,
The BioImaging Core at UDel has the iLabs interlock connected to the monitor of each scope computer. The users login via a chromebook near the works station that has the iLabs website bookmarked. There they start the session which turns on the monitor. From there the users are trained to start the system and when they are finished they shut down the system and logout.
I think the system works pretty smoothly.

I hope that helps.

-Tim

On Wed, Feb 21, 2018 at 7:32 PM, Stanislav Vitha <[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.
> *****
>
> Deal All,
> I have a question for those who have the iLabs scheduling/billing
> platform in their imaging facilities - how do you keep track of the
> real use of a microscope?
> We are in process of setting up iLabs for our Center  and would prefer
> not to rely on the users to correctly enter the start and end time of
> their imaging session when they check in and check out of the reservation system.
> We would rather prefer to start counting when users log into the
> imaging computer and stop counting time when users log out from the
> imaging computer.
> Any advice much appreciated!
>
> Sincerely,
>
> Stan Vitha
> Microscopy and Imaging Center
> Texas A&M Unibersity
>

--
Tim Chaya
Delaware Biotechnology Institute
Caplan Lab
15 Innovation way
Rm 147
Newark, DE 19702
p. 302-831-3422

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End of CONFOCALMICROSCOPY Digest - 20 Feb 2018 to 21 Feb 2018 (#2018-47)
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