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Fiji imagej

Manufactured by Leica

Fiji/ImageJ is an open-source image processing software for biological image analysis. It provides a wide range of tools and functions for image acquisition, processing, analysis, and visualization. The software is designed to be extensible, allowing users to develop and integrate custom plugins to suit their specific needs.

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6 protocols using fiji imagej

1

Microscopy Protocols for Cell Imaging

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Phase-contrast images were acquired on a Zeiss microscope (Axiovert 25) at 10x (NA 0.25) or 20x (NA 0.3) magnification, using a Zeiss CCD camera (Axiocam MRC) and Zeiss Mr. Grab 1.0 software. Quantification of cell area and circularity was performed using Fiji/ImageJ (version 1.52e).
For confocal microscopy of fixed cells, cells were prepared on coverslips as previously described [39] , and images were acquired on an inverted confocal microscope (Leica AOBS or SP8) using 20x (NA 0.7) dry, 40x (NA 1.25) oil, and 63x (NA 1.32) oil objectives (Leica). Images were processed using Leica Application Suite X and Fiji/ImageJ (version 1.52e) software.
For confocal microscopy of sprouting assays, fibrin gels with beads were permeabilized for 5 mins in 0.5% Triton X-100, and blocked in 5% BSA in PBS containing 1 mM CaCl2 and 0.5 mM MgCl2 for 2 h at RT. Afterwards the gels were washed 3 times with PBS++ and DAPI and phalloidin were incubated overnight at 4 °C. The following day the gels were washed 3 times with PBS++ for 10 min. The beads were visualized using a 25x long-distance water objective on a Leica SP5 confocal microscope, creating z-stacks of 1.5 µm per slice, resulting in 150-200 slices per bead. A maximum projection of the image stacks was created using Fiji/ImageJ.
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2

Multimodal Analysis Workflow

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Statistical analyses were performed with GraphPad Prism version 9.0.0 (471). Microscopy images were acquired with Leica LAS AF software (v2.6.3.8173) and analysed with ImageJ/Fiji (v1.52n). Western blots were quantified using Bio-Rad Image Lab (v3.0.1.14). Cell sorting was performed using BD FACSDiva software (v8.0, FACSAria I). Proteomics data analysis was performed with MaxQuant (v1.6.14.0) and the R-package limma (v3.44.3).
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3

Immunofluorescence Microscopy of Cultured Cells

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Cells seeded on coverslips were fixed in 4% paraformaldehyde, permeabilized with 0.1% Triton X-100 and blocked with 1% BSA in PBS for at least 30 min. 100 µl of primary antibody diluted in 1% BSA and 0.1% Triton X-100 in PBS was added for 1 h followed by washing and secondary antibody (1:200) addition for 1 h. Coverslips were rinsed with PBS, inverted onto a glass slide with anti-bleaching sealant and sealed with fingernail polish. Labeled cells were imaged on an Olympus FluoView FV10i laser scanning confocal microscope with 405, 473, 559 and 635-nm lasers, in the xyz and xzy planes or with a Leica TCS SP2 AOBS laser scanning confocal microscope with 458, 477, 488, 514, 543 and 633-nm lasers. Images were prepared for publication using Olympus FluoView, Leica Imaging and ImageJ Fiji software.
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4

Histological Analysis of Kidney and Heart

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Heart and kidney samples fixed in 4% PFA were processed to paraffin and sectioned at 4 μm. Representative midline sections from each kidney and heart were stained with Periodic acid–Schiff (PAS) and Masson’s Trichrome by Monash Histology Platform. The Aperio Scanscope AT Turbo scanner (Leica Microsystems, NSW, Australia) was used to generate digital images of the sections (20 × magnification). All analyses were performed by a researcher blinded to treatment groups using Aperio ImageScope software (Leica, RRID:SCR_020993), Fiji ImageJ (RRID:SCR_002285) or QuPath version 0.2.3 (RRID:SCR_018257) [19 (link)].
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5

Immunostaining of Drosophila VNC

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VNC were dissected in 1× PBS. Tissues were then fixed for 1 h in 4% formaldehyde in 1× PBS at room temperature. After fixation, brains and VNCs were washed three times (30 min per washing) in PBS with 0.3% Triton X-100 (PBTx) and incubated at 4°C overnight with primary antibodies. The following primary antibodies were used: mouse monoclonal anti-Ubx (FP3.38 (5 (link)) 1:500) from the Developmental Studies Hybridoma Bank), rabbit anti-TH (Novusbio), mouse anti-nc82, and chicken anti-GFP (Abcam Probes, 1:3,000). The secondary antibodies were anti-mouse Alexa Fluor 555 (Invitrogen Molecular Probes, 1:1,000), anti-rabbit Alexa Fluor 647 (Invitrogen Molecular Probes, 1:1,000), and anti-chicken Alexa Fluor 488 (Invitrogen Molecular Probes, 1:1,000). Images were acquired with a Leica SP8 confocal microscope, processed, and analyzed using FIJI ImageJ (NIH).
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6

Ultrastructural Imaging of Activated Gametocytes and Ookinetes

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Purified gametocytes were activated for 4 to 5 min and 15 min; activation was stopped by adding 1X ice-cold PBS. Activated gametocytes and mature ookinetes were sedimented onto 12-mm round Poly-D-Lysine (A3890401, Gibco) coated coverslips for 10 min (gametocyte procedure was performed on ice), fixed in methanol at −20°C for 7 min, and then prepared for U-ExM as described previously [45 (link),74 (link)]. Immuno-labelling was performed using primary antibody against α-tubulin and β-tubulin (1:200 dilution, source: Geneva antibody facility) and secondary antibody anti-guinea pig Alexa 488 (1:400 dilution, source: ThermoFisher). Images were acquired on a Leica TCS SP8 microscope; image analysis was performed using Fiji-Image J and Leica Application Suite X (LAS X) software.
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