Hi @spunjani, is there a detailed workflow described anywhere in terms of how to use volume alignment tools to recenter and re-extract in conjunction with signal subtraction, especially in a context where one wants the subtracted particles in a smaller box?

Subtraction follows several important patterns. It is anticommutative, meaning that changing the order changes the sign of the answer. It is also not associative, meaning that when one subtracts more than two numbers, the order in which subtraction is performed matters. Because 0 is the additive identity, subtraction of it does not change a number. Subtraction also obeys predictable rules concerning related operations, such as addition and multiplication. All of these rules can be proven, starting with the subtraction of integers and generalizing up through the real numbers and beyond. General binary operations that follow these patterns are studied in abstract algebra.


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Methods used to teach subtraction to elementary school vary from country to country, and within a country, different methods are adopted at different times. In what is known in the United States as traditional mathematics, a specific process is taught to students at the end of the 1st year (or during the 2nd year) for use with multi-digit whole numbers, and is extended in either the fourth or fifth grade to include decimal representations of fractional numbers.

Some European schools employ a method of subtraction called the Austrian method, also known as the additions method. There is no borrowing in this method. There are also crutches (markings to aid memory), which vary by country.[14][15]

The minuend is 704, the subtrahend is 512. The minuend digits are m3 = 7, m2 = 0 and m1 = 4. The subtrahend digits are s3 = 5, s2 = 1 and s1 = 2. Beginning at the one's place, 4 is not less than 2 so the difference 2 is written down in the result's one's place. In the ten's place, 0 is less than 1, so the 0 is increased by 10, and the difference with 1, which is 9, is written down in the ten's place. The American method corrects for the increase of ten by reducing the digit in the minuend's hundreds place by one. That is, the 7 is struck through and replaced by a 6. The subtraction then proceeds in the hundreds place, where 6 is not less than 5, so the difference is written down in the result's hundred's place. We are now done, the result is 192.

The Austrian method does not reduce the 7 to 6. Rather it increases the subtrahend hundreds digit by one. A small mark is made near or below this digit (depending on the school). Then the subtraction proceeds by asking what number when increased by 1, and 5 is added to it, makes 7. The answer is 1, and is written down in the result's hundreds place.

There is an additional subtlety in that the student always employs a mental subtraction table in the American method. The Austrian method often encourages the student to mentally use the addition table in reverse. In the example above, rather than adding 1 to 5, getting 6, and subtracting that from 7, the student is asked to consider what number, when increased by 1, and 5 is added to it, makes 7.

The partial differences method is different from other vertical subtraction methods because no borrowing or carrying takes place. In their place, one places plus or minus signs depending on whether the minuend is greater or smaller than the subtrahend. The sum of the partial differences is the total difference.[17]

I prepared a mask (using segger in chimera - which worked well to generate masks for the 3DVA), resampled on a correct volume, imported it, dilated by 5 and padded by 5 using the volume tools, but then the particle subtraction runs and the particles look the same as before.

The other potential cause I can think of is if the window inner/outer radii were changed during any of the processing. This can cause discrepancies with the multiplicative scale, so the subtraction job has to know what window radii were used in the previous refinement to correct the scale (some more info on the subtraction job is here).

As I checked everything:

2) Particle scales look ok.

3) Inner/outer radii are always the same (0.85 and 0.99 for the local refinement job with the subtraction mask, and for the subtraction job).

Glad to help! Looks like the mask was definitely the issue here. You can also check the subtraction by running a local refinement and checking for density in the subtracted region. Typically at this point, any residual density left over after subtraction would be due to suboptimal pose estimates, or heterogeneity/disorder (a recent discussion of this is here Particle subtraction of detergent belts still maintain low level signal of the belt).

If you are age 65 or older, or have a permanent and total disability, you may qualify for a subtraction to lower your Minnesota taxable income. This applies even if you do not qualify for the federal credit (Schedule R).

Looking at the Python source, I can make a guess. This is handled in ceval.c, in PyEval_EvalFrameEx. INPLACE_ADD has a significant extra block of code, to handle string concatenation. That block doesn't exist in INPLACE_SUBTRACT, since you can't subtract strings. That means INPLACE_ADD contains more native code. Depending (heavily!) on how the code is being generated by the compiler, this extra code may be inline with the rest of the INPLACE_ADD code, which means additions can hit the instruction cache harder than subtraction. This could be causing extra L2 cache hits, which could cause a significant performance difference.

