Downloaded by guest on September 25, 2021 rist hs ftesroniglmsoeo ooiematrix, dolomite or limestone surrounding the of those to erties most However, (9–11). from dissolution acid isolated Cloudina via be study for can rock host specimens the individual and phosphatized or within Rarely, individuals required. of is orientation aggregates and structure the about mation evolu- ecology, on architecture. had platform reefs and such construction sedimentology, effect tion, the the and and biomineralization frameworks; both of to led evolutionary that the environ- journey behavior; the such emerged; cultivated how building that reef conditions into of mental insight act the provide why) can perhaps (and reefs of metazoan-mediated timing the first environments Constraining the biodiversity. the surrounding species high be formed alter contain built and organically to that reefs extensive, regarded structures oceans, laterally widely wave-resistant comprise modern are metazoans In which by reefs. Cam- 8), Lower metazoan-mediated ref. before the first of Ma, Ma buildups (521 20 archaeocyathan some brian the of reefs advent framework the calcified that produced proposed preferred have have basis workers exhibit the observations, field On clusters, of (6). growth aggregated that growth in that its and horizontal-to-subhorizontal–oriented found suggested altering 6) when have by (5, viduals, Researchers to changes end (7). attached apical environmental strategy that an to 4) through responded (3, substrates feeder microbial suspension sessile epibenthic, Ediacaran techniques. density of imaging reconstruc- lack tomographic a 3D precludes and contrast require impossible is that techniques separation physical problems These where systems. tions to reef applicability Ediacaran wide in have outcrops role minor reef a studied played the detrital that only contain detailed demonstrate while observations remains transported field of composed are that show aggregates reconstructions neural Our developed classifier. recently image a network with coupled system imaging and of ing reconstructions 3D present most we Cloudina earlier Here, and much thought. bioconstructions previously oceans—emerged than modern largest in the environments is of diverse that some behavior for complex responsible building—a reef framework organ- metazoan tubular as distributed globally known possi- and ism abundant (and suggested an dominated been by were has built) associ- reefs bly It strata microbial reefs. Ediacaran in microbial some Ma) that water (635–541 shallow appeared Period with biomineralization Ediacaran ated late and of Denmark, the M., capable Odense during Denmark, metazoans Southern of earliest University 2017) Evolution, The 14, Earth November for review Center for Nordic (received and 2018 Biology 19, of January Institute approved Canfield, E. Donald by Edited constructions reef a situ in Mehra Akshay not and detritus are www.pnas.org/cgi/doi/10.1073/pnas.1719911115 fos- index millimeter-to-centimeter–scale (2), sil, the strata them Ediacaran among within chief metazoans biomineralizing several A biomineralization that reveals approach Multiscale eateto esine,PictnUiest,Pictn J08544 NJ Princeton, University, Princeton Geosciences, of Department odtriewhether determine To Cloudina. tog h daaaboalreyaepeevda soft- are there as (1), preserved sediment are fine-grained in largely impressions biota bodied Ediacara the lthough | ouain,poue sn natmtdsra grind- serial automated an using produced populations, ean r acfidadhv iia hsclprop- physical similar have and calcified are remains reefs ftu,ti nepeainipisthat implies interpretation this true, If Cloudina. | Cloudina a,1 al life early n dmMaloof Adam and Cloudina | a endsrbda gregarious, a as described been has Cloudina he-iesoa reconstructions three-dimensional ulus ugsigthat suggesting buildups, Cloudina ul ef,i iu3 infor- 3D situ in reefs, built a pcmn r silicified are specimens Cloudina Cloudina Cloudina Cloudina | indi- may ue r ujc oalredge ferr(sgeta 5;Fig. 35%; as great (as error of elliptical degree and/or large 1 a curved to subject through are cross-sections tubes on made ments 1 (Fig. structures cross-sections tubular 2D from of tion case the as in such that, can- syn- reveal Furthermore, distributions (12). experiments size cross-sections thetic noted 2D and from as estimated spatial Unfortunately, be 3D not 7). researchers, 4, previous (3, by planes bedding and measurements situ sections, make in to researchers produce of led to has inability reconstructions The 3D techniques. computed (CT) traditional of tomography use the or separation physical precluding ulusa er ie amsuho akut aii ( Namibia Naukluft, of microbial south sheet Farm and River patch Zebra the at S2B); Reho- buildups and near S1 Farm (Figs. Driedoornvlakte Namibia at beth, complex reef pinnacle the Ediacaran three from collected (see Methods