large image depository?

[Stanislav Vitha-2]

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Hallo,
Is there some depository for 3D light microscopy datasets, analogous to  
the EMPIAR (Electron Microscopy Pilot Image Archive)?
 
I have a somewhat large z-stack from a Structured Illumination scope that
I would like to share as supplemental data with the manuscript I am about
to submit.

the z-stack is about 1 GB, even with some cropping and LZW compression
it will be larger than the publisher's limit.

Hints and suggestions appreciated.

Stan Vitha
Microscopy and Imaging Center
Texas A&M University

[DamirSudar]

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Hi Stan,

You can check out "The Cell Image library" at
http://www.cellimagelibrary.org/  which may be able to take your
dataset. I'm not sure what their criteria are for accepting data and
whether there are costs for the contributor.

One other thought: you might consider whether your paper is appropriate
for the Journal of Cell Biology and if so, they provide a very
impressive "original image data" respository on:
http://jcb-dataviewer.rupress.org/

Good luck,
- Damir

On 7/16/2015 4:41 PM, Stanislav Vitha 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.
> *****
>
> Hallo,
> Is there some depository for 3D light microscopy datasets, analogous to
> the EMPIAR (Electron Microscopy Pilot Image Archive)?
>  
> I have a somewhat large z-stack from a Structured Illumination scope that
> I would like to share as supplemental data with the manuscript I am about
> to submit.
>
> the z-stack is about 1 GB, even with some cropping and LZW compression
> it will be larger than the publisher's limit.
>
> Hints and suggestions appreciated.
>
> Stan Vitha
> Microscopy and Imaging Center
> Texas A&M University

--
Damir Sudar - Staff Scientist
Lawrence Berkeley Laboratory / Life Sciences Division
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: [hidden email]
WWW: http://www.lbl.gov/lifesciences/labs/sudar_lab.html

Visiting Scientist, Oregon Health & Science University

[George McNamara]

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Hi Stan,

If the image or its zip file is under 1 Gigabyte (maybe back to 800 Mb
limit?) you could post on your free personal account at bepress -- see

http://works.bepress.com/gmcnamara/70/
for one of my Tiki_Goddess posts.

At least one part of TAMU is a bepress subscriber -
http://digitalcommons.bepress.com/subscriber_gallery/
and UT MDACC is not on that page, so simplest is to sign up.

Damir's suggestions are also good.

Enjoy,

George



On 7/16/2015 6:41 PM, Stanislav Vitha 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.
> *****
>
> Hallo,
> Is there some depository for 3D light microscopy datasets, analogous to
> the EMPIAR (Electron Microscopy Pilot Image Archive)?
>
> I have a somewhat large z-stack from a Structured Illumination scope that
> I would like to share as supplemental data with the manuscript I am about
> to submit.
>
> the z-stack is about 1 GB, even with some cropping and LZW compression
> it will be larger than the publisher's limit.
>
> Hints and suggestions appreciated.
>
> Stan Vitha
> Microscopy and Imaging Center
> Texas A&M University
>
>    

--



George McNamara, Ph.D.
Single Cells Analyst
L.J.N. Cooper Lab
University of Texas M.D. Anderson Cancer Center
Houston, TX 77054
Tattletales http://works.bepress.com/gmcnamara/42

[George McNamara]

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Hi Les,

You may not be subscribed to the Confocal Listserv, in which case it
would not send you an "are you sure you want to post this?" request. I
am copying the listserv and will click yes.

You did not include the direct web link to your and your colleagues
editorial, so here it is:
http://www.cell.com/biophysj/abstract/S0006-3495(15)00230-1


I am all for reproducibility! Also transparency - of both our specimens
and science. Too bad Science has not not figured out open access (which
B.J. has) - this recent policy forum is not O.A.
http://www.sciencemag.org/content/348/6242/1420


George
p.s. the same issue of Science did have a guest editorial, "Solving
reproducibility" that is open access,
http://www.sciencemag.org/content/348/6242/1403.long
too bad the related content -- including content authored by its editor
in chief -- is not.

