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These sites provide kuzushiji and hentaigana reference, such as charts and guides to be used by those who have already learned some kuzushiji and hentaigana.
These are more comprehensive dictionaries of kuzushiji, hentaigana, and calligraphic kanji forms.
Texts with Honkoku
These digital archives contain page images of documents written in kuzushiji with hentaigana and kanji, and many also include honkoku 翻刻 that can be viewed alongside or superimposed on the original documents.
Josei Kanren Shiryō 女性関連資料
This collection features books related to women and provides honkoku in a pop-up window along with them. Note that the encoding of the honkoku is mostly EUC-JP.
Ise Monogatari no Sekai 伊勢物語の世界
A variety of early modern books on Ise monogatari, accompanied by honkoku in a popup window. Note that you need to scroll through the honkoku as you turn pages, rather than receiving a new honkoku for each page.
Edo-jidai Kikō Bunshū 江戸時代紀行文集
An interactive map with travel accounts from the Edo period, each accompanied by a honkoku.
Shibai Kinmō Zui 劇場訓蒙図彙
This kabuki-related text by Shikitei Sanba, from 1803, is accompanied by a honkoku next to images of the original document. The texts are displayed as PDFs within the web browser.
Genji Monogatari Gazō 『源氏物語』画像
This site provides high-quality scans of a copy of Genji Monogatari held by the Library of Congress, along with a transcription in tyeset Japanese either superimposed on the image or displayed alongside it.
Kasuga Gongen Genki Emaki 春日権現霊験記繪巻
A picture/text scroll accompanied by honkoku in a popup window; you must scroll down in the honkoku as you page through the images of the scroll, rather than receiving a new popup for each image.
Bunbuku Chagama 分福茶賀間
The UK Early-Modern Japanese Texts Research Group is working on a honkoku of the rare book Bunbuku Chagama 分福茶賀間, available freely on their website.
Nara Ehon Muromachi Jidai Monogatari 奈良絵本室町時代物語 (Hiroshima University)
Hiroshima University's collection of Nara ehon, including kaisetsu 解説 and honkoku + image viewer 翻刻+画像.
Princeton has scanned some archival documents and provided honkoku for them on this digital archive. It includes a lengthy prefatory essay.
Other digital archives which contain materials relevant to kuzushiji and hentaigana reading, but not necessarily images of texts and/or honkoku.
These sites and other resources provide tutorials and guides on learning kuzushiji in a structured way, rather than just serving as reference tools.
A search engine for inkan, indexed by personal name of artists, scholars, and calligraphers from the Edo period.
NIJL Collectors' Seal Database 蔵書印データベース
A database of seals stamped in books by collectors. The advanced search function is extremely detailed and allows you to search by size, color, title, author, etc. It provides high-quality digital images of the seals and notes which institution holds the book that was scanned.
These are sites with information about premodern books, or kotenseki 古典籍.
Berkeley Kotenseki Workshop Presentations
The Kotenseki Workshop sponsored by C. V. Starr East Asian Library and the Center for Japanese Studies, University of California, Berkeley, and the National Institute of Japanese Literature was held at the C. V. Starr East Asian Library on March 11, 2016. This guide contains PDFs of the presentation slides from that workshop.
Japanese Culture Through Rare Books MOOC
A MOOC taught by Sasaki Takahiro and Ichinohe Wataru from Keio University on traditional Japanese books and book culture. This is an introductory course and is open to anyone with an interest in the history of Japanese books. A basic knowledge of the history of Japan and Japanese literature will be helpful but is not required. The course makes use of a number of visual resources; course videos are in Japanese with English subtitles.