A voter casts a ballot at Smelser Town Hall in Georgetown, Wis., on Nov. 8, 2016. Credit: Nicki Kohl/Telegraph Herald via AP

I’ve been following voting machine technology and Wisconsin’s election since our Oct. 22 episode, “How to (really) steal an election.”

Starting this morning, Wisconsin’s counties have 12 days to recount all their ballots from the Nov. 8 general election.

Why is there a recount in Wisconsin?

Wisconsin was one of the closest states in the presidential election – only 22,177 out of nearly 3 million votes cast separated Donald Trump from Hillary Clinton in the state’s official canvass. And some election security experts, like University of Michigan computer science professor Alex Halderman, have said they saw statistical patterns favoring Donald Trump in counties that relied more on “direct-recording electronic voting machines” than on traditional paper ballots. Though Halderman didn’t say he sees proof of hacking, he said the patterns were worth looking into.

Other journalists and members of the general public have pointed to other anomalies in at least two Wisconsin counties that made them suspicious. (More on those cases below.)

In Wisconsin, recounts can be demanded only by candidates. After Hillary Clinton’s campaign signaled it would not be seeking a recount, Green Party candidate Jill Stein stepped in to raise money to fund a statewide recount in Wisconsin and at least two other states. Clinton campaign officials then released a statement saying they would join the recount to ensure that their interests were being represented. They also said they did not expect the results to change in Wisconsin.

How will the votes be counted?

Wisconsin uses three types of voting machines.

The first, and most common, is paper ballots, which are marked by voters with a pen and then run through an optical scanner, which tabulates the votes automatically.

The second, which is used primarily by voters with disabilities, is called a ballot-marking device. This is a computer that can, for example, read choices out loud to a voter with impaired vision. The computer then prints marks on a physical ballot, which is run through the same scanner as other paper ballots.

For both of those types of ballots, local elections officials, sometimes with the help of vendors, will reprogram their optical scanners to count only presidential votes for a recount. They will do test runs with sample ballots to see if the reprogramming leads to accurate counts.

The third type of voting machine, which is the focus of those who think Wisconsin’s election may have been hacked, are called “direct-recording electronic voting machines,” or DREs. Rather than marking a paper ballot, a voter’s choices are stored on memory cards.

Will all the votes be counted by hand?

No. A county circuit court judge ruled Tuesday that even though a hand recount would be more thorough, the Stein campaign had not shown that there was “clear and convincing” evidence of fraud that would warrant requiring hand-counting under Wisconsin’s recount laws.

That means it’s up to each county’s Board of Canvassers to decide if they will do a hand recount or use machines – at least for the votes cast on paper ballots.

How do you do a recount with electronic voting machines?

In Wisconsin, all DRE machines also have “voter-verified paper audit trails.” This is a paper tape that is visible to the voter as choices are made. It shows that the choice the voter intended to make is the same one that is recorded.

Votes cast on the DRE machines must be recounted from the paper tape, according to the Wisconsin Election Commission. Otherwise, it’s impossible to verify that a malicious program or software error wasn’t miscounting or flipping votes.

To count the electronically cast votes, workers will cut the paper tapes from each machine into individual pieces representing a single voter’s choices – a sort of virtual ballot. Those pieces are then shuffled, so no one could deduce from the order of the ballots whose vote was being counted.

Will any recount be done by hand?

Outagamie County, where an error in some towns led to reports of more votes for president than the total number of votes cast, will not be doing a full hand recount. That’s according to the Wisconsin Election Commission.

The Wisconsin Election Commission spokesman, Reid Magney, emphasized that all the paper ballots will still be looked at, and representatives from campaigns are welcome to count along as they go, but the final recount tabulation will be by optical scanner. He also noted that the problems reported were not with the scanner, but with the adding together of results by municipal staff.

As with the rest of the state, direct-recording electronic votes will still have to be counted by hand by cutting up the paper audit trail tape. (Touchscreens were at the center of the hacking concerns raised by election security experts.)

In another county where election night problems had raised eyebrows, officials will count by hand. Rebecca Evert, the Sauk County Clerk, told the Baraboo News Republic that the city of Baraboo had problems sending results from one precinct by modem. So votes were saved on two memory sticks, which ended up both being counted by mistake.

Evert told Reveal from The Center for Investigative Reporting that even though she doesn’t have to, she wants to put any doubts to rest and will count all the county’s votes by hand.

“I’d just as soon do the hand count, so everyone can see it’s all good,” she said.

There’s a full list of recount methods by county on the Wisconsin Election Commission’s website.

So the recount is going ahead. Could anything stop it?

The Republican Party of Wisconsin has filed a complaint with the Federal Election Commission against the Stein and Clinton campaigns, alleging that Stein improperly coordinated her fundraising efforts for the recount with the Clinton campaign.

Magney told Reveal in an email that “the FEC complaint will have no effect on the Wisconsin Elections Commission’s order for a presidential recount.”

The Stein campaign told the Milwaukee Journal Sentinel that it thinks the complaint is essentially a public relations move that won’t affect the recount.

If you have other questions about the recount process in Wisconsin, email me and I’ll try to find the answer and update this explainer.

Michael Corey can be reached at mcorey@revealnews.org. Follow him on Twitter: @mikejcorey.

Michael Corey is Reveal's senior data editor. He leads a team of data journalists who seek to distill large datasets into compelling and easily understandable stories using the tools of journalism, statistics and programming. His specialties include mapping, the U.S.-Mexico border, scientific data and working with remote sensing. Corey's work has been honored with an Online Journalism Award, an Emmy Award, a Polk Award, an IRE Medal and other national awards. He previously worked for the Des Moines Register and graduated from Drake University. He is based in Reveal's Emeryville, California, office.