University and Princeton rials at (GIRI) Instrument struction traced and 1073/pnas.1719911115/-/DCSupplemental. at online information supporting emailing contains article by This request on provided be will 1 data image raw [email protected]. original all constraints, size aadpsto:Temaueetdt n h opttoa orecd reported in code deposited source been computational have the paper and this data in measurement The deposition: Data the under Published Submission. Direct PNAS a is article This interest. of conflict no declare the wrote authors Maloof The A. and Mehra A. performed and Mehra data; A. analyzed paper. Maloof research; A. designed and Maloof Mehra A. A. research; and Mehra A. contributions: Author and reef; stratigraphic the GPS-constrained of differential extent the meter-scale, evaluate ( (ii) to of mapping consisting drone-assisted approach multiscale scale a to outcrop Each subject S5). was and S4, S2A, (Figs. Canada in Mountain Salient S2B owo orsodnesol eadesd mi:[email protected]. 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Fig. 1. Synthetic tube experiments. (A and B) One hundred tubes of equal diameter and length are randomly distributed within XY space with their centers at Z = 0. In A, all of the tubes exhibit a plunge of 15◦ and a trend of 180◦ ± 15◦, while in B, tubes are evenly subdivided into two populations, both with the same plunge but with one having a trend of 180◦ ± 15◦ and the other having a trend of 0◦ ± 15◦. C demonstrates that the cross-section at Z = 0 is the same for both populations. (D) Variations in cross-sectional eccentricity and curvature of a synthetic tube lead to measurement error (here, error is the percentage of difference between the median measured area and the known cross-sectional area). Errors result from treating measured semiminor axis size as the true diameter based on the assumption that tubes have a circular cross-section. (E) Sixty-four randomly selected sections through a straight open tube with a circular cross-section. The shapes are similar to those observed on bedding planes, including what are interpreted as closed apical ends (circled).

sedimentological observations to identify where Cloudina can be The reef at Driedoornvlakte Farm is a 500-m-thick, 10-km- found; (iii) centimeter-scale petrographic and stable isotope anal- long outcropping that dips ∼25◦–40◦ to the south and that, on ysis to contextualize depositional and diagenetic histories; and the basis of changes in reef geometry, has been divided into (iv) submillimeter-scale 3D reconstructions of in situ Cloudina three distinct units (17). The third—and youngest—unit, which populations to quantitatively describe the aggregates. was deposited in an environment of increasing accommoda- We find that Cloudina specimens primarily are preserved as tion before drowning by the Urikos shales (17), has been the detrital assemblages consisting of transported individuals within focus of multiple studies (17–19), including several that pro- the fill between microbial buildups; that Cloudina thicket, when posed evidence for in situ Cloudina growth (4, 6, 7). The third found, makes up 3% of the host reef; and that Cloudina was unit contains pinnacle reefs made up of coalescing decimeter- easily deformed and may have been composed of a weakly or to-meter–scale microbial mounds. The mounds are composed nonbiomineralized shell. We conclude that Cloudina likely was of both columnar or encrusting stromatolites and columnar or a minor component of microbial reefs during the Ediacaran and massive thrombolites. Fill between the stromatolites and throm- suggest that Cloudina populations may have had an analogous bolites, when present, often contains the skeletal remains of habit to that of present-day serpulid worm buildups, which exist Cloudina and the goblet-shaped biomineralizer Namacalathus in a wide range of modern environments but are distinct from (20). Remains of both organisms, along with the modular meta- large-scale, wave-resistant, structural framework constructions. zoan Namapoikia (21), also can be found within neptunian dikes distributed throughout the reef. On the fore slope of the reef Field Observations and Reconstruction Results are meter-scale dolomitized clinoformal grainstones consisting In Namibia, the Driedoornvlakte and Zebra River Farm reefs solely of the skeletal remains of Namacalathus and Cloudina. represent Neoproterozoic age Nama Group sediments that were Cloudina thicket, a dense aggregate of individuals without evi- deposited on a carbonate ramp in the northern Zaris subbasin dence of internal microbial fabrics that has been suggested to following the Damara and Gariep orogenies (13, 14). The Kuibis represent framework reef building (4, 6), is present in several subgroup, which comprises the lowest Nama and contains Cloud- mounds within the reef. A detailed survey of the reef reveals ina-bearing sediments, has a