DOI: 10.5061/dryad.nzs7h4525
title: Stuck in the mud: experimental taphonomy and computed tomography demonstrate the critical role of sediment in three-dimensional carcass stabilization during early fossil diagenesis - TIFF stack data

description: Exceptionally preserved fossils provide critical information on the
 morphology and ecology of extinct organisms, but their formation remains
 poorly understood. Experimental taphonomy has produced critical insights
 that allow us to better understand preservation biases, but they typically
 do not reflect realistic depositional environments, employ destructive
 sampling, and are restricted to a two-dimensional setting. Here, we
 utilize micro-computed tomography to non-invasively visualize the process
 of decay of carcasses of the branchiopod Triops longicaudatus for a year
 of post-burial decay. The earliest stages of post-burial diagenesis are
 dynamic and produce marked differences in relative density within each of
 the experimental replicates affecting both the carcass and the surrounding
 sediment. After 64 weeks, specimens are still detectable as
 three-dimensional voids that capture the body in life position and
 external morphological features. Sediment plays a critical role in carcass
 stabilization and the resulting voids provide sites for mineral
 precipitation needed for exceptional three-dimensional fossilization.
description: <strong>Dryad Archive of Tiff
 Stacks</strong> The week 2 scans were completed
 at the Digital Imaging Facility (DIF) at the Museum of Comparative
 Zoology, Harvard University, with a Bruker SkyScan 1173 micro-CT scanner.
 Scans were performed as 180° scans with Al 1 mm filter, 100 kV, 100 µA
 current, 32 µm voxel size, 12mm stage positioning with 0.4 angle step size
 and frame averaging of 3. Due to an update on the DIF facilities taking
 place during the duration of the experiment, week 20, week 42, and week 64
 scans were produced on a new Bruker Skycan 1273 using 180° scans with Cu
 .5 mm filter, 120 kV, 125 µA current, 25.3 µm voxel size, 0.4 angle step
 size and frame averaging of 3. All scans were reconstructed as TIFF stacks
 in NRecon (Bruker Corporation). These reconstructed TIFF stacks are
 archived here. File types: The
 compressed ZIP files were compressed using Windows and will be unzipped to
 folders of .tif image files. Folders of reconstructed
 .tif stacks may be visualized in many programs. Authors used Dragonfly
 2019 4.0 (Object Research Systems, Montreal, Canada), please see the
 associated Dryad repository for this archive. Other visualization tools
 can import the images here including the free software Drishti, cited
 below. Ajay Limaye; Drishti: a volume exploration and
 presentation tool. Proc. SPIE 8506, Developments in X-Ray Tomography VIII,
 85060X (October 17, 2012). https://github.com/nci/drishti/wiki
description: ### \*\*Note to users:\*\* This README file includes combined instructions
 for two complementary Dryad datasets: 1. **The Dryad Archive of**
 **Dragonfly Sessions** works best when opened with the eponymous software
 ([https://dragonfly.comet.tech/;
 ](https://dragonfly.comet.tech/?uh=6b5ae8a230a2d222ba13a0f50f3f8cd0a88dea543e4694f4b763e4b6b372d5fc "https://dragonfly.comet.tech/")see details below), and includes all the information regarding the parameter used for visualizing the data used on the results and discussion of the published manuscript. **The Dryad Archive of Dragonfly Sessions can be accessed at DOI: 10.5061/dryad.k98sf7mcq** 2. **The Dryad Archive of TIFF Stacks** contains the raw data (after minimal processing / reconstruction from the micro-CT scanner) consisting of grayscale TIFF files that correspond to the tomographic sections of all the datasets analyzed. This option allows users to examine the data without the need to use Dragonfly, and can be accessed with other freeware options including SPIERS ([https://spiers-software.org/](https://urldefense.proofpoint.com/v2/url?u=https-3A__spiers-2Dsoftware.org_&d=DwMCAw&c=WO-RGvefibhHBZq3fL85hQ&r=RoBtBqLfBvA75aSCZXNUmOA0Zr30pao7udBKnzN6xJUFmq4F6NtAwHAvzg0J0Inr&m=oIs6PvI83yxVCgUqWr2ezfCDB0v30emCuEn7MMOituL8g9WrpLGfIPsRdoBF3qkM&s=1RQ0V1p2Yv5Ftf9DPkJLXaEdCpH3NOnhWi6T2mi2j1c&e= "https://urldefense.proofpoint.com/v2/url?u=https-3A__spiers-2Dsoftware.org_&d=DwMCAw&c=WO-RGvefibhHBZq3fL85hQ&r=RoBtBqLfBvA75aSCZXNUmOA0Zr30pao7udBKnzN6xJUFmq4F6NtAwHAvzg0J0Inr&m=oIs6PvI83yxVCgUqWr2ezfCDB0v30emCuEn7MMOituL8g9WrpLGfIPsRdoBF3qkM&s=1RQ0V1p2Yv5Ftf9DPkJLXaEdCpH3NOnhWi6T2mi2j1c&e=")), and Drishti ([https://github.com/nci/drishti](https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_nci_drishti&d=DwMCAw&c=WO-RGvefibhHBZq3fL85hQ&r=RoBtBqLfBvA75aSCZXNUmOA0Zr30pao7udBKnzN6xJUFmq4F6NtAwHAvzg0J0Inr&m=oIs6PvI83yxVCgUqWr2ezfCDB0v30emCuEn7MMOituL8g9WrpLGfIPsRdoBF3qkM&s=Fu-jwrajAOA3OGIX__PCs7UID_tL4wWrTgsNe247KcE&e= "https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_nci_drishti&d=DwMCAw&c=WO-RGvefibhHBZq3fL85hQ&r=RoBtBqLfBvA75aSCZXNUmOA0Zr30pao7udBKnzN6xJUFmq4F6NtAwHAvzg0J0Inr&m=oIs6PvI83yxVCgUqWr2ezfCDB0v30emCuEn7MMOituL8g9WrpLGfIPsRdoBF3qkM&s=Fu-jwrajAOA3OGIX__PCs7UID_tL4wWrTgsNe247KcE&e=")). **The Dryad Archive of Tiff Stacks can be accessed at DOI: 10.5061/dryad.nzs7h4525.** ## **Dryad Archive of Dragonfly Sessions** The week 2 scans were completed at the Digital Imaging Facility (DIF) at the Museum of Comparative Zoology, Harvard University, with a Bruker SkyScan 1173 micro-CT scanner. Scans were performed as 180° scans with Al 1 mm filter, 100 kV, 100 µA current, 32 µm voxel size, 12mm stage positioning with 0.4 angle step size and frame averaging of 3. Due to an update on the DIF facilities taking place during the duration of the experiment, week 20, week 42, and week 64 scans were produced on a new Bruker Skycan 1273 using 180° scans with Cu .5 mm filter, 120 kV, 125 µA current, 25.3 µm voxel size, 0.4 angle step size and frame averaging of 3. All scans were reconstructed as TIFF stacks in NRecon (Bruker Corporation) and visualized using the software Dragonfly 2019 4.0 (Object Research Systems, Montreal, Canada). The Dragonfly Session files are archived here. ## File types: The compressed ZIP files were compressed using Windows and will be unzipped to .ORSSession files. .ORSSession files maybe be opened in Dragonfly using a free noncommercial license. Dragonfly 2024.1 [Computer software]. Comet Technologies Canada Inc., Montreal, Canada; software available at [https://dragonfly.comet.tech/](https://dragonfly.comet.tech/?uh=6b5ae8a230a2d222ba13a0f50f3f8cd0a88dea543e4694f4b763e4b6b372d5fc "https://dragonfly.comet.tech/") ## Uploaded files and descriptions Triops_refscan_Fig2D.ORSSession This file corresponds to the stained *Triops longicaudatus* anatomical scan in Figure 2D. The Dragonfly Session may be opened in the Dragonfly program. week2_viala.ORSSession This zipped file corresponds to the scan of vial a after 2 weeks of decay, in Figure 3A. The Dragonfly Session may be opened in the Dragonfly program. week2_vialb.ORSSession This zipped file corresponds to the scan of vial b after 2 weeks of decay, in Figure 3B. The Dragonfly Session may be opened in the Dragonfly program. week2_vialc.ORSSession This zipped file corresponds to the scan of vial c after 2 weeks of decay, in Figure 3C. The Dragonfly Session may be opened in the Dragonfly program. week2_viald.ORSSession This zipped file corresponds to the scan of vial d after 2 weeks of decay, in Figure 3D. The Dragonfly Session may be opened in the Dragonfly program. week2_viale.ORSSession This zipped file corresponds to the scan of vial e after 2 weeks of decay, in Figure 3E &F. The Dragonfly Session may be opened in the Dragonfly program. week20_viala.ORSSession This zipped file corresponds to the scan of vial a after 20 weeks of decay, in Figure 4A. The Dragonfly Session may be opened in the Dragonfly program. week20_vialb.ORSSession This zipped file corresponds to the scan of vial b after 20 weeks of decay, in Figure 4B. The Dragonfly Session may be opened in the Dragonfly program. week20_vialc.ORSSession This zipped file corresponds to the scan of vial c after 20 weeks of decay, in Figure 4C. The