Hematoma assessment was conducted after sacrificing the mice. The brains of six mice in each group were quickly removed and cut into 1mm thick brain sections after perfusion with PBS. The sections were then imaged with an Epson Perfection V370 Photo scanner (Epson China, Beijing, China) and the hematoma volume of each section was analyzed using the Image-Pro Plus software. Hematoma volume in cubic millimeters was calculated as the mean of the summation of the hematoma areas multiplied by the interslice distance (1mm).
Perfection v370
Manufactured by Epson
Sourced in China, Japan
The Epson Perfection V370 is a flatbed scanner that can digitize various types of media, including photos, slides, and documents. It features a maximum optical resolution of 4800 dpi and can scan at up to 48-bit color depth. The scanner is capable of operating at USB 2.0 speeds.
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Lab products found in correlation
Lsm 700 confocal microscope, by Zeiss (2 mentions)
Xcalibur 2, by Thermo Fisher Scientific (1 mentions)
Nitrofurantoin, by Merck Group (1 mentions)
Amikacin disulfate salt, by Merck Group (1 mentions)
Orca flash4.0 v3, by Hamamatsu Photonics (1 mentions)
Plan apochromat, by Zeiss (1 mentions)
Csu w1 t2, by Yokogawa (1 mentions)
V700 flatbed scanner, by Epson (1 mentions)
Zen blue, by Zeiss (1 mentions)
Visiview software, by Visitron (1 mentions)
Statistica v 7, by StatSoft (1 mentions)
19 protocols using perfection v370
1
Brain Hematoma Volume Quantification
2
Floral Petal Preparation and Imaging
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After a flower was harvested, the corolla was dissected along the middle vein of the two lateral petals. From the ventral half of the corolla, the remaining lateral lobes were removed, and a necessary cut was made at the remaining lateral tube region to properly flatten the petal (Figure 1 ). An image of the adaxial surface of the petal was captured using a flatbed color scanner (Perfection V370, Epson, Nagano, Japan). The resolution ranged from 600 to 9,600 dpi. During scanning, the petal was flattened at the scanning stage and covered with a black cloth. The detailed procedure was reported by Hung et al. (2020) (link). Subsequently, the scanned fresh petal was carefully moved to a fixative solution.
3
Automated Time-Lapse Imaging for Plant Growth
4
FTICR MS Analysis of Metabolite at m/z 400.3
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A 12 T SolariX FTICR MS (Bruker Daltonics) was used to acquire high mass accuracy spectra for the ion of interest at m/z 400.3, previously detected by MALDI-TOF-MSI. Slides with infected and uninfected tissue sections prepared for MSI were used and matrix applied as previously described. Areas of the tissue sections to be analysed were identified using the MSI results and an optical image of the slide taken using a flatbed scanner (Epson Perfection V370). The laser diameter was set to medium and 50 μm areas of tissue were ionised by random walk. A spectrum with a mass range of m/z 200–2000 was acquired for each sample position and continuous accumulation of selected ions (CASI) was used to increase the signal-to-noise of the ions in the range m/z 400.34 ± 5. Data was analyzed using Xcalibur 2.2 (Thermo Scientific) to gain an accurate mass of the molecule at 400.3 and the m/z ratio was searched on the online human metabolome database (http://www.hmdb.ca/ ) to gain a preliminary identity.
5
Scanning Bacterial Growth Dynamics
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Aliquots of bacterial cultures grown as described above were taken at time points indicated in the text, washed twice in sterile phosphate-buffered saline, diluted between 10−5 to 10−6, and 100 μL spread on either LB agar plates with or without specified antibiotics (2 μg/mL amikacin disulfate salt or 7 μg/mL nitrofurantoin [both Sigma-Aldrich]) or 50% (vol/vol) healthy female human urine containing 1.5% (wt/vol) agar. Plates were incubated at 33°C in a standard office scanner (Epson Perfection V370 photo scanner, J232D) placed in an incubator, and images were taken every 20 min over a 48-h period. Analysis of appearance time and apparent growth rate of colonies was adapted from Levin-Reisman et al. (18 (link)) using a modified code by Miles Priestman available at https://github.com/mountainpenguin/NQBMatlab . At least two independent experiments were conducted for each ScanLag experiment shown in the figures.