maximum age of 620–590 Ma (13) that Cloudina thicket is sparsely distributed within the outcrop and a minimum age, on the basis of a uranium–lead zircon date area. Although ∼52% of all surveyed points exhibit some form of in the overlying Schwarzrand subgroup, of 545.1 ±1 Ma (15). microbial texture, only ∼14% have any sort of skeletal remains An additional geochronological constraint is provided by an ash present, and fewer than 3% have been identified as Cloudina bed 270 m above the base of the Kuibis at Zebra River Farm, thicket (Fig. 2). located in an interbedded microbialite succession above Cloud- Two samples of thicket from Driedoornvlakte (named thicket ina-bearing thrombolites (Fig. S2D), which has a reported age of A and thicket B) consist of Cloudina tubes surrounded by a fine- 548.8 ± 1 Ma revised to 547.32 ± 0.31 Ma (15, 16). grained, dark micrite matrix that lacks any apparent microbial

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Movie ,5,ma horizontal mean 1,254, = kltlmtra,and material, skeletal B) eiso otes-onrhettedn omlfutblocks fault normal ( southeast-to-northwest–trending 18 of approximately series dip that reef. the exposures for Cambrian Early of age minimum (Skolithos a (28) provides beds fossils and reef trilobite-bearing below immediately trace the post- strata 607.8 in contains Cruziana) a Supergroup, of of formation age Windermere dating McNaughton maximum Re-Os breakup the a of the in has basis following the shale Formation setting On Marinonan Byng margin (24–26). the passive Rodinia of a of were and in Platform (23) Supergroup) deposited Salient Windermere Group, the Miette (Upper to belong tain trend predominant no have 4G). individuals (Fig. and 1), (Table plane ding ribbed either Larger smooth. be can micrite. or tubes smaller with while surfaces filled hollow, external smooth are and interiors 1). walled, present, (Table smooth When size distinguishable. smaller always axis not in semimajor especially in cavities, change Internal appreciable no have ecie svral ietoso igebs-tpaewt a with plane best-fit single 055.2 a of be on can strike lineations measurements variable plunge 25 as and trend described between of trending distribution The usually 4E). while and, 240 1) and (Table the plane both ding B. thicket A, in dolomitized thicket partially ina is In matrix the the 1). only along while (Table size axis tube ina semimajor the consistent of a length have and sections, calcite. blocky agr(ue eiao xssize axis 3H size semimajor axis (outer semimajor larger (outer smaller into 3 divided (Fig. matrix micrite fine-grained extremely both includes S2D) (Fig. Namacalathus Farm River Zebra at unit buildups. microbial stratigraphy. individual between fill No skeletal the contain and within stromatolites. elongation material associated directional that exhibit and plane mounds bedding thrombolites The resistant of a mounds forms the and exposes while sheetlike retention is fabric reef iso- poor as upper appears with microbialites occurrence biostromes reef interbedded mounding lower of lated The sequence S2D). (Fig. a shales by and overlain are which turn buildups, in reef river alternat- microbial interrupted of dolomitized, twice often of are consists meter-scale, that and by system grainstones canyons coarse-grained Kaines the to a fine- the of ing in bottom overlies the succession exposed at stratigraphic quartzite are The that (22). canyons strata (1 northwest) near-horizontal the of composed is Driedoornvlakte, dom- a exhibit not 4F do (Fig. and trend 1) (Table inant plane bedding the to relative B, thicket In 4E). (Fig. otistoti ooiie oios ohwt vdneof which the evidence Although with succession, S2C). both (Fig. sandstone stromatolites horizons, preserved upper dolomitized poorly an thin two by contains overlain are by herms unit capped (including a is material is that skeletal sandstone horizon pink massive the elongated and meter-scale, Above shale material. horizon interbedded stromatolite skeletal of and visible oncolite no an with into transition sandstones alternating shales of and series A succession. stratigraphic same .Ec lc xiisvral xoueo the of exposure variable exhibits block Each S5). and S4 Figs. h ef nSletMuti uco sgailypolished glacially as outcrop Mountain Salient on reefs The Moun- Salient on reefs biohermal isolated the Canada, In ilbtentotrmoiemud oae nteuprreef upper the in located mounds thrombolite two between Fill of up-ramp located Farm, River Zebra at outcrop The ue ntiktAplunge A thicket in tubes n 4G and ean n urudn arxaeprilydolomitized, partially are matrix surrounding and remains Cloudina ◦ h pcmn ontehbtadmnn rn (Fig. trend dominant a exhibit not do specimens the , Cloudina and ◦ hceswr dnie ihnteZbaRiver Zebra the within identified were thickets rsre sdr,rcytlie od nalight, a in molds recrystallized dark, as preserved Cloudina n i f22.3 of dip a and ,ehbtelpia rs-etos and cross-sections, elliptical exhibit S2), Movie ). plunge Cloudina eual ed aeelpia cross- elliptical have bend, regularly Platella nfil The fill. in Cloudina) 31.6 21.5 niiul plunge individuals ± ◦ ◦ m iefatos(Figs. fractions size mm) >3 ◦ eaiet h edn plane bedding the to relative . a(7.Teoverlying The (27). Ma 4.7 ± ± toaoieboem with bioherms stromatolite 17.5 ◦ 10.4 Cloudina NSLts Articles Latest PNAS otesuheto a on southwest the to ◦ ◦ eaiet h bed- the to relative F eaiet h bed- the to relative ). Cloudina .5m)and mm) <1.25 pcmn,are specimens, Cloudina 35.8 Cloudina Platella ◦ –2 ◦ ◦ ± Platella Cloud- Cloud- | a be can i to dip 18.9 have f9 of 3 bio- and and ◦ ◦

