Overview
Our Scopes | Setup | Timeline | Updates
Our Scopes
Talos L120C G2
- 120 kV LaB6 transmission electron microscope with a Ceta CCD camera
- Shared between the cryoEM SR and Cellular Imaging SR
- Used for room temperature and cryo samples
Glacios Cryo-TEM
- 200 kV FEG transmission electron microscope with a Gatan K3 direct electron detector
- Part of the newly established cryoEM Shared Resource
- Used for cryo samples
cryoEM Shared Resource Timeline
Please note all dates are tentative and may change. For the most up-to-date info please check the updates below. [Timeline last updated March , 2021]
April 1, 2021: Received estimated shipment dates for the computers the vendor – 4/09-4/12 (original date when ordered: late-January 2021).
March 22, 2021: Cellular Imaging data is streaming off the Talos via Steve & Bobbie. For single particle work, if you're familar with collecting manual data using the low-dose kit, please contact Caleigh for instructions on setting up training.
March 19, 2021: Internet and remote access to the K3 server has been verified and tested.
March 18, 2021: Caleigh collected ~2 hours of data and in less than half a day after singing off on the Glacios we have a 100% homegrown 2.76 Å map of apoferritin (expressed & purified on site, collected here, processed here).
March 18, 2021: Talos for Cellular Imaging is LIVE! Reach out to Steve and Bobbie for all of your cellular imaging needs. Thanks to Yan Liu from the Bai for being our pacient guniea pig as we all get used to a new system.
March 17, 2021: If it weren't COVID times, I'm sure we would be celebrating in person, but we have...
Signed off on Booth of the Microscopes!
Unfortunately due to hardware delays we are unable to open them up for automated data collection (we are waiting for the storage servers to come in, so there is no where to store collected data) but we plan to open up the Talos to the Cellular Imaging Core as soon as Steve & Bobbie familiarize themselves with the new software (it a completely separate program from what was on the JEOL). Caleigh has hit the ground running characterizing & optimizing performance, setting up multiscale imaging, calibrating pixel sizes, and finalizing best-use data collection parameters and specifications.
March 12, 2021: The Talos passes all of its SATs!
March 11, 2021: Right on schedule: The cryo-EM Shared Resource website is live! Check it out here! We're thrilled at how it came together it was great to work with a whole team (thanks Jeremy, Regina, Sabrina, Sara, Stuart & Heather)! Can't wait to replace some of these place holder images of ferroportin, rotavirus, and integrin with structures and images collected here at the Hutch!
March 8, 2021: From Thermo: 1:30 pm: the Glacios will be finished on Wednesday! 6:00 pm: the Glacios will not be finished on Wednesday... no timeline. Peter from Colorado should get here tomorrow to work on the Talos. We're still being told Friday.
March 5, 2021: The Glacios has passed all of its system acceptance tests (SATS) with flying colors-- should be all finished this week!
March 5, 2021: Good news: The cryoEM Shared Resource website is almost complete (thanks to the whole team!) and is scheduled to go live on March 11, 2021!
March 5, 2021: Last two pieces (fingers crossed) have arrived! A foot for the Talos and a valve block for the Glacios.
March 4, 2021: Not good news. Still waiting for the Talos foot, SATs cannot be started until it's here because the wooden 2x4's are (expectedly) unstable. Thermo still estimates Talos will be up and SATs completed by next week. At least the good news is that the same engineer (Peter) will be flown back out from Colorado next week to finish the Talos, so at least there is that consistency.
Glacios finish now pushed to end of next week. :(
March 2, 2021: Well. One day out and we're behind schedule. Talos: The foot came for the microscope, but the screw needed to install it did not. It has been 'expedited' and should be coming in from Eindhoven either this week or next. There was also found to be a problem with the filament (LaB6), so the column was vented and the filament realigned. Currently resuming vaccume so the high tension can be conditioned. Should have a beam again soon. Glacios: New valve block controller is on order to try and fix the slamming-down-flu screen issue. New sensor for autoloader is now scheduled to be installed tomorrow (instead of today).
March 1, 2021: New month, new timelines from Thermofisher:
March 1, 2021: Today we should receive the final missing piece for the microscopes. A "foot" for the Talos. Can't wait to get rid of these two by fours...
February 27, 2021: Good News: Center IT has installed the 10 GbE connection between the Thomas and Eastlake Building! This will enable users to rapidly transfer, access, and process their data using the Hutch cluster.
