The histology of spinal cord was evaluated by hematoxylin and eosin (HE) staining and Pischinger methylene blue staining (Khedkar et al., 2012 (link)). The left ventral section of spinal cord was fixed in formalin and embedded into paraffin. The 6 μm coronal sections were cut from the tissue block and stained with HE stain or Pischinger's methylene blue before evaluated microscopically with an Olympus IX71 Inverted Fluorescence Phase Contrast Microscope (Olympus, Shanghai, China). The areas of cavities were assessed using Digimizer software (MedCalc Software bvba, Ostend, Belgian) and number of dendrites was quantified with ImageJ software (NIH, Bethesda, MD).
Digimizer software
Manufactured by MedCalc
Sourced in Belgium
Digimizer is a software application designed for image analysis. It enables users to measure and quantify various aspects of digital images, such as distances, areas, and angles. The software provides a range of tools and functionalities to support image processing and data extraction tasks.
Automatically generated - may contain errors
Lab products found in correlation
Fm4 64, by Thermo Fisher Scientific (3 mentions)
Ix71 inverted fluorescence phase contrast microscope, by Olympus (1 mentions)
Fluorescent mounting medium, by Agilent Technologies (1 mentions)
Spot rt slider camera, by Nikon (1 mentions)
Coreldraw x4, by Adobe (1 mentions)
Eclipse e600 microscope, by Nikon (1 mentions)
Prism 9, by GraphPad (1 mentions)
Spss statistic, by IBM (1 mentions)
Szx16, by Olympus (1 mentions)
Cd 15cp, by Mitutoyo (1 mentions)
Axioimager a1 light microscope, by Zeiss (1 mentions)
S 800, by Hitachi (1 mentions)
Shuttle pix, by Nikon (1 mentions)
Isomet, by Buehler (1 mentions)
26 protocols using digimizer software
1
Spinal Cord Histology Analysis
2
Wound Healing Assay with miR-223
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Cells were seeded and grown to confluence in 6-well dishes, and transfected with either miR-223 or anti-miR-223. 24 h later, an artificial wound was scratched into the confluent cell monolayer using a 200-μl pipette tip. To visualize cell migration and wound healing, images were captured 0 and 48 h after scratching. The distance between the two edges of the wound was measured using Digimizer software (MedCalc Software, Ostend, Belgium).
3
Immunofluorescence Staining of NMJs
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The average CSA and fiber-size distributions were determined using the Digimizer software (MedCalc Software, Mariakerke, Belgium). Immunohistochemistry was performed as described previously (Piecha et al., 1999 (link)). Primary and secondary antibodies used for immunofluorescence of acetone-fixed 10-µm cryosections and cells grown on coverslips are listed in supplementary material Table S1 . Nonspecific binding of the antibodies was blocked with 10% proper normal serum. Nuclei were stained with DAPI. NMJs were detected with tetramethylrhodamine α-bungarotoxin (Invitrogen, 1∶200). The specimens were mounted with fluorescent mounting medium (Dako), viewed with a Nikon Eclipse E600 microscope equipped with epifluorescence and photographed with a Spot RT Slider camera. The images were processed using SPOT software (version 4.0.9 for Windows; Diagnostic Instruments). Figures were created with Adobe Photoshop 8.0 and CorelDraw X4 softwares.
4
Quantifying Zebrafish Developmental Parameters
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Rotated brightfield images with segmented animal and black background were used to evaluate developmental parameters, such as length, eccentricity, pericardial area, tail-head angle, and yolk sac area. Length and eccentricity were determined using CellProfiler (Version 4.2.6, Broad Institute Inc.). Briefly, the animal was identified as an object (“IdentifyPrimaryObjects” function) with a manual threshold of 0.01, and values were obtained by applying “MeasureObjectSizeShape” function (pipeline “MorphologyAndMpeg_quantification.cppipe” available at https://github.com/nBTTlab/beatrizcustodio_PAMAM ). Pericardial area, head–tail angle, and yolk sac area were quantified using Digimizer software (version 4.1.1.0, MedCalc Software, Ostend, Belgium). Measured areas and larvae contour were manually defined.
5
Standardized Radiographic Evaluation of Shoulder
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Standard true AP radiographs (ie, oblique view) with the arm in the neutral position and the hand in the anatomic position (ie, external rotation) were selected and retrieved from the hospital's picture archiving and communication system. Radiographs were made with the patients standing at a film distance of approximately 120 mm and with 15° of craniocaudal tilt. Radiographs were processed with CXDI Control Software NE (Canon Europe, Amstelveen, The Netherlands), stored in DICOM (Digital Imaging and Communications in Medicine) file format, and assessed using Digimizer software (version 4.6.1 [2005-2016]; MedCalc Software, Ostend, Belgium). Each measurement was conducted on a blank radiograph. Two observers (A.K. and C.L.O.) independently assessed the outcome parameters on each of the 280 radiographs in a random sequence. At 1 to 7 days (median, 3 days) after the first session, both observers assessed the outcome parameters in a second session. In total, each outcome measure was rated 4 times, resulting in 1120 observations per method.
