Jewish-American Emily Henochowicz recalls how she lost an eye at a protest in Israel after the storming of the Gaza aid flotilla

As a student artist, Emily Henochowicz has always been fascinated by the way the brain processes visual signals to form images of the physical world around us. That has been a theme of her work at the prestigious New York art college, Cooper Union, which she joined three years ago.

In her first term she made a costume out of papier-mache for the inaugural freshman's parade that neatly expressed that fascination. It was meant to be a monster cyclops, but the way it came out it resembled a giant eyeball with her arms and legs sticking out of it.

For more than a year she has used a photograph of that eyeball as the icon of her art blog, thirsty pixels. It is all too ironic, she laughs now. The irony is that in May Henochowicz became – in her own words – a cyclops. She lost her left eye as she was demonstrating against Israeli government policy in the Palestinian occupied territories.

With her loss, she became yet another casualty of the ongoing Israeli occupation. But what makes Henochowicz's story singular was that her experiences were filtered through the lens, the eye, of an artist.

It was art that took her to the Middle East in the first place. She signed up to an animation course in Jerusalem that suited her passion for drawing.

Her choice of Jerusalem had little to do with the fact that she was the granddaughter of Holocaust survivors, or that her father was born in Israel and that she herself was Jewish and an Israeli citizen. It had even less to do with any political beliefs she might have on either side of the Israeli-Palestinian divide, though she had been disturbed by Israel's conduct in the Gaza war of 2008-9.

It was all about art. But a month after she arrived in Jerusalem, an Israeli friend and peace activist took her into Palestinian East Jerusalem. That day changed everything.

"It was a little bit shocking," she says, recalling the event in a Manhattan cafe. "Suddenly a huge group of Hassidim came down the street. These little Palestinian kids – just five or six years old – linked arms and were standing in the middle of the street. The Hassidim were on the other side, singing prayers at them. It was such a powerful image for me: that line of children, so strong and defiant, this huge group of adults in front of them."

The next day Henochowicz captured the moment in a dramatic painting that shows the children in front of a swirl of black-clad Jewish men. And then she acted on impulse – something that as an artist she says she is wont to do. She went to Ramallah on the West Bank and joined the protest campaign the International Solidarity Movement.

Over the next few weeks Henochowicz threw herself into the fray, protesting outside Israeli settlements in the West Bank and along the separation wall. She was aware of the dangers, not least because it was with the ISM that fellow-American Rachel Corrie had been demonstrating in 2003 when she was crushed to death by a bulldozer.

"I had a fear the whole time I was going to get hit with tear gas," Henochowicz says. "I knew the way that it was used. Forget UN regulations, this is Israel, the rules don't apply here – tear gas is fired directly into crowds."

At first she kept what she was doing from her parents, certain that they would disapprove. But eventually she told them.

"They were incredibly upset, particularly my dad. He had been to Yeshiva, Jewish school, and speaks Hebrew.' How could you do this to me?' he said, but I wasn't doing it to him."

Paradoxically, shortly before the incident in which she lost her eye, Henochowicz decided, partly out of concern for her parents, that she would avoid demonstrations and dedicate herself instead to teaching art to Palestinian children. But on the morning of 31 May she awoke to the news that a Turkish flotilla attempting to break the Israeli blockade of Gaza had been raided and nine activists killed.

Mayhem and confusion ensued. She was swept along by the reaction, and found herself at a protest rally at the Qaladiya checkpoint, facing Israeli soldiers. "I was scared in a way I'd never been before."

It was so quick, maybe just a minute from the first stones being thrown to the tear gas canister striking her in the face.

"I remember a weird crunch feeling and thinking, 'Oh, I've been hit!' Then there was the thought: 'Hey guys, my brain's ok! My brain's ok!"

"And then I remember falling back and being held, and cameras rushing to me and clicking away and me thinking 'Oh, I've become one of those images'."

She was treated in a hospital in Ramallah and Jerusalem before returning to Maryland in the US. She has had multiple operations for a fractured skull as well as losing the eye.

The Israeli government has refused to pay thousands of dollars in medical costs, on the grounds that Henochowicz chose to put herself at risk and that she was hit by mistake by a ricochet.

"That's preposterous," she says. "A ricochet? From what wall? Where? How? This was no ricochet."

Henochowicz is now preparing for term to start at Cooper Union. She wears a pair of glasses, the left lens of which she has painted with swirls to obscure the empty socket behind it.

She says she has adapted with amazing speed to the loss. "I go through a lot of my days not even thinking that I'm seeing only through one eye. I'm so fine in other ways, I'm perfectly healthy."

She stresses how unfair she thinks it is that she gets so much attention, while Palestinians who are injured with depressing frequency go without notice. "I'm white, I'm Jewish, I'm an Israeli citizen and American. When I'm hit by tear gas there are articles, the Israeli government gets involved. When Palestinians are hit, who gives a shit?"

She doesn't know what the longer-term impact will be on her art. She remembers telling the doctor who informed her she had lost an eye: "But I'm an artist, that's not supposed to happen!"

"I've been sad because this is a moment in my life I can never escape, and that's what gets me more than the loss of my eye," she says. "Twenty years from now I will still carry this moment, and I desperately don't want it to be the end of my story."