Lightroom

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Lightroom is a photo processing and management software developed by Adobe. It provides tools for importing, organizing, editing, and exporting digital images.

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Lab products found in correlation

Ace200, by Leica (2 mentions) Abode illustrator, by Adobe (2 mentions) Gt450, by Leica (1 mentions) Geforce gtx 1080, by NVIDIA (1 mentions) Hoechst 33342, by Merck Group (1 mentions) 6d camera, by Canon (1 mentions) Mpe 65 mm 1 5x micro photography lens, by Canon (1 mentions) Sp8 inverted microscope, by Leica (1 mentions) E400 microscope, by Nikon (1 mentions) Toluidine blue o, by Merck Group (1 mentions) Diamond knife, by Electron Microscopy Sciences (1 mentions) Ultracut r microtome, by Leica (1 mentions) Smz25 stereomicroscope, by Nikon (1 mentions) Axiocam erc5s camera, by Zeiss (1 mentions) Axioscope microscope, by Zeiss (1 mentions) D3x slr camera, by Leica (1 mentions) Power sybr green pcr master mix, by Thermo Fisher Scientific (1 mentions) Odyssey fc imager, by LI COR (1 mentions) Eclipse 80i compound microscope, by Nikon (1 mentions) Infinity 2 microscope camera, by Teledyne (1 mentions)

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Lightroom CC (7 citations) Lightroom Classic (7 citations) Lightroom Classic CC (3 citations) Lightroom 3.6 (2 citations) Lightroom 2 (2 citations) Lightroom 5 (2 citations)

17 protocols using lightroom

Whole-Slide Image Capture Optimization

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All slides were batch imaged in whole-slide scanners using supplied autoloader racks under three conditions [Details in Supplemental Data]: (1) Hamamatsu S210 using default brightfield (“default”) profile settings; (2) Hamamatsu S210 using profile settings empirically optimized (“opt”) to minimize tissue dropouts; and (3) Leica GT450 standard settings. Scan time was estimated from file timestamps (S210) or scanner log (GT450) and the resulting file size was read from the destination computer operating system (Windows 10). Measurements of file size were captured as actual bytes per file, and scaling of units was performed on a decimal scale (e.g., 1 byte = 1000⁰ bytes; 1 KB = 1000¹ bytes, 1 MB = 1000² bytes; 1 GB = 1000³ bytes).
Full-frame tiff images of the entire field captured by the scanner were generated by opening each whole-slide image file (ndpi = S210 file type, svs = GT450 file type) in a multiformat viewer (NDP.View Plus v2.7.43 + Hamamatsu Photonics K.K., 2019), and exporting the screen contents as recompiled from the source wsi to a tiff file that was cropped to the margins of the captured field. TIFF files were imported into Adobe Lightroom for adjustment of contrast and brightness, and conversion to gray scale.

Mutter G.L., Milstone D.S., Hwang D.H., Siegmund S, & Bruce A. (2022). Measuring digital pathology throughput and tissue dropouts. Journal of Pathology Informatics, 13, 100170.

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Dissection and Imaging of Genitalia

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The genitalia from wildtype and crispants were dissected using fine forceps and placed in 10% solution of sodium hydroxide for 30 min to 1 h to soften the attached nonsclerotized tissues. They were then moved to PBS and the sclerotized structures were separated from the underlying tissues using forceps. Genitalia were embedded in low melting agarose to maintain orientation while imaging. Imaging was done using an Ocellus microscope (Dun Inc.) consisting of a Canon 7D Mk II DSLR body, Mitutoyo objectives and a P-51 Camlift stacking rail. Individual image slices were processed with Lightroom (Adobe Inc.), stacking of images with Zerene Stacker and postprocessing with Photoshop CS5 (Adobe Inc.).

Prakash A, & Monteiro A. (2020). Doublesex Mediates the Development of Sex-Specific Pheromone Organs in Bicyclus Butterflies via Multiple Mechanisms. Molecular Biology and Evolution, 37(6), 1694-1707.