On 7/17/2015 10:14 AM, Loew,Leslie M. wrote:

> Stan, George and Damir,
> This didn't seem to appear on the confocal listserve, so I thought I'd send it to you directly. I'm pretty excited about these development for BJ, so please spread the word.
> Best,
> Les
>
> -----Original Message-----
> From: Loew,Leslie M.
> Sent: Friday, July 17, 2015 8:15 AM
> To: [hidden email]
> Subject: RE: large image depository?
>
> Hi Stan,
> This issue of access to large datasets has been a hot topic and a challenge for scientific journals. Take a look at the " Guidelines for the Reproducibility of Biophysics Research" published earlier this year by the Biophysical Journal (BJ) and the Biophysical Society (you can google it).  BJ is about to partner with Mendeley to provide a permanent archive for large datasets that are not covered by community-driven repositories (like EMPIAR or PDB).  This also prompts me to inform the microscopy community that starting some time in August, BJ will be supporting an online multidimensional image viewer capable of navigating through x,y,z,t, multichannel microscopy data.
> Best,
> Les Loew
> U. Conn. Health
> Editor in Chief, Biophysical Journal
>
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of George McNamara
> Sent: Thursday, July 16, 2015 9:29 PM
> To: [hidden email]
> Subject: Re: large image depository?
>
> *****
> 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 Stan,
>
> If the image or its zip file is under 1 Gigabyte (maybe back to 800 Mb
> limit?) you could post on your free personal account at bepress -- see
>
> http://works.bepress.com/gmcnamara/70/
> for one of my Tiki_Goddess posts.
>
> At least one part of TAMU is a bepress subscriber - http://digitalcommons.bepress.com/subscriber_gallery/
> and UT MDACC is not on that page, so simplest is to sign up.
>
> Damir's suggestions are also good.
>
> Enjoy,
>
> George
>
>
>
> On 7/16/2015 6:41 PM, Stanislav Vitha 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.
>> *****
>>
>> Hallo,
>> Is there some depository for 3D light microscopy datasets, analogous
>> to the EMPIAR (Electron Microscopy Pilot Image Archive)?
>>
>> I have a somewhat large z-stack from a Structured Illumination scope
>> that I would like to share as supplemental data with the manuscript I
>> am about to submit.
>>
>> the z-stack is about 1 GB, even with some cropping and LZW compression
>> it will be larger than the publisher's limit.
>>
>> Hints and suggestions appreciated.
>>
>> Stan Vitha
>> Microscopy and Imaging Center
>> Texas A&M University
>>
>>
>>      
>
>    

--



George McNamara, Ph.D.
Single Cells Analyst
L.J.N. Cooper Lab
University of Texas M.D. Anderson Cancer Center
Houston, TX 77054
Tattletales http://works.bepress.com/gmcnamara/42

[Stanislav Vitha-2]

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*****

Thank y'alls all for your suggestions and comments.
I will be looking into these options for the next paper.
For this one I ran out of time, I had to wrap thing up before my leave.

Stan Vitha
Microscopy and Imaging Center
Texas A&M University

[White, Silke /DZNE]

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Dear all,

we are currently in the planning process for a new building for our institute, which is also going to host our Imaging Facility.

Right now, we are trying to define the properties of the air conditioning unit. Next to obvious parameter like temp range, temp gradient and thermal load, the company responsible for the air conditioning now asked us to also provide them a specific rate for the air flow.
I do not have a glue and I can't seem to find the number anywhere, least of all in the companies specs.

Can any of you help me here? Do you happen to know the air flow rate of your own microscope rooms? And if so, are you happy with it or would you define it differently if you had the chance?

I'll be grateful for any help!