Dragonfly Session may be opened in the Dragonfly program. week20_viald.ORSSession This zipped file corresponds to the scan of vial d after 20 weeks of decay, in Figure 4D. The Dragonfly Session may be opened in the Dragonfly program. week20_viale.ORSSession This zipped file corresponds to the scan of vial e after 20 weeks of decay, in Figure 4E &F. The Dragonfly Session may be opened in the Dragonfly program. week42_viala.ORSSession This zipped file corresponds to the scan of vial a after 42 weeks of decay, in Figure 5A. The Dragonfly Session may be opened in the Dragonfly program. week42_vialb.ORSSession This zipped file corresponds to the scan of vial b after 42 weeks of decay, in Figure 5B. The Dragonfly Session may be opened in the Dragonfly program. week42_vialc.ORSSession This zipped file corresponds to the scan of vial c after 42 weeks of decay, in Figure 5C. The Dragonfly Session may be opened in the Dragonfly program. week42_viald.ORSSession This zipped file corresponds to the scan of vial d after 42 weeks of decay, in Figure 5D. The Dragonfly Session may be opened in the Dragonfly program. week42_viale.ORSSession This zipped file corresponds to the scan of vial e after 42 weeks of decay, in Figure 5E &F. The Dragonfly Session may be opened in the Dragonfly program. week64_viala.ORSSession This zipped file corresponds to the scan of vial a after 64 weeks of decay, in Figure 6A. The Dragonfly Session may be opened in the Dragonfly program. week64_vialb.ORSSession This zipped file corresponds to the scan of vial b after 64 weeks of decay, in Figure 6B. The Dragonfly Session may be opened in the Dragonfly program. week64_vialc.ORSSession This zipped file corresponds to the scan of vial c after 64 weeks of decay, in Figure 6C & D. The Dragonfly Session may be opened in the Dragonfly program. week64_viale.ORSSession This zipped file corresponds to the scan of vial e after 64 weeks of decay, in Figure 6E &F. The Dragonfly Session may be opened in the Dragonfly program.   ## **Dryad Archive of Tiff Stacks** The week 2 scans were completed at the Digital Imaging Facility (DIF) at the Museum of Comparative Zoology, Harvard University, with a Bruker SkyScan 1173 micro-CT scanner. Scans were performed as 180° scans with Al 1 mm filter, 100 kV, 100 µA current, 32 µm voxel size, 12mm stage positioning with 0.4 angle step size and frame averaging of 3. Due to an update on the DIF facilities taking place during the duration of the experiment, week 20, week 42, and week 64 scans were produced on a new Bruker Skycan 1273 using 180° scans with Cu .5 mm filter, 120 kV, 125 µA current, 25.3 µm voxel size, 0.4 angle step size and frame averaging of 3. All scans were reconstructed as TIFF stacks in NRecon (Bruker Corporation). These reconstructed TIFF stacks are archived here. ## File types: The compressed ZIP files were compressed using Windows and will be unzipped to folders of .tif image files. Folders of reconstructed .tif stacks may be visualized in many programs. Authors used Dragonfly 2019 4.0 (Object Research Systems, Montreal, Canada), please see the associated Dryad repository for this archive. Other visualization tools can import the images here including the free software Drishti, cited below. Ajay Limaye; Drishti: a volume exploration and presentation tool. Proc. SPIE 8506, Developments in X-Ray Tomography VIII, 85060X (October 17, 2012). [https://github.com/nci/drishti/wiki](https://github.com/nci/drishti/wiki) Triops_recon *[NOTE that for size constraints, this file is uploaded to this DRAGONFLY dataset, not the TIFF dataset]* This file corresponds to the stained *Triops longicaudatus *anatomical scan in Figure 2D. The .tif files may be opened in Dragonfly, Drishti, or other 3D image processing software. week_2_viala_recon This zipped folder of reconstructed .tif images corresponds to the scan of vial a after 2 weeks of decay, in Figure 3A. The .tif files may be opened in Dragonfly, Drishti, or other 3D image processing software. week_2_vialb_recon This zipped folder of reconstructed .tif images corresponds to the scan