Inside the ScholarThread reader
One reading surface for PDFs and EPUBs, five highlight colors with an inline note on every highlight, and deep links that take you from a note back to the exact passage it came from.
Most reference managers hand off reading to whatever PDF viewer is already on your machine, and treat EPUBs as an afterthought if they're supported at all. That split is where annotation habits fall apart — a highlight in one app, a note in another, no connection between the two beyond whatever you remember to copy-paste. ScholarThread reads both formats in the same surface, with the same tools, so a highlight is never more than a click from a note you can actually write from.
One reader, two formats
Open a PDF or an EPUB from your library and you land in the same reading surface either way — the same highlight colors, the same notes, the same left-hand panel for finding your way around (page thumbnails are the one exception: they're for PDFs only). You shouldn't have to relearn how to annotate just because a publisher shipped one book as an EPUB and the paper you're reading alongside it as a PDF.
Highlight in five colors, and mean something different by each one
A highlight in ScholarThread isn't just a yellow rectangle. You get five colors — yellow, green, blue, red and purple — and you can change a highlight's color later from the same small toolbar that appears when you select text or click an existing highlight. That toolbar also has an Inline note button: it opens a note attached to the highlight, with its own title, text and tags, so the moment you notice something worth keeping you can say why right there, rather than scrambling to remember later. If the note deserves more room, Expand to sidebar turns it into a standalone note in your Notes (in the Unfiled bucket), anchored to the highlighted passage. The toolbar also has a dictionary lookup for a single selected word and, on a highlight you made yourself, a Delete highlight button. Using colors consistently (evidence in one, a claim you disagree with in another, a term to look up in a third) turns a single pass through a long paper into something you can scan for structure afterward, not just re-read start to finish.
Deep links: the other half of the citation trail
A highlight is only useful later if you can get back to it fast. Highlights are listed in the reader's Annotations tab, and click-through works from there, and from any note or piece of evidence that is anchored to a passage: the link opens the reader on that page (for PDFs) or at that exact location (for EPUBs), not just the paper's detail view. Click a note's source link months later and you land in the same place, not a re-search through a fifty-page PDF trying to relocate the sentence you meant. Citation chips in a grounded chat answer work a little differently: they open the cited paper, with a hover preview of the page and excerpt when available, rather than jumping to a highlighted passage.
That's the mechanism behind ScholarThread's whole "notes should point at their source" idea: the deep link is what makes "point at their source" a real, one-click thing instead of an aspiration.
Finding your way around a long document
A hundred-page PDF or a full monograph isn't something you navigate by scrolling. The reader's left-hand panel has three tabs: Table of contents, Annotations and, for PDFs, Page thumbnails. The table of contents is built from the document's own outline — PDF bookmarks or an EPUB's own structure, whichever the file provides; a file without an outline shows "No table of contents available." The thumbnails tab does the visual version of the job, for the times you remember roughly what a figure or a page layout looked like but not which section it was in. And the Annotations tab collects your highlights and bookmarks so you can jump to any of them.
Neither replaces reading in order the first time through. Both matter enormously the second and third time, when you're back in a paper looking for one specific thing.
Pick up where you left off
Open a paper on one device, close it, open ScholarThread somewhere else, and the reader puts you back on the same page — no scrolling back through a hundred pages of a monograph to find your spot. Reading state follows your account, not the device you happened to open the file on.
Doing this in ScholarThread
Open any paper or EPUB from your library and the reader is already there — highlight a passage in whichever of the five colors fits what you're marking, add an inline note in the same motion if it's worth keeping, and trust that clicking back to it later (from a note, the Annotations tab, or just your own history) lands you on the exact passage, not the general vicinity of it.
The reading surface is the same regardless of format on purpose: the tool shouldn't be the thing you have to think about. The passage should be.