Thanks,

Silke



**********************
Silke White

Imaging Platform - Microscopy Manager
German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association
Arnoldstraße 18 / 18b
01307 Dresden
 t  0049 351 210 463 16
f  0049 351 210 463 99
e  [hidden email]
web   http://www.dzne.de

***********************

Executive Board: Prof. Pierluigi Nicotera, MD PhD (Chairman of the Executive Board and Scientific Member of the Executive Board) and Dr. Sabine Helling-Moegen, LL.M. (administrative member of the executive board)
The DZNE is registered in the association register of the Bonn District Court (Amtsgericht Bonn) (Az. VR 9021).

***********************

[Doube, Michael]

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Hello Silke!

I have reasonably limited experience of air flow specifics but usually for human comfort (and non-sleepiness) you need to do several (~6) room-changes per hour of fresh air, to get rid of the CO2 produced by respiring human occupants and to supply some O2. Air-con units usually do a pretty good job of getting temperature and humidity right, but they often do not supply fresh air all by themselves (unless they are air-con units are attached to fresh-air ventilation inlet, or are some kind of pass-through heat exchanger).

So a rough guess would be volume of room * 6 to get m^3/hour of air going through the microscope room.

(I only know this through various estates departments in London attempting to stop us from complaining about the laboratory temperature by shutting off the fresh air supply - eventually the complaining, and all other signs of life, would stop using this approach).

Very best greetings from London,

Michael


On 22/07/15 10:45, White, Silke /DZNE wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Dear all,
>
> we are currently in the planning process for a new building for our institute, which is also going to host our Imaging Facility.
>
> Right now, we are trying to define the properties of the air conditioning unit. Next to obvious parameter like temp range, temp gradient and thermal load, the company responsible for the air conditioning now asked us to also provide them a specific rate for the air flow.
> I do not have a glue and I can't seem to find the number anywhere, least of all in the companies specs.
>
> Can any of you help me here? Do you happen to know the air flow rate of your own microscope rooms? And if so, are you happy with it or would you define it differently if you had the chance?
>
> I'll be grateful for any help!
>
> Thanks,
>
> Silke
>
>
>
> **********************
> Silke White
>
> Imaging Platform - Microscopy Manager
> German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association
> Arnoldstraße 18 / 18b
> 01307 Dresden
>  t  0049 351 210 463 16
> f  0049 351 210 463 99
> e  [hidden email]
> web   http://www.dzne.de
>
> ***********************
>
> Executive Board: Prof. Pierluigi Nicotera, MD PhD (Chairman of the Executive Board and Scientific Member of the Executive Board) and Dr. Sabine Helling-Moegen, LL.M. (administrative member of the executive board)
> The DZNE is registered in the association register of the Bonn District Court (Amtsgericht Bonn) (Az. VR 9021).
>
> ***********************
>

--
Michael Doube
BPhil BVSc PGCert(Vet Ed) PhD FHEA MRCVS
Lecturer, Comparative Biomedical Sciences
The Royal Veterinary College, University of London
London NW1 0TU
United Kingdom

[phone] (Internal: 5503)
@mdoube

<http://www.rvc.ac.uk>

This message, together with any attachments, is intended for the stated addressee(s) only and may contain privileged or confidential information. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Royal Veterinary College.

[Ekaterina PAPUSHEVA-2]

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*****

Dear Silke,

Here is ours, for one of the rooms-with total heat production of 4.5 kW:

rate of airflow
in: 970m³/h
out: 950m³/h
Cooling power: 4690W
Roomtemp.: 21°C (+-1,5°C)


Good luck :-)
Katja

[Smith, Benjamin E.]

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We've had issues also having our room transiently heating up when equipment is turned on (we have 2 computer work stations, two confocals, and one compound microscope in the room), and then the air handler over-compensating by cooling the room too much.  This was fixed by having the blower run at 80%speed  continuously (unfortunately I'm not sure what this translates to in cubic feet), rather than have the blower speed ramp based on demand.  We also warmed up the chill water supply to the air handler to 15oC, so that we could further reduce thermal cycling.  I've also installed a HEPA filter that blows over the thermostat, so that the thermostat can respond much faster to thermal deviations, and have also carefully aimed each vent (using kim wipe strips to track the airflow) so that they blow along the ceiling , over all the equipment, and then down the far wall where the computers are.  With all this combined, we have been able to keep the air around the microscopes within 22oC +/- 0.1oC and the humidity at exactly 40%.  