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Fig. 3. Neural network image segmentation technique, sample images, and 3D reconstructions. (A–J) White bars in lower left represent 0.5 cm. T.A., T.B., Z.R., and S.F. refer to thicket A, thicket B, Zebra River fill, and Salient Mountain fill, respectively. (A) Superpixel oversegmentation. (B) Likelihood image illustrating the network-calculated probability of superpixels belonging to a given class (in this case, fossil). (C) Outlines of thresholded superpixels bounding fossils. (D) Slice of thicket A from Driedoornvlakte: 1 depicts dolomitization present throughout the sample while 2 illustrates blocky calcite fill. (E) Slice of thicket B from Driedoornvlakte. (F) Slice of fill from Zebra River Farm. (G) Slice of fill from Salient Mountain: 1 shows a truncated shell. (H) Side view of 3D reconstruction of Cloudina from Zebra River fill. The red dashed lines highlight several “larger” tubes while the yellow dashed lines highlight the more numerous “smaller” tubes. (I) Comparison demonstrating how a single cross-section can appear to be the basal end of a tube (Left) but instead turn out to be a fragmented, open cup (Right). (J) Reconstruction of a single Cloudina tube with flared rims from Salient Mountain.

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Zebra Salient completely in are outcroppings extensive and laterally Farm the Driedoornvlakte at reef the that Field reveal 31). (30, observations transportation and fragmentation, lithified mechani- destruction, to within cal prone position are 50%) dwellers growth reef in secondary, as other, or while situ blocks high in preserved as be most is to the (in likely are number present constructors framework that rock primary Furthermore, of reefs, reef-building (29). volume Cambrian dominant the Lower of the other 38% CA, up make Mill, archaeocyaths Stewart’s of at portion Poleta Cambrian large Formation Lower the a in compose example, For builders remains. reef reef lithified true record, rock the Organism In Deformed Easily an of Remains Transported and distributed, 4H widely (Fig. northeast are measurements Cloudina plunge and reconstruction. Trend during identified (Table ina were tube the also of apertures, length (n the Several along 3 1). size (Fig. axis rims semimajor flared sistent with funnels connected I cemented, of posed sub- and grains. with micrite, quartz pink filled millimeter material, and skeletal 3 G). hollow, detrital (Fig. of walled, combination layers smooth a cases, microbial are certain cavities overlying tube by in Internal truncated and, be incomplete, to fragmented, appear are remains tal % length, tube along change Mean eccentricity Cross-sectional mm Length, mm axis, Semiminor mm axis, Semimajor Count ewe irba ulus(i.3G (Fig. buildups microbial between Namacalathus of evidence no exposed, found. was well thicket laterally are bioherms length. tube along size values. axis percentile semimajor 25th/50th/75th of the change represent of shills *Percentage by separated values with Fields Location reconstructions 3D Parameter from observations Aggregated 1. Table Dolomitization composition Fill % volume, by Shell enplunge, Mean and vnif Even apefo the from sample A poie h tutr o efsystems. reef for structure the Cloudina—provided plunge J .Tbshv litclcosscin n xii con- a exhibit and cross-sections elliptical have Tubes ). Cloudina niiul a edsrbda ral lnigt the to plunging broadly as described be can individuals Cloudina 45. ◦ 4 )1m imtrshrs ihzr otwo to zero with spheres, diameter 1-mm 3) = ean htaefudwti okt ffill of pockets within found are that remains ◦ ± ). a ete oiatmtza component metazoan dominant a neither was 19.0 i o ul daaa ef,tepossibil- the reefs, Ediacaran build not did Platella ◦ Cloudina Cloudina eaiet aehrzna Tbe1). (Table paleohorizontal to relative ihrscontains bioherms Cloudina ∗ niiul pert ecom- be to appear individuals hcescmoeol %of 3% only compose thickets lcyclieado micrite and/or calcite Blocky and ol eepce to expected be would reorvat amDidonlkeFr er ie am ain Mountain Salient Farm, River Zebra Farm Driedoornvlakte Farm Driedoornvlakte hlsadmatrix and Shells oi S3 Movie 0.73/0.78/0.83 12.4/15.2/19.8 21.5 2.7/3.3/3.6 3.5/4.4/5.0 