6
Characterization of Inorganic Hydrogel Particles
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The inorganic phases were characterized by scanning electron microscopy, in an electronic analytical field emission microscope model S-800 FE, brand Hitachi (Tokyo, Japan), operated at 30 kev. The micrographs obtained were studied using the Digimizer software (version 5.8.0, MedCalc Software, Ostend, Belgium), using descriptors of shape and size to characterize the particles.
To study the porosity, the hydrogels were exposed to deionized water, which they absorbed until reaching physicochemical equilibrium. The samples were observed in the Quanta FEG 250 electron microscope (Saragossa, Spain), operated under low vacuum.
To study the porosity, the hydrogels were exposed to deionized water, which they absorbed until reaching physicochemical equilibrium. The samples were observed in the Quanta FEG 250 electron microscope (Saragossa, Spain), operated under low vacuum.
7
Histological Analysis of Ovarian Follicles
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Dehydration of the ovaries was donebygraded concentrations of ethanol and xylene. Then, they were embedded in paraffin wax. The ovaries were serially sectioned at thicknesses of 10 μm. Paraffin removal was done on one of every 10 serial sections in 60 °C. Then, selected sections were rehydrated in of xylene and decreasing serialconcentrations of ethanol. Finally, ovarian slices were stained with hematoxylin and eosin. To assess the type of follicles [23 ] and counting secondary, tertiary, and atretic follicles and corpora lutea, ovarian slices were observed with a light microscope (CX21, Olympus, Japan). Selected areas were photographed by a digital camera (AM423U Eyepiece Camera, Dino-Eye, Taiwan). Diameters of various structures including entire follicle, follicular antrum, granulosa and theca layers of secondary and tertiary follicles and corpus luteum were measured by Digimizer software (MedCalc Software bvba, Belgium)[21 ].
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Dehydration of the ovaries was donebygraded concentrations of ethanol and xylene. Then, they were embedded in paraffin wax. The ovaries were serially sectioned at thicknesses of 10 μm. Paraffin removal was done on one of every 10 serial sections in 60 °C. Then, selected sections were rehydrated in of xylene and decreasing serialconcentrations of ethanol. Finally, ovarian slices were stained with hematoxylin and eosin. To assess the type of follicles [23 ] and counting secondary, tertiary, and atretic follicles and corpora lutea, ovarian slices were observed with a light microscope (CX21, Olympus, Japan). Selected areas were photographed by a digital camera (AM423U Eyepiece Camera, Dino-Eye, Taiwan). Diameters of various structures including entire follicle, follicular antrum, granulosa and theca layers of secondary and tertiary follicles and corpus luteum were measured by Digimizer software (MedCalc Software bvba, Belgium)[21 ].
8
Membrane and DNA Staining of Bacteria
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For staining procedures, cells were washed three times with PBS buffer (pH 7.4) and collected by centrifugation at 5,000 rpm for 5 min at 4°C. Membrane dye FM4-64 (Thermo Fisher) and DNA dye DAPI (Beyotime) were added into bacterial suspension at 37°C for 10 min in the dark. Bright-field microscopy images were acquired using a microscope with 100× oil immersion lens. Cell length and cell wall thickness quantitative measurements were made using Digimizer software (MedCalc, Ltd., Ostend, Belgium) (57 ). An unpaired t test was used for statistical analysis. The branched cells were not included in the cell length measurement analysis.
9
Antenna Morphometrics Compared
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The morphometrics were measured with Digimizer software (MedCalc Software, Ostend, Belgium). The measurements were expressed as mean ± standard error. Differences in antenna length and sensillum size and number between sexes were analyzed using t test with SPSS statistics (20.0, IBM, Chicago, IL, USA). Bar graphs were drawn with GraphPad Prism 9 software (GraphPad Software Inc. San Diego, CA, USA).
10
Morphological Descriptions of New Plant Species
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The morphological descriptions of the two new species were based on observation of living plants and specimens collected from the type localities in 2021. We also examined specimens in the herbaria KB, KH, KIOM , and SNU (Thiers 2022 ) to compare them with related species. Type and voucher specimens were deposited in the Korean Herbarium of Standard Resources, Korean Institute of Oriental Medicine (KIOM ). Measurements of morphological structures were performed using a digital vernier caliper (CD-15CP; Mitutoyo, Kawasaki, Japan). Digital images of floral parts were captured by using an Olympus SZX16 stereomicroscope (SM: Olympus, Tokyo, Japan), equipped with an attached Olympus DP21 digital camera (Olympus, Tokyo, Japan). Quantitative data of floral structures obtained from SM images were determined using Digimizer software (version 5.4.3; MedCalc Software, Mariakerke, Belgium).
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