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10 protocols using infinity capture software

1

Cytospins and Histopathology Protocols

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For cytospins, 1×106 cells were collected in 100ȝL PBS/2% FBS from single cell preparations of BM, added to Shandon Single Cytofunnels (Thermo Scientific #1102548) clipped to glass slides (FisherScientific #12–550-20), and centrifuged using a Cytospin 3 centrifuge (Shandon) set at 500 rpm for 5 min at medium acceleration. After drying, cells were stained with the Hema 3 stat pack (Fisher Scientific #23–123869) and images captured with a Nikon Eclipse E200 microscope equipped with an Infinity 2 color camera (Lumenera) controlled by Infinity Capture software (Lumenera).
For histopathology, mouse tibia and spleens were fixed in 10% neutral buffered formalin (Fisher Scientific #SF100–4) overnight at 4oC or 1 hr at room temperature, respectively. Spleens were inoculated in 35% sucrose (Fisher Scientific #525590A) overnight, whereas bones were decalcified (Calrite from Richard-allen Scientific #5501) for 12 days prior to overnight inoculation in 35% sucrose. Both tibias and spleens were rinsed with PBS and processed for paraffin embedding and sectioned at 5 μM. Both H&E and reticulin staining was performed by the Histology Lab of Washington University. Images were captured using an inverted microscope and analyzed with NIS-Elements software from Nikon.
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2

Adipocyte Morphometry in Mice

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A portion of the mesenteric fat collected at euthanasia from VEH, BPA and DES treated mice fed the HFD was fixed immediately in 4% formaldehyde. Tissue from n = 4 mice/group was cryoprotected in 30% sucrose in PBS overnight, equilibrated in PBS for ∼4 h and then frozen in OCT (Tissue Tek, Torrance, CA) overnight at −20 °C. Sections, 5 μm, were cut using a cryostat at −24 °C and stained with Oil Red O [36] (link). Photographs were taken of 5 random fields/section using Infinity Capture software (Lumenera, Ottawa, Ont.). The outline of at least 100 fat cells/mouse was measured using Image J software. The cross-sectional area of VEH male mice adipocytes was arbitrarily designated 100%.
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3

Histological Analysis of Rat Brainstem

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At the end of the experiments, the rats were overdosed with 5% isoflurane for 20 min. The heart was then perfused with 30 mL of 0.9% saline and 30 mL of 10% formalin. The brainstem was removed and fixed in 10% formalin for a minimum of 24 h at room temperature for subsequent histological processing. Three days prior to tissue sectioning, the brainstem was transferred into a 30% sucrose solution for cryoprotection and stored at − 4 °C. Sectioning of the brainstem was performed in − 20 °C at 50 μm thickness using a cryostat (Leica, CM 1850, Wetzlar, Germany). The histological sections were then mounted on plus microscope slides (VWR, PA, USA), sealed with Cytoseal 280 (Thermo Scientific, Waltham, MA), and stained with neutral red dye (neutral red powder, 1 M CH3COOH, 1 M NACH3COO, 50% ethanol). A bright field microscope attached to a charge-coupled device (CCD) camera (Infinity 1 and BX-41, Olympus, Center Valley, PA, USA) was used to capture images using the Infinity Capture software (Lumenera, Ottawa, ON, Canada). The captured images of stained sections were cross referenced to a standard stereotaxic atlas of the rat brain79 to identify the anatomical placement of the microdialysis probes.
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4

Antiviral Efficacy of A-3302-B against HSV-2

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The assays evaluate the antiviral activity of the compound when administered before, during or after HSV-2 infection. Cells were incubated with different concentrations of A-3302-B (from 100 μM to 0.4 μM) in a 24-well plate at 37 °C for 2 h before infection (pretreatment), for 2 h during infection (cotreatment) or 24 h after removal of virus inoculum (post-treatment). Cells were concurrently infected with HSV-2 at MOI of 0.001 PFU/cell and treated for plaque reduction assay. Plaque size was measured with an Axiovert 200 inverted microscope (Zeiss, Jena, Germany) equipped with Infinity3 microscope camera (Lumenera, Ottawa, ON, Canada) and Infinity Capture software (Lumenera), and was analyzed with Infinity Analyze software (Lumenera) and ImageJ software (Bethesda, MD, USA).
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5