February 27, 2021: The autoloader on the Glacios is not initializing properly :(
February 26, 2021: The screen lift issue on the Glacios has been fixed by adjusting the pressurized air from 6 bar to 5 bar. (It used to slam down). The IGP has been installed on the Talos and the enclosure is being reassembled.
February 25, 2021: The Elsa cryo-holder for the Talos has made it out of customs and is now on site and ready to be used. Also, all column alignments on the Glacios should be finished today.
February 24, 2021: Good News (subject to change)! A little worried to jinx this, but we may be back at 'final' alignments for the Glacios again (it still won't be ready for large scale data collection for a while, but at least the microscope itself might be complete). The IGP and crane attachment were rushed from the Netherlands, it was received today and now we're waiting for the vacuum to condition.
February 23, 2021: The Glacios will not need to be split. This is very good news, because that would have taken a month at least. No progress other than that. The new IGP has been shipped, but we have not gotten an update on where the crane attachment is or if that has been shipped, which is necessary for the IGP replacement.
February 22, 2021: We were promised last Thursday we would have a definitive answer as to whether or not the Glacios would need to be split. This was bumped to Friday, now Monday, and still no answer from ThermoFisher.
February 21, 2021: Good News: Caleigh has installed SerialEM on the Glacios. As soon as the scope is up, we're ready to collect data!
February 18, 2021: Turns out the o-ring was not the issue on the Talos: after the column was vented to clean the detector the IGP was turned off and now will not turn back on. It was likely faulty. A new IGP has been ordered but this equipment is on backorder there is no ETA. New estimated up time for the Talos is mid-March, but that is very preliminary.
February 17, 2021: Still no definitive answer on whether the column for the Glacios will need to be split. We're either very close to completion of the installation or in for at least another month... :( (and after the microscope installation is finished we begin connecting the computers, calibrating software, and benchmarking...)
February 17, 2021: The Ceta camera is clear-- no more fluff! Now we can't pull a vacuum so a new o-ring is on order.
February 15, 2021: There's a little piece of dust on the Ceta camera. It will be blown off with N2 gas.
February 12, 2021: Good News: First image on the Ceta camera from the Talos.
February 12, 2021: Computers are delayed: storage drives were discontinued, looking for alternatives.
February 11, 2021: There is a beam on the Talos (no image on the camera, yet, but a beam)! If things continue to go smoothly ThermoFisher projects the Talos microscope will be completed by the first week of March. Kyle from TX and Mar worked on the Talos this week. Next week Peter from CO will be flown in to continue the work. The Glacios installation continues to struggle and we do not have an updated timeline.
February 9, 2021: We've signed off on the K3 detector!
February 2-3, 2021: Bobbie, Steve, Caleigh, Peng and Melody complete a virtual Talos training with Lindsey Brock from ThermoFisher. This session was a highlight-- can't wait for the scope to be up and running...
February 1, 2021: The installation of the Talos has FINALLY begun!
January 31, 2021: The cryo loading station is set up.
January 29, 2021: K3 installation on the Glacios is *almost* complete... hit a couple hiccups with the microscope connection but an engineer will be back next Thursday to finish the final tests.
January 28, 2021: The K3 computer is installed in its server rack in the accessory room. This computer is so powerful (loud) it can't be kept in the sever racks behind the microscope because the vibrations will compromise the quality of the images collected. We learned this right before our blueprints for the microscope suite were finalized, and thanks to the engineering and design teams at the Hutch, new plans were quickly drawn up and we built an extra room specifically for this computer.
January 27, 2021: Site survey for the Talos begins.
January 26, 2021: K3 installation begins.
January 25, 2021: The Leginon computers are in and are currently being formatted-- thanks Chris!
January 24, 2021: Apoferritin is purified. This test sample will be used to benchmark the microscope and processing pipeline that we set up.
January 22, 2021: Glacios is prepped for the K3 installation-- and the two crates containing the parts for the K3 direct detector have been taken out of storage and delivered to the Glacios room
January 19, 2021: Bobbie and Steve return at full capacity! They are ramping up sample prep and we're counting down the days until imaging can re-start! Fun fact: Between Bobbie, Steve, Melody and Caleigh collectively we have EIGHTY NINE YEARS of electron microscopy experience (36, 35, 10, 8 years respectively).
January 14, 2021: The negative stain bench is set up.