hce A Thicket 6.0 False 7.5 Cloudina 29 ± ± 4.2 10.4 Cloudina Cloudina .Skele- ). Cloud- and ol xli h rsneo aiecmnsa ecie by described as cements 36). marine which (4, of workers porosity, previous presence high the with explain assemblages would detrital transportation produced following likely Deposition sourced. proximally be may suggesting (35), occurrence in common that a assemblages is death environments of large modern over movement assemblages plunges, shell cur- habitat-adjacent transport of tidal to distances, range rare or is a unidirectional it have Although turbulent rent. a but by direction reworking one suggesting in point specimens broadly Mountain, settling Salient do rapid at suggesting Finally, trend, (35). lack and transport a following plunge exhibit both River, in Zebra coherence from contrast, those of In with along buildup. B, the thicket microbial at reori- from deposition by a following explained of are current be edge unidirectional can but a which plane by direction, bedding entation one the in to tubes pointing relative individual not A, inclinations thicket similar In the have predom- processes. contrast, hydraulic single, In by a angles. explained in plunge of plunges similar oriented and with trends be (4) an all direction of would tubes inant framework individual (6), situ above), researchers from in previous matter organic by of suggested rain steady as a or current by deposi- trolled before transported If 4 were tion. probably of (Fig. compo- assemblages distributions orientation metazoan studied Furthermore, minor tube systems. a individual reef most, 3D Ediacaran at was, of it nent that of possi- suggests absence the areas the Although inhabitant. out, reef ruled situ in that an bility of remains ken 34). 33, same 10, (5, the Brazil assemblages, and Nevada, detrital Paraguay, described likely are previously samples as the tubes result, individual a that whole of imply segments incomplete measurements represent size axis that suggest semimajor surfaces microbial to (Fig. the previ- cross-section attachment 2D as of in lack ends—which, misidentified 1E)—and easily apical be of can absence noted, ously The measure- 1). and size 4D), (Table axis (Fig. semimajor ments outer size unchanging axis consistent, rela- semimajor have no and have substrate, length any between to tionship attached not are 3D ends, However, apical basal (32). that workers ontoge- reveal previous from reconstructions by resulting demonstrated length as axis nesis, semimajor in increase ciable tcudb rudthat argued be could It Cloudina Cloudina 0.78/0.83/0.89 11.1/16.7/25.4 35.8 3.8/4.2/5.0 3.2/3.7/4.2 hce B Thicket Cloudina 6.4 Micrite Matrix False 39.8 Cloudina 24 ± ± 18.9 4.2 r o rwn hr hyaefud hl the while found, are they where growing not are grgts hnfudi daaa efsystems, reef Ediacaran in found when aggregates, okavnaeo uretflx(hte con- (whether flux nutrient of advantage took a aebe efihbtn antbe cannot inhabitant reef a been have may Cloudina Cloudina Cloudina Cloudina Cloudina hoblt l toaoiefill Stromatolite fill Thrombolite pe efunit reef upper .708/.10.77/0.82/0.87 0.77/0.85/0.91 6.4/8.4/10.6 31.6 0.9/1.0/1.8 1.1/1.2/2.3 9.4 nalfu eosrcin a be can reconstructions four all in Micrite None False 24.8 30 ± ± grgtsrpeettebro- the represent aggregates grgtsi pi,China, Spain, in aggregates 17.5 8.2 rmalfu ape lack samples four all from hce naltrestudy three all in thicket NSLts Articles Latest PNAS Cloudina ugs htthe that suggest E–G) Cloudina irt n shell and Micrite raim.As organisms. 45.4 fragments 3.5/5.3/7.4 1.9/2.8/3.7 2.3/3.2/4.3 8.2 Matrix individuals True 18.8 27 ± ± | 19.0 6.4 f9 of 5

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Fig. 4. Data from 3D reconstructions. (A) Comparison of reported Cloudina diameters, including measured semimajor and semiminor axis size from this study. (B) Plot of eccentricities of Cloudina individuals from all three samples. Median, maximum, and minimum measurements refer to measurements within each individual. (C) Plot of aspect ratios, comparing tube length to outer diameter semimajor axis measurements. (D) Distribution of minor axis plunge angles from all three individuals. µ (mean) and σ (SD) refer to values obtained by fitting a normal distribution to the data. Dashed lines with labels refer to expected distributions for different compaction scenarios. D, Inset illustrates length and semimajor and semiminor axes on an idealized tube. (E–H) Directional and semimajor axis size distributions of thicket A, thicket B, Zebra River fill, and Salient Mountain fill, respectively. E–H, Top show stereonets depicting the mean plunge and trend vector of each specimen with α95 confidence limits; unique color and symbol combinations represent individual tubes, some of which bend, thereby yielding larger α95 confidence limits. E–H, Bottom show histograms of median outer diameter semimajor axis size.