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Automated 3D Model Creation From Photos

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The rest of the process to create a 3D model is carried out by a largely automated process (Fig 2) that requires minimal supervision (e.g., opening software programs, starting batch processing, etc.), except for a small amount of manual mesh processing (see below). For processing the scan data, we use a Windows PC with an intel i7 processor, 16 gigabytes of ram, and a Nvidia GeForce GTX1080 graphics card. The approximate time to completion of each step is listed in Table 2. The 288 photos (96 photos x 3 angles) are imported into Adobe Lightroom for image processing. Exposures and white balances are standardized using the 75% gray color chip, and photos are corrected for distortion and color aberrations using a color profile generated from the standard color chart. Photos are exported as high-quality JPGs. Then, within Adobe Photoshop, masks are created using a batch process that obscures the backdrop and isolates the subject in preparation for the next step: alignment of the 2D images to create a 3D model (image registration). The images are exported from Adobe Photoshop as JPGs with the “_masked” suffix.

Medina J.J., Maley J.M., Sannapareddy S., Medina N.N., Gilman C.M, & McCormack J.E. (2020). A rapid and cost-effective pipeline for digitization of museum specimens with 3D photogrammetry. PLoS ONE, 15(8), e0236417.

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Immuno-Detection of RANKL in Cells

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Cells were fixed in 3% paraformaldehyde in Tyrode's salt solution at 4°C for 20 minutes and rinsed with wash buffer (0.1% BSA in Tyrode's salt solution). Cells were then permeabilized with 0.01% digitonin in Tyrode's salt solution for 20 minutes and rinsed in wash buffer. Blocking of non- specific antibody interaction was carried out using a 10% serum solution based on secondary antibody species. Blocking was carried out for 30–50 minutes. Anti-RANKL primary antibody in 10% goat serum was added for 1–2 hours at room temperature. For co-staining, RANKL primary antibody was added in a blocking solution with mouse derived antibodies for either Runx2, PPARγ1/2, SH2 antibody [43] (link), [44] , anti-CD90 antibody (gift from Michael Sorrell), or goat anti-C/EBPα. After washing, cells were incubated for 2 hours at room temperature with fluorophore-conjugated secondary antibodies. Cell were washed, and counterstained with 3 µg/mL Hoechst 33342 (Sigma) prior to imaging. Quantitative analysis was done by counting RANKL positive cells in 4–5 random fields (n = 3–4 donors). All images were processed using Image J for quantitative analysis and Adobe Lightroom for contrasting.

Holt V., Caplan A.I, & Haynesworth S.E. (2014). Identification of a Subpopulation of Marrow MSC-Derived Medullary Adipocytes That Express Osteoclast-Regulating Molecules: Marrow Adipocytes Express Osteoclast Mediators. PLoS ONE, 9(10), e108920.

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Macro-Imaging of Ethanol-Fixed Specimens

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For macro-images, one specimen was fixed in 70% ethanol and documented using the BK PLUS Lab system (Dun Inc., http://www.duninc.com/bk-plus-lab-system.html) with a customized Canon MPE 65 mm 1–5x micro-photography lens mounted on a Canon 6D camera. Image stacks were captured with Adobe Lightroom and processed using Zerene Stacker under PMax value.

Kenning M., Schendel V., Müller C.H, & Sombke A. (2019). Comparative morphology of ultimate and walking legs in the centipede Lithobius forficatus (Myriapoda) with functional implications. Zoological Letters, 5, 3.

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Microscopy and Image Processing Protocol

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Chromogenic images were acquired by using a Nikon E400 microscope and NIS-Elements BR imaging software (Nikon Instruments, Melville, NY, USA). Immunofluorescence images were captured using a Leica SP8 inverted microscope (LeicaMicrosystems, Mannheim, Germany) and further processed using ImageJ (Wayne Rasband, National Institutes of Health, USA). Color adjustments were made by Lightroom (Adobe, San Jose, CA, USA). InkScape 0.92 was used for subsequent image orientation and cropping.

Thorsvik S., Bakke I., van Beelen Granlund A., Røyset E.S., Damås J.K., Østvik A.E, & Sandvik A.K. (2018). Expression of neutrophil gelatinase-associated lipocalin (NGAL) in the gut in Crohn’s disease. Cell and Tissue Research, 374(2), 339-348.

