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Roof, who police say gunned down nine black worshippers at Emanuel African Methodist Episcopal Church last year, is facing the death penalty in the federal trial, which began Wednesday.
The self-professed white supremacist admitted to carrying out the attack in an FBI interview, and his lawyers have offered for him to plead guilty in exchange for a life sentence.
The presiding judge presented photos from the crime scene Thursday afternoon, revealing the extent of the carnage to the jury.
"There's no shame in stepping out for this," the judge said before showing the images, according to the Charleston Post and Courier. Fifty of the victims' family members were in attendance, with all but one remaining in the courtroom through the whole presentation.
The jury saw photos of the bodies of victims, each of whom had been shot with multiple rounds. Susie Jackson, 87, was shot 11 times, while other victims were hit between three and eight times each.
The presentation came one day after jurors heard emotional testimony from Felicia Sanders, one of three survivors of the shooting.
Sanders said she hid with her granddaughter under a table after Roof began shooting the worshippers. She saw her son, Tywanza, and Jackson, who was her aunt, lying next to them, both shot.
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"I could feel the warm blood flowing on either side of me," she said in court.
Tywanza stood up, she said, begging Roof to stop shooting. Roof allegedly responded, "I have to do this because y'all are raping our women and taking over the world," according to Sanders' testimony. Roof then shot Tywanza multiple times, killing him.
"Then we watched him take his last breath," Sanders said. "I watched my son come into this world, and I watched my son leave this world."
The trial comes just days after the conclusion of another racially charged trial in Charleston. The trial of Michael Slager, a former North Charleston police officer who was filmed shooting unarmed black motorist Walter Scott, controversially ended in a mistrial on Monday after the jury reported it could not reach consensus.