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30 protocols using perfection v600 photo

1

Root and Shoot Analysis of Plant Accessions

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Each day at the same time, for 9 days, plates were scanned with CCD flatbed scanners (EPSON Perfection V600 Photo, Seiko Epson, Nagano, Japan), and the images were used to quantify root parameters using Brat 2.0 (as described in [25 (link)]). After 10 days, roots and shoots from 4 plants of each accession were weighed and frozen. For anion measurements in the initial screening, frozen plant material from 4 biological replicates was then homogenized in 1 mL of deionized water, and the anions -nitrate, phosphate and sulfate- were separated by the Dionex ICS-1100 chromatography system on a Dionex IonPac AS22 RFIC 4x250 mm analytic column (Thermo Scientific, Darmstadt, Germany) with 4.5 mM NaCO3/1.4 mM NaHCO3 as running buffer. Extraction with 1 mL 10 mM HCL did not affect the measured phosphate values. Total P was determined by inductively coupled plasma mass spectrometry (ICP-MS) from ca. 10 mg lyophilized shoot tissue by the Biocenter MS Platform Cologne, University of Cologne, using an Agilent 7700 ICP-MS (Agilent Technologies, Santa Clara, CA, USA) [14 (link)].
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2

High-Resolution Root Imaging Protocol

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Root images were obtained using CCD flatbed scanners (EPSON Perfection V600 Photo, Seiko Epson Co., Nagano, Japan). The BRAT (Busch-lab Root Analysis Toolchain) image acquisition tool on a standard desktop computer running Ubuntu Linux allowed the simultaneous control of the scanners (Slovak et al., 2014 (link)). Scans were performed with a resolution of 1200×1200 dpi, resulting in an image size of 6000×6000 pixels (36 MP) for each of our 12×12 cm agar plates. To enhance image quality, scanning was performed in a dark room and with the scanner lid open.
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3

Root Phenotyping of Arabidopsis Natural Accessions

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The 134 natural accessions (12 plants were used for each accession) were grown on −Fe agar plates under long day conditions (16 hours light) at 21 °C. Plant images were acquired with CCD flatbed scanners (EPSON Perfection V600 Photo, Seiko Epson CO., Nagano, Japan) every 24 hours for 5 days (2 DAG—6 DAG). Root image analyses and phenotype quantification were performed using the BRAT software40 (link). Median total root length values of 134 natural accessions were used for GWA studies. We conducted GWA mapping using a mixed model algorithm41 (link) which has been shown to correct for population structure confounding42 (link) and SNP data from the RegMap panel28 (link)43 (link)44 (link). SNPs with minor allele counts greater or equal to 10 were taken into account. The significance of SNP associations was determined at 5% FDR threshold computed by the Benjamini-Hochberg-Yekutieli method to correct for multiple testing45 .
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4

Quantifying Root System Architecture

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After 3 days of treatment, plates were scanned with CCD flatbed scanners (EPSON Perfection V600 Photo, Seiko Epson, Nagano, Japan), and images used to quantify root parameters with FIJI, by using the tool ‘segmented line’ (Schindelin et al., 2012; Figure S2) as described in Ristova and Busch (2017). In particular, we quantified: primary root length on day 10 (P), growth rate of P after treatment (P2), branching zone or the length of P between the first and last visible lateral root (R), average lateral root length (LRL), and visible lateral root number (LR.No). Length was measured in millimeters. Other traits were calculated: lateral root density of P, LRD_P (LR.No/P), lateral root density of R, LRD_R (LR.No/R), total lateral root length, TLRL (LR.No*LRL), total root length, TRL (TLRL + P), and length ratio, LRR (TLRL/P). For detailed protocol, see Ristova and Busch (2017).
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5

Quantifying Arbuscular Mycorrhizal Fungal Colonization

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Plates with mycelia were scanned with an Epson scanner (Perfection V600 Photo, Epson, Germany), and the files imported into ImageJ (Schindelin et al., 2012 (link)). Mycelial coverage on each plate was delineated using a free-hand selection tool and measured with the built-in “Measure” function.
AMF colonization was determined by the “magnified intersections method” described in detail by McGonigle et al. (1990) (link). In brief, roots were cut in about 1 cm pieces and we counted the fungal structures of 150 intersections per sample after staining with Trypan Blue.
For determination of AMF colonization marker 11-carboxyblumenol, three leaf disks per AMF inoculated of the first and second stem leaf were harvested 6 and 8 weeks after AMF inoculation. 11-Carboxyblumenol levels were determined as markers of arbuscule colonization and quantified following the protocol of Wang et al. (2018a) (link).
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6