The key is to explain the problem of thermal creep to the air handler people, so they understand the importance of tight thermal control.  To make sure their program works, make sure you start with everything turned off, then turn everything on (we even turned on a space heater just to be sure how the system would respond).  This allows the PID autotuner to know exactly what it is up against.  Then, I mopped the whole floor to put on a humidity load, to make sure the system could also completely dehumidify the room under a worst case scenario.

It takes about a day to get a room dialed in, but it is very much worth it, as microscopy equipment definitely performs at it's very best in a highly stable environment.

Hope this helps,
  Ben Smith
________________________________________
From: Confocal Microscopy List [[hidden email]] on behalf of Ekaterina PAPUSHEVA [[hidden email]]
Sent: Wednesday, July 22, 2015 7:31 AM
To: [hidden email]
Subject: Re: new facility planning … flow rate air conditioning

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Dear Silke,

Here is ours, for one of the rooms-with total heat production of 4.5 kW:

rate of airflow
in: 970m³/h
out: 950m³/h
Cooling power: 4690W
Roomtemp.: 21°C (+-1,5°C)


Good luck :-)
Katja

[kspencer007]

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Hi Silke;
        I definitely endorse the DuctSox idea. They are great for air flow without causing currents. http://www.ductsox.com/
        When you first turn them on though, they do create a lot of dust. Don't move your equipment in right away...let the dust settle first.
        Kathy

The Scripps Research Institute
Dept of Molecular and Cellular Neuroscience
10550 N. Torrey Pines Road
DNC 210
La Jolla, Ca 92037



-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of White, Silke /DZNE
Sent: Wednesday, July 22, 2015 2:31 AM
To: [hidden email]
Subject: new facility planning . flow rate air conditioning

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Dear all,

we are currently in the planning process for a new building for our institute, which is also going to host our Imaging Facility.

Right now, we are trying to define the properties of the air conditioning unit. Next to obvious parameter like temp range, temp gradient and thermal load, the company responsible for the air conditioning now asked us to also provide them a specific rate for the air flow.
I do not have a glue and I can't seem to find the number anywhere, least of all in the companies specs.

Can any of you help me here? Do you happen to know the air flow rate of your own microscope rooms? And if so, are you happy with it or would you define it differently if you had the chance?

I'll be grateful for any help!

Thanks,

Silke



**********************
Silke White

Imaging Platform - Microscopy Manager
German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association Arnoldstraße 18 / 18b
01307 Dresden
 t  0049 351 210 463 16
f  0049 351 210 463 99
e  [hidden email]
web   http://www.dzne.de

***********************

Executive Board: Prof. Pierluigi Nicotera, MD PhD (Chairman of the Executive Board and Scientific Member of the Executive Board) and Dr. Sabine Helling-Moegen, LL.M. (administrative member of the executive board) The DZNE is registered in the association register of the Bonn District Court (Amtsgericht Bonn) (Az. VR 9021).

***********************

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Dear Silke,

when we rebuilt the BIC facility labs in Constance this year, although
the actual calculations were done by an  engineering company, as Peter
indicated, they were essentially based on heat load, room size and
temperature drift.
It should be best to specify the parameters you want to have (Temp
stability) and provide the engineers with room volume and heat load.
Although I don't have them on paper, the exchange rates to get to a
stable +- 1 K in the OMX lab were surprisingly high, much higher than
the usual air exchange rates in a research lab.
The air sock system mentioned by Peter is also a very good idea, as it
equalizes the air flow, it does not only improve stability, but also is
more comfortable for the users, as the draft is almost not feelable,
even for high air flows.
One important thing to take into account is the temperature of the fresh
air, as it can bring an additional heat load which has to be taken into
account, especially during summer times.

