The photo, which has been deleted, was posted Monday and featured a close-up photo of U.S. District Judge Amy Berman Jackson's face, along with her name adjacent to a symbol that resembled the crosshairs of a gun sight near her head. Stone added an appeal for donations.
On Tuesday, Stone posted a photo of a book he received from a supporter, writing in an Instagram post that he was praying that it "protects me from the fake news media who are smearing me and purposely misinterpreting everything I say".
He later apologized for the post in an official filing to the court. Stone has since posted two subsequent images that contained statements, trying to clarify where he found the original photo and what it meant.
Mr Stone later deleted the image and reposted it without the crosshairs, before removing it again, according to other media outlets. In the post, Stone said the judge would be presiding over a "show trial".
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Stone later said that the picture had been "misinterpreted" and that any suggestion he meant to threaten Jackson was "categorically false". "Stone recognizes the impropriety and had it removed".
"If you look at that posting, he has a picture of the judge".
Beneath the photo, he wrote: "Now an Obama-appointed Judge wants to gag me so I can't defend myself from the many media leaks by the Mueller hit squad. My lawyers are fighting this effort to abridge my First Amendment Rights".
In court documents submitted Friday, prosecutors alleged that in 2016 Stone had direct contact with transparency organization WikiLeaks and Russian hackers who stole thousands of emails from Democrat National Committee servers and leaked them to the site. She underlined the sentence for emphasis.
Last week, Jackson ordered him not to speak publicly in and around the courthouse.