January 12, 2021: We finally have a date for the installation of the Talos to begin: February 1st.
January 7, 2021: Apoferritin is expressed. This test sample will be used to benchmark the microscope and processing pipeline that we set up.
January 6, 2021: The field cancellation unit is installed.
December 22, 2020: The expected delivery for the computers is first week of February 2021-- perfect timing!
December 21, 2020: The computers have been ordered! This includes 2x Lenovo "Tinies" to run Leginon on each scope, a webserver and database server to store the Leginon data, ~300 TB of storage space for temporary data storage, and a WARP processing box so that data can be processed on-the-fly. Huge thank you to SciComp and CIR-SR including Ben McGough, Chris Rogers, Loren Greenen, Irina Kalmus, Jeff Delrow, Jim Rudd, Al Spencer, and Dirk Peterson for working us to sort out the specifics of not just the hardware but all of the networking and physical infrastructure that will be needed to get everything communicating the way it needs to! Also thank to external input and suggestions on computing from Matt Harrington, Paul Thomas, and Daniel Asarnow at UCSF; David and Justin at UW; and Michael Cianfrocco at Michigan.
December 15, 2020: First system acceptance test for the Glacios... it did not pass :(
December 11, 2020: First grids are frozen (thank you to Dr. Betty Shen)!
December 11, 2020: The vitrobot station is set up.
December 10, 2020: The Glacios has its first beam!
December 4, 2020: Vitrobot installed. Thanks also to Steve MacFarlane for helping reorganize the space and so that we could move this new equipment in!
December 3, 2020: The Glacios is almost ready for the field emission gun (FEG)! The FEG is the electron source for our microscope and has a maximum accelerating voltage of 200,000 eV. It provides the small coherent beam of electrons that we use to image our samples at high resolutions.
November 20, 2020: Glacios is plugged in, powered on, and the stage can move!
November 12, 2020: The results of the site survey are in...The monitoring equipment was set up to perform a complete set of measurements every 4 minutes over a ~24 hour period. A total of 290 surveys were performed. As we had expected based on previous measurements, the amount of electromagnetic interference (EMI) could compromise our image quality once the microscope is up and running.
However, this can be fixed in a straight-forward way by 'cancelling' the interference. A three axis magnetic field sensor measures the ambient AC and DC magnetic fields around the microscope column. This is linked to a controller that then generates a near perfectly equal-- but opposite-- field through three cable loops. These two opposing fields cancel each other out, much in the way noise-cancellation headphones work by responding to ambient noise.
Although these cables used to be positioned throughout the room, now they can be neatly tucked within the microscope casing, and you can't even see them when the microscope is fully assembled.
We will have this equipment delivered and installed in January when the microscope is complete.
November 12, 2020: Installation of the Glacios progress:
November 9, 2020: Caleigh arrives!
November 9, 2020: The Glacios, Talos, and Vitrobot are delivered! Other than a small parking snafu for the riggers hired to unload the boxes from the truck, everything went very smoothly!
November 8, 2020: Final punch, right on schedule-- the renovations are complete and we're ready to receive the microscopes (thanks SO MUCH to the whole team, especially Al Spencer!)
November 6, 2020: Thermofisher Scientific conducts a site survey on the newly renovated rooms to check for vibrations, acoustic, and electromagnetic interference.
September 28, 2020: We received a timeline from Thermofisher Scientific with a timeline for the microscope installation! The Glacios installation should be largely finished by the end of the year (December 23) with the first two weeks of January for system acceptance tests and the third week as extra buffer time in case we run into issues. January 22nd is the projected big day.
September 8, 2020: The JEOL JEM-1400 microscope is dismantled and moved into storage. (It's not goodbye, it's until we meet again... and/or until we have the demand for an additional electron microscope and find a room that is up to spec).
August 17, 2020: Renovations are in full swing
August 10, 2020: Renovation starts in the existing DE-level electron microscopy suite to get rooms up to specifications for the new microscopes
July 31, 2020: Caleigh hired
July 15, 2020: We're getting ready to take down our existing electron microscope
July 1, 2020: Melody arrives
June 16, 2020: The K3 detector is delivered and safely stored in the Fred Hutch Lea warehouse onsite until we need it in January
March 3, 2020: Melody hired
December 16, 2019: The Microscopes (a Glacios and a Talos 120C) and the detector (K3 Direct Detector) have been purchased!