Black circle covering figures in a journal article

fadi_abouzeid
I was trying to open the following article using the Zotero PDF reader:

B. J. Tauro et al., ‘Comparison of ultracentrifugation, density gradient separation, and immunoaffinity capture methods for isolating human colon cancer cell line LIM1863-derived exosomes’, Methods, vol. 56, no. 2, pp. 293–304, Feb. 2012, doi: 10.1016/j.ymeth.2012.01.002.

My institution gives me access to this article, so I have no problem viewing it online using my browser, but when I import it from the browser PDF viewer to Zotero using the Edge plugin, the circles appear inside the application.

I've attached some screenshots in a Twitter post:

https://twitter.com/fadi_abz/status/1452617800137252868?s=20

I'm using the latest beta build (5.0.97-beta.51+6206209ed).
  • dstillman
    edited October 25, 2021
    Can you provide a Report ID?

    What kind of computer is this, and what graphics card? If you go to the Config Editor in the Advanced pane of the Zotero preferences and toggle layers.acceleration.disabled to true, and then restart Zotero, does that fix the problem? (We don't recommend leaving that permanently set to true, but it'd be good to know for testing purposes whether it affects this.)
  • fadi_abouzeid
    I toggled layers.acceleration.disabled to true and now it's working fine, thanks!

    If you're still curious, here's the report:

    [JavaScript Error: "zp.Zotero_Tabs is undefined" {file: "chrome://zotero/content/xpcom/recognizePDF.js" line: 306}]

    [JavaScript Error: "Downloaded PDF was not a PDF"]

    [JavaScript Error: "zp.Zotero_Tabs is undefined" {file: "chrome://zotero/content/xpcom/recognizePDF.js" line: 306}]

    version => 5.0.97-beta.51+6206209ed, platform => Win32, oscpu => Windows NT 10.0; WOW64, locale => en-GB, appName => Zotero, appVersion => 5.0.97-beta.51+6206209ed, extensions => Zotero LibreOffice Integration (5.0.25.SA.5.0.97-beta.51+6206209ed, extension), Zotero Word for Windows Integration (5.0.19.SA.5.0.97-beta.51+6206209ed, extension)

    I'm using an Asus Vivobook Pro 14 with an integrated AMD Radeon Vega 8 card (on Windows 11).

    For my curiosity as well, what does this toggle do? And why would it be bad to keep it on? (assuming that by changing it back I'll have the black circles again).
  • dstillman
    Setting it to true disables hardware acceleration, which will result in worse rendering performance in Zotero and potentially slightly worse battery life.

    Can you email the PDF in question to support@zotero.org with a link to this thread?

    We'll investigate this issue to see if we can get it working for you with acceleration enabled.
  • CarlAndersson
    I've got another pdf with the exact same issue, in case you need more examples to troubleshoot this. This is on Zotero 6.0.9 on windows 10. Let me know if you'd like me to send the pdf!
  • bmorey89
    Hello, I also have multiple papers with the same issue as well when they are uploaded to Zotero. When viewing the actual PDF they are not there. It didn't happen before then started with one paper I downloaded about two weeks ago and again when downloading another paper today. I have Zotero 6.0.13 on Windows 10
  • dstillman
    @bmorey89: As above, we'd need to see the PDF in question.
  • tallish_paul
    Hi, I have the same problem, only noticed so far with this paper, open source at:
    https://repository.lboro.ac.uk/articles/journal_contribution/Irradiance_modelling_for_individual_cells_of_shaded_solar_photovoltaic_arrays/9561218

    I am using Zotero 6.0.13 on:
    (a) (home office) Dell Latitude E6410 laptop, with Intel HD Graphics (Core i5), running Windows 10 Pro v 10.0.19044 Build 19044, i5 M560 CPU, and
    (b) (work office) Lenova desktop, Thinkstation P520 (model 30BFS0A500), with NVIDIA Quadro P4000 graphics, running Windows 10 Enterprise v 10.0.19044 Build 19044

    When I open the paper on (a) in Zotero pdf reader, some figures have a black ellipse quadrant partially covering them, from the top left corner of the image. This is for figures 1, 3, 4, 5, 11a, 13, 14a, 14b, 15, 16. When I open the storage folder to allow me to open in other pdf readers there is no problem (Sumatra pdf, Foxit Reader, Adobe Acrobat DC). Toggling layers.acceleration.disabled to true fixes the problem.

    When I similarly open the paper on (b) there is no problem. I checked that layers.acceleration.disabled is set to false.

    FWIW I noticed this link below reported the same problem for a non-Zotero pdf reader from a while back but still seemingly an irritant:
    https://bugzilla.mozilla.org/show_bug.cgi?id=858128
    I checked with the pdf of comment 19 and it does have the problem on my computer (a) but not (b). There are some suggestions, including that it is an Elsevier issue - my problem paper happens to be an Elsevier journal as well and it seems that the open repository is a copy of the Elsevier published one as oppose to a university made one.

    I can work around it of course, but I thought you might want the additional information.

    By the way, Zotero is absolutely amazing!
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