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It to detritus. due essentially respect are between with distinctions aggregates that evaluated the sible that be fact must the samples to between 1) (Table explain ogy as well as material skeletal situ observations in detrital why for of account amounts up—could large broken of easily be could that sedi- for and habit remains ina analogous shelly An spatially fragmented (38). be produce ments to to both and shown environments, extensive been lagoonal have moderate-energy frame- bioconstructions to to serpulid proximal low- and In within reefs. environments work sub- in hard to exist attach and that strates that feeders filter niche annelid ecological gregarious of tubular, sort the for Cloudina analog pro- appropriate may an still were communities vide which (32)—serpulid study of this neither in tubes, examined daughter expanding pres- rapidly the and of ultrastructure ence shell of comparisons on previous based Although largely that reefs. suggested microbial have that Ediacaran researchers near likely or is in niches it assemblages, tal inter- fluid template. rock-buffered organic a an by with acting diagenesis during thickened and 3) lhuhicnlsv,tesmlrt fseladmatrix and shell of similarity diagenesis the δ and/or inconclusive, precipitated), (i.e., Although is mineralogy (37). calcite primary type, or shell aragonite of whether combination a by trolled mean similar that suggests that deformed reveal easily so be Cloudina could tubes fact The individual deposition. that or transportation either during compaction, that likely is eiio xspug nls ihmasrnigfo 24.0 from ranging means 42.7 with angles, plunge axis semiminor or about verti- 90 distributed to be near would subvertically angles oriented plunge semiminor be (i.e., would cally tubes individual of axis when of range researchers wide by the ina If assumed measurements. previously diameter 2D as making 4D) (Fig. sections 13 h bevddfeecsi ie(i.4 (Fig. size in differences observed The all If Reconstructed ausmysgetthat suggest may values C rdcddneageain fwal imnrlzdtubes biomineralized weakly of aggregations dense produced setrto eetersl fcmato,tesemiminor the compaction, of result the were ratios aspect ◦ (1σ Cloudina ◦ .Hwvr l orsmlshv omlydistributed normally have samples four all However, ). a ekyboieaie.Itaapemeasurements Intrasample biomineralized. weakly was a aeocpe.Tdy epldrescnitof consist reefs serpulid Today, occupied. have may agn rm15.3 from ranging Cloudina Cloudina Cloudina δ 13 grgtsae nfc,poial ore detri- sourced proximally fact, in are, aggregates i.S6 (Fig. values C Cloudina Cloudina r aei daaa efsystems. reef Ediacaran in rare are hlsadtesronigmti have matrix surrounding the and shells niiul eedfre eoeburial before deformed were individuals δ Cloudina 13 niiul onthv iclrcross- circular have not do individuals ieadsaeas a eetthe reflect may also shape and size ◦ at S2C) (Fig. chemostratigraphy C Cloudina o22.7 to Cloudina Cloudina Cloudina .The ). rmNmbaadCanada. and Namibia from i which Cloudina—in ◦ .A eut it result, a As 4D). 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Zebra DSM Farm, point was and sparse cloud image the point in graphic the features to georeferencing, points Trim- Following corrected control differentially of matching measurements by and ble accomplished detecting was georeferencing dataset by Absolute the produced images. of was overlapping in cloud software present point photogrammetry features sparse a matching a Pix4D, which into after loaded package, were package. .TIFFs software processed processing and The .TIFFs flight-planning 12-bit proprietary to a converted pho- eMotion, and aerial in geotagged blue then hand- and were loca- green, images each 0.69-kg, red, These at raw tographs. flights a overlapping Multiple of Sensefly, hundreds used. modified collected was Ebee specially tion camera, a the S110 with Cannon areas, megapixel equipped 12 study drone aerial three programmable all launched, mod- of surface digital (DSMs) and els imagery orthographic high-resolution produce To Methods and Materials serial GIRI the without pipeline. possible image-processing been and have sectioning between not contrast would density work this low the to Due nti ae Di iumaueet loe o rca rein- crucial a for role allowed the measurements of situ terpretation in 3D alone. case, cross-sections this 2D In from mea- collected situ be in cannot accurate that of surements extraction the enable High-resolution reconstructions dimensions. 