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Tissue Preparation and Imaging Protocol

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Cross sections of about 2 mm width and 4 mm length were cut and were fixed for 4 h with 2.5% paraformaldehyde and 0.4% glutaraldehyde in 0.1 M McIlvaine citrate-phosphate buffer, pH 7.0. After dehydration in a graded series of ethanol, samples were embedded in medium grade LR White resin (London Resin Company Ltd, UK). Semi-thin sections (1 μm thick) were collected with a diamond knife (Diatome, Biel, Switzerland) installed on an ultracut R microtome (Leica, Rueil-Malmaison, France), placed on slides, fixed by heating at 120°C for 2 min and stained with Toluidine Blue O 0,1% (w/v in water) (Sigma-Aldrich, T0394).
Cross sections for the ablation experiment were cut and fixed with the same protocol but were included in paraffin. Section of 10μm were made with a rotary microtome (369 Yamato Kohki, Japan) and stained with Toluidine Blue O 0,1% (w/v in water) (Sigma-Aldrich, T0394).
Images were assembled using MosaicJ plugin of ImageJ [18 (link)] and treated with Photoshop and Lightroom (Adobe) in order to adjust contrast and white balance, and for cropping.

Guiguet A., Hamatani A., Amano T., Takeda S., Lopez-Vaamonde C., Giron D, & Ohshima I. (2018). Inside the horn of plenty: Leaf-mining micromoth manipulates its host plant to obtain unending food provisioning. PLoS ONE, 13(12), e0209485.

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Lightroom Photographic Workflow Protocol

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Adobe Lightroom (Lightroom.html">https://www.adobe.com/products/photoshop-Lightroom.html) was used for cropping, calibrating, retouching, adding image metadata, and exporting different file formats, and was selected for the project due to its integration with Helicon Focus.

, & Braker E.M. (2022). Phototank setup and focus stack imaging method for reptile and amphibian specimens (Amphibia, Reptilia). ZooKeys, 1134, 185-210.

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Multimodal Imaging of Art Objects

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Visible diffuse light photography (Vis) was achieved by using two 800W Ianiro Varibeam Halogen lamps (Ianiro, New Taipei City, Taywan), placed at an angle of approximately 45° to the surface, and with the aid of umbrellas for light diffusion purposes. Photographs were taken using a Nikon D810 Full-Frame DSLR camera (CMOS 7360 × 4912 pixels).(Nital Spa, Moncalieri, Turin, Italy)).
The UV-induced visible fluorescence (UVF) was acquired via a Nikon D810 full-frame DSLR camera (CMOS 7360 × 4912 pixel) and a Hoya UV-IR Cut filter (Hoya, Tokyo, Japan), irradiating the painting with two UV Labino^® lamps (365 nm-emission peak). The NIR reflectography was performed using a Nikon D810 full-frame DSLR camera (CMOS 7360 × 4912 pixel), modified to extend the sensor sensitivity range up to 1000 nm, and with a B+W 093 (87c) filter, illuminating the painting using Ianiro Varibeam Halogen 800 W lamps (Ianiro, New Taipei City, Taywan) with indirect diffused light.
Image processing was carried out by means of Adobe Lightroom and Adobe Photoshop software (Version C6S) and included a color correction conducted by inserting a 24-color ColorChecker Classic reference in the field of view.

Cavaleri T., Pelosi C., Ricci M., Laureti S., Romano F.P., Caliri C., Ventura B., De Blasi S, & Gargano M. (2022). IR Reflectography, Pulse-Compression Thermography, MA-XRF, and Radiography: A Full-Thickness Study of a 16th-Century Panel Painting Copy of Raphael. Journal of Imaging, 8(6), 150.

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Imaging and Measurement Protocol for Insect Wings

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Wings flattened on microscope slides were imaged with a Zeiss Axioscope microscope with a Zeiss AxioCam ERc 5s camera attached. For higher magnification images of the body surface and hair, we used a Nikon SMZ25 Stereomicroscope. Images were also taken with a Nikon D3X SLR camera and Leica Z16 APO lens. Wing dimensions and other body measurements were estimated using the built-in scale, ImageJ, or MATLAB with the mean and standard deviation of several measurements reported herein. High speed photography was accomplished with a color Phantom V710 camera. Focus stacking for the images in Fig. 1a,c,d was accomplished in Adobe Photoshop. The histograms of many of the SLR and high-speed photography images were adjusted in Adobe Lightroom to correct the white balance and provide minor brightening.

Speirs N.B., Mahadik G.A, & Thoroddsen S.T. (2020). How drain flies manage to almost never get washed away. Scientific Reports, 10, 17829.

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