Jonas Mekas in 2011. (Joel Ryan/AP)

Jonas Mekas, the Lithuanian-born director, critic, patron and poet widely regarded as the godfather of modern American avant-garde film and as an indispensable documenter of his adopted New York City, died Jan. 23 at his home in Brooklyn. He was 96.

The New York-based nonprofit Anthology Film Archives, a leading avant-garde cinema and center for film preservation, announced the death but did not provide a cause. Mr. Mekas was the longtime artistic director of the institution.

Mr. Mekas, who arrived in the United States in 1949 as a refugee, was weighted by the scars of wartime Europe and energized by postwar America. He was at the center of a historic era for the avant-garde. He published poetry and memoirs, made hundreds of films and videos, wrote an influential column for the Village Voice and opened Anthology Film Archives, where future filmmaker Martin Scorsese was a frequent attendee in his youth.

Scorsese, John Waters and James Franco were among Mr. Mekas’s admirers, and although he never approached mainstream popularity, his friends and collaborators included some of the most important artists of his time and some of the most famous people in the world.

Jacqueline Kennedy allowed him to film her and her family, a rare gesture by the private former first lady and the basis of the 1999 Mekas documentary “This Side of Paradise.” He was an early supporter of Andy Warhol and helped film Warhol’s underground classic “Empire” (1965), an eight-hour silent portrait of the Empire State Building. He shot some of the earliest known footage of rock’s prototypical punk/avant-garde band, the Velvet Underground.

He was close to Allen Ginsberg and other beat poets, and Mr. Mekas’s first full-length release, “Guns of the Trees,” was a 1961 documentary that featured Ginsberg’s narration. He knew artist Yoko Ono years before she met Beatle John Lennon and later became friends with both, filming a Lennon birthday where guests included Beatles drummer Ringo Starr and jazz trumpeter Miles Davis. Mr. Mekas also helped Lennon and Ono settle into New York after they moved from London in the early 1970s.

Mr. Mekas’s adaptation of a play about life in a military prison, “The Brig,” won the grand prize at the Venice Film Festival in 1963. Other notable works included “Diaries Notes and Sketches” (1969), a three-hour documentary about the New York art scene of the 1960s that features shots of Lennon and Ono, author Norman Mailer and Harvard University psychologist and LSD advocate Timothy Leary; “Reminiscences of a Journey to Lithuania” (1972); and “Lost, Lost, Lost” (1976), reflections on his early years in New York, with footage of Ginsberg as well as poets Frank O’Hara and Amiri Baraka.

Many of his projects were collaborations with his brother and fellow refugee, Adolfas Mekas, who died in 2011.

Using film as a diary, never far from a 16-millimeter Bolex camera, Mr. Mekas defied the rules of commercial movies while reaching back to the earliest days of moving images, when filmmakers simply recorded scenes of everyday life. Some works were as intimate and dreamlike as a home movie, with abrupt cuts and disjointed sound. The technique often reinforced the story; the harsh lighting and blurred images of his Velvet Underground film seemed to capture the jarring, foggy ambiance of the music.

Mr. Mekas was also revered among fellow poets, especially for the cycles “Idylls of Semeniskiai,” about his early years in rural Lithuania, and “Reminiscences,” verse about his years after World War II.

Mr. Mekas was born in the farming community of Semeniskiai on Dec. 24, 1922. The Soviet Union annexed Lithuania in 1939, only to have the Nazis seize the country two years later.

In June 2018, the New York Review of Books featured an interview and essay that accused Mr. Mekas of long obscuring or minimizing his involvement with two anti-Semitic newspapers in his youth during the Nazi occupation. He contributed poems and reviews to the publications and denied he shared their noxious political views. Mr. Mekas told the New York Times that the Review article was “dirty” and inaccurate.

Mr. Mekas, who said he spent time doing forced labor in Germany during the war, arrived on a refu­gee ship in New York in 1949. Already fascinated by movies, he initially thought he could adapt avant-garde sensibilities to commercial films. But he decided within a few years that the mainstream was hopeless. In the early 1960s, he helped establish the New American Cinema Group, through which Mr. Mekas, writer-filmmaker Peter Bogdanovich, photographer-filmmaker Robert Frank and others called for an independent system of making and distributing movies.

“The official cinema all over the world is running out of breath. It is morally corrupt, esthetically obsolete, thematically superficial, temperamentally boring,” the group announced in its founding manifesto.

Over the following decades, Mr. Mekas championed the avant-garde in every way possible — as a director, fundraiser, critic, publisher, programmer, distributor and agitator, even spending a night in jail in 1964 for exhibiting Jack Smith’s explicit “Flaming Creatures.” He was the Village Voice’s original film reviewer, and his Film Culture magazine (which ended in the 1990s) included contributions from Bogdanovich, Andrew Sarris and Manny Farber.

He grew more prolific with age. In 2007, when he turned 85, he posted a new short film online for every day of the year. In his 90s, he was still regularly adding videos to his website, whether shots of rain falling in Brooklyn or a mealtime conversation with fellow documentary maker Agnès Varda.

In an interview with the Times published earlier this month, Mr. Mekas calmly ruminated about death.

“It’s a very normal transition,” he said. “What’s beyond that line, it’s where the mystery begins, where it becomes interesting. There are glimpses in the mes­sages that come from there, some of the old Scriptures. Indications are there, and I believe it all. I believe it much more than anything that’s written since the 12th century.”

— Associated Press