3D three in evaluated be must struction as nature biomineralized, outcroppings weakly reef likely of in deformed, easily textures the framework as well of paucity the inter- any with However, record. rock of the pretation in situ in preserved true are that structions possibility a is there structions, mor- the both and of there conditions phology whether environmental indi- between determine enough relationship to a provide is information contextual could and/or reconstructions, rect con- 3D in localities, with multiple from junction observations field environment detailed of between ing link provide a can support location and or to sample evidence one direct no enough detrital, be individual to likely As dif- most and/or regimes. textures, energy microbial specific ferent of presence flux, nutrient nslce tairpi etos etmtrsaecroaesamples carbonate centimeter-scale sections, stratigraphic selected In was antenna external an without rover GeoXH6000 Trimble handheld A vnwt xesv edosrain n eald3 recon- 3D detailed and observations field extensive with Even 2 Cloudina a nlzduigaSro RSculdwt aBnhI tPrince- at II GasBench a with coupled IRMS Sercon a using analyzed was Cloudina Cloudina ue.Ms motnl,aycamo nst con- situ in of claim any importantly, Most tubes. opooy oee,adtoa tde,consist- studies, additional However, morphology. 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EARTH, ATMOSPHERIC, PNAS PLUS AND PLANETARY SCIENCES Decimeter-scale in situ hand samples of Cloudina and associated organ- ing the image (Fig. 3A). For each superpixel, a column vector, consisting of isms were collected for thin sectioning and serial sectioning. Each sample pixel color and texture value statistics, as well as the corresponding statistics was assigned a unique GPS point using a Garmin GPSmap 64, a Garmin of superpixels located directly above and directly below the one of inter- GPSmap 60cx, or a Trimble GeoXH6000 handheld GPS unit and was contex- est, is produced and stored. Following this preprocessing, a user defines the tualized with respect to the environment in which it was deposited. When- classes of interest (e.g., fossil and matrix) and selects representative super- ever possible, orientation (either bedding plane up or the strike and dip) pixels for each class within a subset of images from the stack. The result- was marked directly on multiple faces of the extracted sample. Samples des- ing collection of classified superpixels is divided into training, verification, ignated for serial sectioning and reconstruction were slabbed (∼5.4 × 4.0 × and testing datasets, which are then used to train and verify a two-layer 5.0 cm) and mounted using two-part epoxy onto steel plates in preparation feed-forward neural network. The trained network outputs the probability for grinding. that a superpixel belongs to a given class (Fig. 3B) and predicts the cor- The GIRI at Princeton University is a fully automated system that requires rect class with greater than 90% accuracy. Finally, superpixels are thresh- minimal operator intervention. GIRI is a computer numerical control (CNC) olded to produce a binary image for use in visualization and measurement Mistui MSG-818PC-NC surface grinder which has been retrofitted with a (Fig. 3C). misting apparatus, retractable rollers, and an imaging stage that consists The stack of processed binary images is loaded into Avizo, a scientific visu- of two LED lamps and an 80-megapixel Phase One digital back coupled to a alization software package. Each slice is given a thickness that corresponds 120-mm Schneider Kreuznach macrolens via an electronic shutter. The CNC to the amount of material removed during a grind cycle (i.e., the step size), grinder is capable of moving in 1-µm increments. The camera sensor mea- thereby turning each pixel into a volumetric pixel, or voxel. sures 40.4 × 53.7 mm and contains pixels that are each 5.2 × 5.2 µm in To isolate and measure individual specimens, a custom graphical user size. When the camera is set up for 1:1 macroimaging, the system is capa- interface (GUI), written in MATLAB, is used. First, a down-sampled stack of ble of resolving objects as small as 10.4 µm over a 40.4 × 53.7-mm field of the original true color images is loaded into the GUI. Next, a user scrolls view. As the CNC grinder has a high degree of repeatability, samples can be through the stack, selects an object of interest, draws a bounding box mosaicked to achieve a higher field of view and/or higher resolutions. around the feature, and inputs the first and last slice in which the feature The CNC grinder processes a list of machine instructions written in G code, can be found. Finally, in the case of cylindrical objects such as Cloudina, the a numerical control code language (40). An optimized grinding and imag- user marks the center of the object in multiple slices. ining routine has been written for GIRI and parameters related to individ- The bounding box coordinates, along with information about the first ual samples (i.e., sample name, sample width, step-down size, and number and last slice, are used to extract a subvolume of the larger dataset in Avizo. of slices) can be edited and the result saved as a valid G-code file for any If center points are provided, a 3D spline is fitted to the points. The length given sample. Using a collection of interactive MATLAB scripts and Apple- of the spline is