of vial b after 2 weeks of decay, in Figure 3B. The .tif files may be opened in Dragonfly, Drishti, or other 3D image processing software. week_2_vialc_recon This zipped folder of reconstructed .tif images corresponds to the scan of vial c after 2 weeks of decay, in Figure 3C. The .tif files may be opened in Dragonfly, Drishti, or other 3D image processing software. week_2_viald_recon This zipped folder of reconstructed .tif images corresponds to the scan of vial d after 2 weeks of decay, in Figure 3D. The .tif files may be opened in Dragonfly, Drishti, or other 3D image processing software. week_2_viale_recon This zipped folder of reconstructed .tif images corresponds to the scan of vial e after 2 weeks of decay, in Figure 3E & F. The .tif files may be opened in Dragonfly, Drishti, or other 3D image processing software. week_20_viala_recon This zipped folder of reconstructed .tif images corresponds to the scan of vial a after 20 weeks of decay, in Figure 4A. The .tif files may be opened in Dragonfly, Drishti, or other 3D image processing software. week_20_vialb_recon This zipped folder of reconstructed .tif images corresponds to the scan of vial b after 20 weeks of decay, in Figure 4B. The .tif files may be opened in Dragonfly, Drishti, or other 3D image processing software. week_20_vialc_recon This zipped folder of reconstructed .tif images corresponds to the scan of vial c after 20 weeks of decay, in Figure 4C. The .tif files may be opened in Dragonfly, Drishti, or other 3D image processing software. week_20_viald_recon This zipped folder of reconstructed .tif images corresponds to the scan of vial d after 20 weeks of decay, in Figure 4D. The .tif files may be opened in Dragonfly, Drishti, or other 3D image processing software. week_20_viale_recon This zipped folder of reconstructed .tif images corresponds to the scan of vial e after 2 weeks of decay, in Figure 4E & F. The .tif files may be opened in Dragonfly, Drishti, or other 3D image processing software. week_42_viala_recon This zipped folder of reconstructed .tif images corresponds to the scan of vial a after 42 weeks of decay, in Figure 5A. The .tif files may be opened in Dragonfly, Drishti, or other 3D image processing software. week_42_vialb_recon This zipped folder of reconstructed .tif images corresponds to the scan of vial b after 42 weeks of decay, in Figure 5B. The .tif files may be opened in Dragonfly, Drishti, or other 3D image processing software. week_42_vialc_recon This zipped folder of reconstructed .tif images corresponds to the scan of vial c after 42 weeks of decay, in Figure 5C. The .tif files may be opened in Dragonfly, Drishti, or other 3D image processing software. week_42_viald_recon This zipped folder of reconstructed .tif images corresponds to the scan of vial d after 42 weeks of decay, in Figure 5D. The .tif files may be opened in Dragonfly, Drishti, or other 3D image processing software. week_42_viale_recon This zipped folder of reconstructed .tif images corresponds to the scan of vial e after 42 weeks of decay, in Figure 5E & F. The .tif files may be opened in Dragonfly, Drishti, or other 3D image processing software. week_64_viala_recon This zipped folder of reconstructed .tif images corresponds to the scan of vial a after 64 weeks of decay, in Figure 6A. The .tif files may be opened in Dragonfly, Drishti, or other 3D image processing software. week_64_vialb_recon This zipped folder of reconstructed .tif images corresponds to the scan of vial b after 64 weeks of decay, in Figure 6B. The .tif files may be opened in Dragonfly, Drishti, or other 3D image processing software. week_64_vialc_recon This zipped folder of reconstructed .tif images corresponds to the scan of vial c after 64 weeks of decay, in Figure 6C & D. The .tif files may be opened in Dragonfly, Drishti, or other 3D image processing software. week_64_viale_recon This zipped folder of reconstructed .tif images corresponds to the scan of vial e after 64 weeks of decay, in Figure 6E & F. The .tif files may be opened in Dragonfly, Drishti, or other 3D image processing software.