High-Resolution Scanning for Tomato Analysis

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To allow equal spacing of Petri dishes on the scanner bed, a black construction paper mask was created by cutting ∼ 2.5-cm circles about 1 cm apart from each other. The mask was accommodated on a flatbed scanner (Perfection V600 Photo, Epson, Suwa, Japan) and the Petri dishes were placed on top of the carved circles. Ninety-six-well plates were placed directly on the scanner bed. Scans were acquired at 600 dpi and by covering the scanner with a cardboard box. All images were saved in jpg format and processed in FireAlpaca v. 2.11.17 on a Windows 11 Home v. 23H2 computer, to replace the original background with a black background (Additional file 6: Fig. S4). The final resolution of the images after editing was maintained at 600 dpi. Image analysis was performed with Tomato Analyzer (TA) v. 4.0 on a Windows 8.1 with Bing computer. Tomato Analyzer calibration was done using a color checker (ColorChecker Passport Photo 2, Calibrite LLC, Wilmington, DE, USA) and setting illuminant D65, observer 10° of the CIELab color space. The Color Test function of TA (TACT) was used to obtain L*, a*, b*, hue, and Chroma of all samples. Parameters a* and b* were used to compute the a*/b* ratio.
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7

Collecting and Characterizing Beetle Specimens

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We collected a total of 75 (50 male and 25 female) beetles from a large metapopulation near Butt Mountain, Virginia, in June 2019. We housed subjects individually in small, plastic containers (5 cm × 2.5 cm × 5 cm) under natural light conditions (14.5:9.5 hr light:dark cycle ± 17 min) and room temperature (22 ± 3°C) at the Mountain Lake Biological Station (Salt Pond Mountain). Containers included a small amount of mulch over a layer of plaster of Paris to help maintain a humid environment and mimic natural substrate. We added a small piece of Ganoderma tsugae (a polypore fungus) fruiting body as a food source and provisioned water ad libitum. Beetles remained in isolation in their containers for 12 days before trials began. All individuals were assigned a unique ID by adding colored dots to their elytra using nontoxic Testors® Enamel paint. We recorded elytra length to the nearest 0.01 mm from images taken with a flatbed scanner (Epson Perfection V600 Photo) in ImageJ (Abramoff et al., 2004; Formica et al., 2012). Age and reproductive status are impossible to determine from wild‐caught B. cornutus, so we did not control for the age or experience of our individuals.
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8

Plant Shoot Morphometric Analysis

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Shoots of Individual plants were cut and their fresh weight was measured first. Shoots were disposed onto white paper, sealed with polyester non-sterile transparent film (VWR, USA), and scanned (Perfection V600 Photo, Epson). Canopy size, petiole length, leaf length, leaf width, leaf numbers, and hypocotyl length were measured using ImageJ (Fiji)87 (link).
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9

Hypocotyl Measurement Protocol

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Six-day-old seedlings were harvested for hypocotyl measurements. A ScanJet3500 (Hewlett-Packard, Palo Alto, CA, USA) or a Perfection V600 Photo (Epson, Nagano, Japan) flat-bed scanner was used to generate TIFF or JPEG format images of the seedlings. National Institutes of Health (NIH) ImageJ 1.48 (Schneider et al., 2012 (link)) was used to measure hypocotyl lengths and data were analyzed and graphs generated using Excel (Microsoft, Redmond, WA, USA) software.
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10

Optimizing Chemotaxis Assay Imaging

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To efficiently capture images of the distribution of worms at the end of each chemotaxis assay, we used flatbed scanners (Epson, Perfection V600 Photo). We captured 8-bit grayscale images at 1200 dpi, with both brightness and contrast set at 50, choosing these settings to maximize contrast and resolution of the worms. The scan-bed on this instrument was large enough to simultaneously scan four assay plates positioned on the scanner surface using a frame cut from a sheet of black foam (9”×12”×1/6”, Cleverbrand Fun Foam, Black). The frame helped to map the four plates captured in a single image to their respective metadata and increased image contrast by setting consistent black levels. In addition, we adjusted the position of the scanner’s camera lens to achieve a sharp image at the surface of the gellan gel media that formed the assay arena. To achieve this goal, we modified consumer-grade flatbed scanners [21 (link)]. Specifically, we used standardized, transparent resolution patterns (USAF, 1951 Test Patterns, Edmund Scientific, #38-710) placed in position mimicking the assay surface, and adjusted the lens position to maximize pattern sharpness.
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