Your experiment is faulty. The way this experiment should be designed is to write 2 different programs - 1 for addition, 1 for subtraction. They should be exactly the same and run under the same conditions with the data being put to file. Then you need to average the runs (at least several thousand), but you'd need a statistician to tell you an appropriate number.

It is so true. Organizations are so much better at adding things than they are at taking things away. We\u2019re better at setting goals and talking about what we\u2019re going to do than we are at talking about what we\u2019re NOT going to do. It's easier to add process than it is to ask why we're still doing that thing that worked great two years ago but mostly isn't relevant anymore. We\u2019re better at adding meetings than we are at removing them. 


In the early years of Facebook, Sheryl Sandberg always made us set \u201Cnon-goals\u201D in addition to goals. The company had a list of the things we weren\u2019t going to do in addition to the things we were trying to do. Even if it sometimes felt perfunctory, I loved that ritual. When I work with start ups, I push that conversation during goal setting: let\u2019s not just set a list of things we\u2019re going to do, let\u2019s also make a list of things we are explicitly NOT going to do this quarter/this half/this year. 


Setting non-goals is a ritual that helps with focus. It should make priorities more clear. It is a great way to decide NOT to start things.


But it is not subtraction. 


Subtraction is the decision to stop doing something \u2014 to take something away. 


Subtraction is usually quite painful to think about for organizations. Inertia is powerful. It is scary to disrupt things that are in motion. We worry about offending people. We worry that the process that feels useless is actually useful. 


I\u2019ll give you an example that has come up 100 times in my work. 


\u201CWe have this meeting. It's got 30 people in it. It started because we needed to coordinate across departments. And then we just kept adding people. And now it's like a weird 30 person stand up every week. I'm not sure we need it any more but I'm nervous to be the one to say - what if we stop doing this?\u201D


This is just the story of one meeting but some version of it is happening inside every company right now. 


My answer: remove the meeting for a month and see what breaks. Chances are that nothing will.


I have five tools and ideas for how companies can get better at subtraction:


1) Make a practice as a leadership team of asking: do we actually need to do this? What would break if we didn't? You can do this through a \u201Cstart / stop / continue\u201D exercise but the most important thing is to both do the exercise AND follow through on it. Actually pick 3 things to stop doing that feel meaningful. Create a culture that rewards people who remove things or even just people who ask the question. There should always be a clean, clear answer for why something exists and why we do it the way we do it. Ask why multiple times and if/when you get to the answer \u201Cbecause that's how we do it,\u201D then you know it's time to subtract. 


2) Even just as a thought exercise, ask how you can do things in half the time. I will never forget the person in IT at Facebook (when it was 10,000+ employees) who told me that they measured productivity inside the company and that it very clearly ground to a halt during peer review season. I know multiple companies that have asked how to make performance reviews less time suck-y and ended up blocking the entire company calendar for one day to write peer reviews versus having it spread over 2 weeks. There are pros and cons to every process design, but even if you ask all the questions and end up redesigning the same thing, at least you feel completely confident on why you're doing it that way. 


3) Calendar bankruptcy: at the end of the year each year, wipe the calendars. I did not come up with this, but it is a great practice for forcing people to evaluate every meeting and whether it truly needs to exist. Yes it is painful for EAs (sorry!) but with subtraction comes pain because you are fighting inertia. It's easy to leave the meeting on the calendar because the room is booked, etc, etc., and it is painful to remove it but it forces you to ask: do we need this meeting? If so, who REALLY needs to be there? Does it really need to be 60 mins?


4) Re-evaluate and refactor all major processes / meetings every 3-6 months. I realize this feels too frequent but given how much collective time things like business reviews take up, you need to think of these processes as iterative not fixed. Try a new agenda, making it shorter, making it asynchronous, remove it and see what breaks, etc. Let me say it again: ALL major processes inside of start ups should be iterative. Your business evolves, your understanding evolves, your priorities evolve... your meetings and processes need to evolve with it! 


5) This last one is wacky and only makes sense for bigger companies but... put someone in charge of subtraction. Eng teams often do this (see: eng efficiency initiative) but what if it happened for the whole company? Someone told me a story about a person who was tasked with reducing time-load on employees and ended up designing things like auto-approving vacation requests of less than 7 days. Imagine how many small things there are like that that eat up time and mental energy? Imagine how many big things go unexamined because people are too afraid to ask the question. It would be an interesting experiment for every company of over 1,000 employees to have someone where half or all of their job was just to look for things to stop doing, someone whose whole job is to ask \u201Cwhy are we doing this?\u201D Someone who was empowered to look for subtraction. 006ab0faaa

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