ceej64.bsky.social
Postdoctoral Scientist @HHMIJanelia by way of @WelsherLab | Microscopist 🥼| Leading Edge Fellow 💪 | Weekday Warrior 🥋 | Openly Autistic | Memes and Motivation 🥇|
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If you are attending the Optica Biophotonics conference in San Diego, be sure to check out Magdalena's talk on this work!
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DeepPD obtains better de-aberrated images without requiring optical correction, and more completely estimates wavefronts by accounting for nonlinearities in our deformable mirror and other assumptions not captured in our original analytic approach.
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In our new preprint, we combine a deep learning framework with our phase-diverse image acquisition called "DeepPD".
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We demonstrated that by acquiring few extra images with added optical aberrations ("phase diversities") wavefront sensing can be achieved using an analytic optimization scheme.
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Last year we published a simple experimental method for image-based wavefront sensing in fluorescence microscopy using phase diversity.
opg.optica.org/optica/fullt...
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Too bad it will involve actual legwork to distinguish against the broader uses of these terms. My research project is literally called "Phase Diversity" - it originated in the 1980's in Astronomy - I study physics, not DEI. Wait until they find out how much cis/trans gets used in Chemistry!
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This is utterly insane. I literally study a method called "Phase Diversity" that originates in Astronomy and deals with physics - not DEI. I am lucky that I will not be affected in the short term but this is absolutely horrifying censorship and it is only the start.
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All of these structures and checks and balances are theoretical: they have never been stress tested in this manner before. Laws are meaningless if not enforced.
The question is: how much will -unelected- Elon Musk be allowed to dismantle the government in this clearly unconstitutional manner.
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This has been the darkest week for science in recent memory. Horrifying to imagine what else is to come.
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I like to think there are others out there on their own improbable journeys. These are the students who perhaps stand to gain the most if successful, and we do them a great disservice when we give up on them before giving them a chance because they deviate from an increasingly-precise template
end/
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The dilemma is not just who fails when we select candidates purely on numbers, but who are we excluding that would have succeeded? What do these metrics inadequately model about what makes someone a successful research scientist?
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Which is to say, academia is not alone in this problem of using indicators of past performance to predict future success - particularly when the past performance insufficiently captures the physical, mental, and emotional tolls to be endured in future training. 7/
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How to select SEAL Candidates who will be successful in training has been a long-standing problem. It turns out that physical fitness scores are not sufficiently predictive: grit is also a critical component - but difficult to measure. 6/
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It reminds me of a similar problem the military faces: How do you assess and select Navy SEALS?
BUD/S, the school for SEAL Candidates, has a physical fitness test that represents a high barrier to entry - and yet up to 90% of those that enter fail to become SEALS.
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What do you do when the answer isn't in the back of the book? When nobody knows the answer and you only have yourself to rely on?
Students used to achieving high scores and riding the coattails of impressive team projects may flounder in conditions of relentless failure and uncertainty. 4/
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I felt intimidated and hopelessly out of my depth the first week among students who were more prepared or from better schools
And yet... All those smart students who knew all the answers week 1? Most of them didn't make it to the end. What I lacked in knowledge I made up for in mental toughness 3/
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I came from a small, unranked public school with poor test scores, a poor math background, and one co-author manuscript in preparation. If you lined me up in class rank I was probably near the bottom. 2/
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I was at a Sonic concert last weekend and it was ground zero for weapons-grade-autism. Literally doesn’t get more autistic than Sonic lol
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I can’t help but think this is a good thing: so many companies latched onto wokeness and DEI as performative virtue signaling: we will now see who is serious about change and improving things and who just wanted to look good while doing nothing.
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The common theme through both of these articles is that becoming the type of person who continually seeks challenge to drive growth will make you a better scientist, labmate, and leader.
These traits are not innate - you develop them over time when you focus on becoming 1% better every day.
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Further, you are shown the fact that teams can accomplish feats - like continuously carrying a 200# sand log for over a mile - that individuals cannot. Building a mindset that is team-oriented will take you farther than being a person who is focused solely on their own priorities.
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This order applies even - and especially if you are personally suffering. You are taught to instead look for a teammate to help. If every teammate is looking out for each other instead of themselves, no one is left behind.
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For my 2nd article I discuss the impact of participating in the GORUCK Challenge - a Special Operation Forces-led military-style rucking challenge which seeks to develop teamwork, leadership, and stress inoculation.
As both a leader and follower you are taught to prioritize: Team > Teammate > Self
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These are all capabilities that scientists need to withstand the challenges that accompany the task of discovering new knowledge through an isolating period of continuous failure. If you have never tried BJJ or any martial art - consider this your sign to take the leap and start!
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In this article I talk about the role Brazilian Jiu-Jitsu has played in my development as a scientist and scholar. BJJ will humble you no matter how smart and strong you are. It requires resilience and humility. It teaches you to problem solve under pressure.
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Adding one more reply for those interested in 3D-TrIm’s high-speed virus tracking: #Academicsky #Science #Microscopy
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You can learn more about 3D-TrIm by reading the paper at: www.nature.com/articles/s41...
or instead check out an article for non-scientists: today.duke.edu/2022/11/watc...
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Further, the large axial range means that 3D-TrIm gives an unprecedented view into the motion of single viruses in 3D tissue environments.
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This detail originates from the high speed: trajectories are sampled every 1 millisecond, yielding 1000 localizations per second.
3D, two-photon images acquired simultaneously give context to the particle motion enabling new insights into the pre-binding motion and contacts of viral particles.
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3D-TrIm decouples acquisition for imaging and particle tracking, allowing both acquisitions to be optimized and enabling multiple orders of magnitude faster tracking that is independent of axial extent. Compare the trajectory detail enabled by 3D-TrIm against conventional spinning disk acquisition:
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Conventionally, single particle tracking is accomplished by acquiring Z stacks and looking at particle motion over time. Because tracking and imaging imaging are acquired frame-by-frame and volume-by-volume, the temporal resolution greatly deteriorates as the volume size expands.
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I think I am in the clear for now but this was a big wakeup call to backup more frequently, & to have enough extra space that I do not need to delete the old one until complete. 2 is 1, and 1 is none but in this case it was more like 3-4 became 1.
Hope this inspires you to review your backup plan!
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Most - but not all files were recovered but many were indeed unrecoverable. Unstoppable Copier to the rescue! This program checks for read errors corruption when copying - a great way to merge the changes from the original drive with the backup.
www.roadkil.net/program.php?...
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Priority #1 was recovering the deleted backup. When you delete files they are not deleted - only freed to be overwritten. As my backup drive had no other write activity & my backup attempt failed early, the chance of recovery was high. I first turned to the free tool, Recuva www.ccleaner.com/recuva
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My first mistake was accidentally deleting my last backup - because I found I was unable to make a new one.
Alarmed - I ran chkdsk and it failed after hours of very slow scanning.
Event viewer showed continual warnings of bad blocks - a sure sign of hard drive failure in progress.
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The result is that you can arbitrarily choose the volume rate and interpolate the remaining unscanned voxels which are closely-spaced. This enables you to choose your desired balance between imaging rate and quality.
Read the paper here: opg.optica.org/oe/fulltext....
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3D-FASTR provides a theoretical framework and experimental validation using a commercial two-photon system with an electrically tunable lens to show that these scans can be timed so that only unique voxels are scanned every frame. This means that every single plane is visited every frame.
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Raster scanning 1 frame at a time is slow. The more planes in your volume the slower it is - and the larger time difference between the bottom and top planes.
In 3D-FASTR, the raster and focus scanning are performed at the same time at a rate that creates linear tessellating patterns.