Best regards

Martin



Am 22.07.2015 um 11:31 schrieb White, Silke /DZNE:

> *****
> 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 all,
>
> we are currently in the planning process for a new building for our institute, which is also going to host our Imaging Facility.
>
> Right now, we are trying to define the properties of the air conditioning unit. Next to obvious parameter like temp range, temp gradient and thermal load, the company responsible for the air conditioning now asked us to also provide them a specific rate for the air flow.
> I do not have a glue and I can't seem to find the number anywhere, least of all in the companies specs.
>
> Can any of you help me here? Do you happen to know the air flow rate of your own microscope rooms? And if so, are you happy with it or would you define it differently if you had the chance?
>
> I'll be grateful for any help!
>
> Thanks,
>
> Silke
>
>
>
> **********************
> Silke White
>
> Imaging Platform - Microscopy Manager
> German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association
> Arnoldstraße 18 / 18b
> 01307 Dresden
>   t  0049 351 210 463 16
> f  0049 351 210 463 99
> e  [hidden email]
> web   http://www.dzne.de
>
> ***********************
>
> Executive Board: Prof. Pierluigi Nicotera, MD PhD (Chairman of the Executive Board and Scientific Member of the Executive Board) and Dr. Sabine Helling-Moegen, LL.M. (administrative member of the executive board)
> The DZNE is registered in the association register of the Bonn District Court (Amtsgericht Bonn) (Az. VR 9021).
>
> ***********************

--
Bioimaging Center
University of Konstanz
P.O. Box 604
D-78457 Konstanz
Germany
[hidden email]
www.uni-konstanz.de/bioimaging

[Craig Brideau]

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Those fabric duct things look pretty neat! Seems like an obvious solution
to a common problem. I wonder if vacuuming them off with a HEPA-filtered
vacuum cleaner before turning them on would help with the initial dust. I
also wonder if the company would consider a clean-room compatible version
with a non-linting synthetic fabric...

Craig

On Wed, Jul 22, 2015 at 9:09 AM, Kathryn Spencer <[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 Silke;
>         I definitely endorse the DuctSox idea. They are great for air flow
> without causing currents. http://www.ductsox.com/
>         When you first turn them on though, they do create a lot of dust.
> Don't move your equipment in right away...let the dust settle first.
>         Kathy
>
> The Scripps Research Institute
> Dept of Molecular and Cellular Neuroscience
> 10550 N. Torrey Pines Road
> DNC 210
> La Jolla, Ca 92037
>
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of White, Silke /DZNE
> Sent: Wednesday, July 22, 2015 2:31 AM
> To: [hidden email]
> Subject: new facility planning . flow rate air conditioning
>
> *****
> 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 all,
>
> we are currently in the planning process for a new building for our
> institute, which is also going to host our Imaging Facility.
>
> Right now, we are trying to define the properties of the air conditioning
> unit. Next to obvious parameter like temp range, temp gradient and thermal
> load, the company responsible for the air conditioning now asked us to also
> provide them a specific rate for the air flow.
> I do not have a glue and I can't seem to find the number anywhere, least
> of all in the companies specs.
>
> Can any of you help me here? Do you happen to know the air flow rate of
> your own microscope rooms? And if so, are you happy with it or would you
> define it differently if you had the chance?
>
> I'll be grateful for any help!
>
> Thanks,
>
> Silke
>
>
>
> **********************
> Silke White
>
> Imaging Platform - Microscopy Manager
> German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz
> Association Arnoldstraße 18 / 18b
> 01307 Dresden
>  t  0049 351 210 463 16
> f  0049 351 210 463 99
> e  [hidden email]
> web   http://www.dzne.de
>
> ***********************
>
> Executive Board: Prof. Pierluigi Nicotera, MD PhD (Chairman of the
> Executive Board and Scientific Member of the Executive Board) and Dr.
> Sabine Helling-Moegen, LL.M. (administrative member of the executive board)
> The DZNE is registered in the association register of the Bonn District
> Court (Amtsgericht Bonn) (Az. VR 9021).
>
> ***********************
>