treated as the length of the object. Coordinates and tangent script functions, the control computer is able to send and receive signals values are evaluated at fixed intervals along the spline (for this study, the from the grinder, trigger the shutter, and verify image capture, all while intervals were at 20%, 40%, 60%, and 80% of the total length of the spline) GIRI is in operation. and the information is used both to produce oriented sections (with the A typical grind cycle begins with the removal of some surface material tangent serving as the normal of the plane that defines the sections) in (as specified by the step size) by a 6-inch diameter diamond or silicon car- Avizo and to calculate the plunge and trend of the tube. bide wheel. Following the grind cycle, the sample passes under a roller to Semimajor and semiminor axes measurements are made directly on these clear off any excess fluid and ensure an even sheen. The sample is then 2D sections using the built-in ruler tool in Avizo. The cross-sectional eccen- positioned under the imaging stage for photographing. At this point, the tricity is calculated by dividing the semiminor axis size value by the semima- grinder sends a signal to the control computer requesting an image capture; jor axis size. The rate of semimajor axis size change is defined as an Applescript command triggers the shutter and the image is downloaded

into Capture One, a software package designed to work with the Phase One (|dn+1 − dn|)/(dn), digital back. After the image has been downloaded and verified, the control computer initiates the next grind cycle by sending a signal to the grinder. where d is the semimajor axis (in millimeters) and n refers to the sectional The process is repeated until the sample has been fully ground and imaged. slice number. All means are reported with 1 SD. A typical 1,500-slice sample (at 30 µm per slice) takes 1 wk to grind and image; during this time, the operator needs to replace machine fluids and ACKNOWLEDGMENTS. We thank C. Husselmann for granting us access to clean the wipers only once every 24 h. Driedoornvlakte Farm, G. and L. Fourie for allowing us to work in Zebra Capture One downloads and stores images as .IIQs, a proprietary raw River Farm, and the Curtis family for opening up Donkergange Farm. image file format. While the .IIQ format preserves unedited sensor data— M. Laflamme and R. Wood provided helpful discussions while in Namibia. thereby enabling postcapture adjustments of settings such as white balance, G. Schneider at the Geological Survey of Namibia granted us permits for exposure, and sharpening—it cannot be opened or processed in programs working in Namibia. J. Eiseb of the Geological Survey of Namibia assisted other than Capture One. Therefore, once a sample has been ground and us with the export permitting process. J. Grotzinger let us use his locker at the Geological Survey of Namibia. We thank BC Parks for granting us a imaged, the .IIQ file for each slice is adjusted and exported as a 16-bit .TIFF permit to conduct fieldwork on Salient Mountain and Matt Morison at Yel- for further processing. The conversion from .IIQ to .TIFF has the downside lowhead Helicopters for logistical support. All of Situ Studio, but especially of dramatically increasing file size by an order of magnitude: A single .IIQ B. Samuels, were instrumental in the development of GIRI. A. Spatzier devel- ranges from 50 MB to 80 MB in size while its corresponding .TIFF is approx- oped the initial routines and operational procedures for GIRI. K. Kellerson at imately 600 MB. As a result, .TIFFs for a typical 1,500-count image stack Millennium Machinery gave us useful advice about machine programming can consume up to 900 GB of disk space. Due to storage space limitations, and grinding processes. A. Tasistro Hart, R. Bartolucci, W. Van Cleve, and and because .IIQ files retain adjustment information, only the .IIQ files are C. Gray provided assistance in the field. S. Gwizd, A. Hager, and D. Okhai archived after a project is completed. helped prepare and run samples for stable isotope analysis. B. Getraer assisted with measuring and electronics fabrication. J. Irving first suggested A user-supervised MATLAB routine was developed to efficiently extract the use of neural networks for fossil segmentation. This paper benefited features of interest from .TIFF image stacks. First, superpixels (i.e., regions from feedback by M. Eddy, B. Schoene, S. Porter, and A. Knoll. We thank the that consist of pixels that have been clustered together on the basis of color editor and two anonymous reviewers for their thoughtful feedback. This and position, ref. 41) are calculated for each image using the MATLAB super- work was supported by NSF Earth Sciences Grant 1028768 to A. Maloof and pixels routine. This effectively preserves feature edges while oversegment- by funding from the Princeton Tuttle Invertebrate Fund.

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