6
Quantifying Fungal Colony Growth
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Prior to a setting up another plate passage (after a 1.5 month incubation period), plates were imaged using an Epson Perfection V370 photo scanner. A ruler was placed in the scanner to scale pixels to millimetres for radial growth measurements. Images were uploaded to ImageJ2 for analysis [21, 22 (link)]. Radial growth was determined by measuring the distance from the centre of the colony to the furthest point of radial growth. Measurements were uploaded to R to generate boxplots using ggplot2 [20 (link)].
7
Tracking Seedling Growth in IAA-treated Arabidopsis
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The petri dishes containing the IAA-grown Col-0 and ralf34-1 seedlings were fixed onto a vertically mounted flatbed scanner (Epson perfection V370) and seedlings were imaged through the layer of medium. Scans were taken automatically every hour using the AutoIt script described previously [48 (link)] at 800 or 1200 dpi. The resulting image series were analysed using StackReg stabilisation and the Manual Tracking plugin in ImageJ.
8
Scanning Methods for Rhizotron Root Imaging
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There are two common types of flatbed scanner, the CIS (Contact Image Sensor) and the CCD (Charge Coupled Device) scanners. A CIS scanner is more compact and requires less power than a CCD scanners and can usually run off battery power or the power from a USB port. CCD scanners, however, provide higher-resolution scans and are capable of scanning with a good depth of field. Accordingly, we used an Epson Perfection V370, high optical resolution of 4800 dpi and CCD technology that relies on a system of mirrors and lenses to project the scanned image onto the arrays. The lid of the scanner can be removed and the scanner connected to the computer via a USB cable and to a 15 V external battery (Fig. 1 ). The scanner can be placed horizontally or vertically. Four horizontal scans and a resolution of 300 dpi are needed for one 50 × 50 cm rhizotron.![]()
Four different methods were used to take images of walnut tree roots in rhizotrons:
9
TRA-1-60 Immunocytochemistry in Cells
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The cells were fixed with 4% PFA for 15 min, incubated with 0.1% Triton X-100/PBS for 15 min, and blocked with 5% BSA/PBS for 1 hour. The cells were incubated with mouse monoclonal anti–TRA-1-60–HRP (horseradish peroxidase) conjugated (1:1000, MA1-023-HRP; Thermo Fisher Scientific) overnight at 4°C. The cells were then washed three times with PBS, and TRA-1-60–positive cells were visualized using the 3,3′-diaminobenzidine (DAB) peroxidase staining kit (Vector Laboratories). The images were scanned using the Epson Perfection V370 photo scanner.
10
Measuring Yeast Colony Size Parameters
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To determine the size parameters for each type, P and S strains were streaked from −80° freezer stocks to isolate colonies on YEA plates. Both P and S strains were grown at 30°, and then cells from individual colonies were again isolated and spread on YEA plates by manual spreading or microscope dissection. These plates were grown at 30° for 6 days (±2 hr). The plates were equilibrated to room temperature, and then scanned at 600 dpi using an Epson Perfection V370 photo scanner. The sizes of each colony was measured using ImageJ software (version 1.47). The average colony sizes for all strains were calculated and checked for normality using a Shapiro-Wilk test (Figure 1 ). In Figure 3A , the colony size was measured after individual cells were dissected and grew on rich medium for 6 days. To ensure a clear distinction between P and S strain colonies, S strains were defined conservatively as those whose colony size was more than six times larger than the average size of P colonies. For genetic analysis shown in Figure 4 and Figure S2, even the colony size of a mutant is slightly smaller than that of the wild-type cells, as long as it is more than six times larger than the elf1Δ P cells, counted as wild-type colony size.
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