Topical Taxol Treatment of Grafted Tumors

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Four days after the grafting (EDD12), available tumors were treated topically with 2.5 μM taxol diluted in culture medium containing 5% FBS or 5% ascites. Eggs were returned to the incubator for 4 days (EDD16). Tumor size was monitored using a Wild Heerbrugg M3Z microscope at 10x magnification with a Lumenera INFINITY2-1 CDD camera with Infinity Capture Software.
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6

Quantifying Dentate Gyrus Dispersion in Mice

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Brains from a randomly selected subset of females and males (8–10 mice per group) were sectioned into 40-μm-thick coronal sections using a freezing microtome (Leica SM 2010R). Every third section from the dorsal hippocampal region was used for histology, with a total of four to six sections evaluated for each mouse. Sections were stained with cresyl violet (Sigma-Aldrich C5042) for 12 min at room temperature, dehydrated using graded ethanol solutions (70–100%), before being cleaned with Xylene and coverslipped with Permount. Images were collected using an Olympus BX43 brightfield microscope with an Infinity 3-6UR Teledyne Lumenera Camera and Infinity Capture software (Lumenera). Dentate gyrus granule cell dispersion ipsilateral to the KA injection was quantified as previously described (Cutia et al., 2022 (link); Lisgaras and Scharfman, 2022 (link)).
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7

Immunohistochemical Analysis of PDAC Tumors

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PDAC tumors were fixed in 10% formalin. Fixed tissue was embedded in paraffin and sectioned by the SBP Histology Core. Antigen retrieval was performed by microwave-heating in 10mM sodium citrate (pH 6) and endogenous peroxidases were quenched in 3% hydrogen peroxide. Sections were blocked in 2% BSA, 10% goat serum in PBS for 1 hour at room temperature and incubated with primary antibodies diluted in 2% BSA/PBS overnight at 4°C. For p53 staining a mouse-on-mouse protocol step was included to blocking endogenous mouse IgG. After washes, sections were incubated with biotinylated goat anti-rabbit secondary antibody (1:1000, Vector, BA-1000–1.5) for 1.5 hours at room temperature followed by incubation with the VECTASTAIN Elite ABC HRP Kit (Vector Labs) and the DAB HRP Substrate Kit (Vector Labs). Nuclear counterstaining was performed by hematoxylin staining. Images were captured with a brightfield Olympus CX-31 microscope coupled with INFINITY camera and INFINITY capture software (Lumenera). The following primary antibodies and dilutions were used: ASNS (1:500, ProteinTech, 14681–1-AP), Cleaved caspase 3 (1:1000, CST, 9664), Ki-67 (1:400, ThermoFisher, MA5–14520), p53 (1:2000, CST, 2524) and phospho Histone H3 (1:200, CST, 9701). For the pHis-H3 and Ki-67 staining quantification, the number of pHis-H3- or Ki-67-positive nuclei per image field was determined.
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8

Quantifying Brain Lesion Characteristics

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Two‐millimetre serial coronal sections of formaldehyde fixed brains were prepared and imaged using Mantis Elite HD dissecting scope (Vision Engineering) to assess total lesion number and size. Total lesion number was measured from images of the anterior plane of each 2 mm section by an investigator blind to sample identity. Lesion size was directly calculated from the image using NIH Image. The third and seventh section of each brain (anterior‐posterior) was then further processed for paraffin embedding and thin sectioning. Three 5‐μm serial sections were taken at 100 μm steps from the embedded coronal slices and stained with haematoxylin/eosin (general histology) and potassium ferrocyanide/nuclear fast red (free iron) as described previously.5, 18 Images were captured at room temperature using Infinity Capture software (Lumenera) with an UPLSAPO 10× (n.a. 0.30) objective on an Olympus IX70 microscope, and an Infinity 2 camera (Lumenera).
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9

Birefringence Imaging for Sarcomere Analysis

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To assess muscle sarcomere morphology in 5 dpf eleutheroembryos (n = 5 per treatment group), a birefringence assay was used as previously described (Berger et al., 2012; Smith et al., 2013) (link). Briefly, 5-6 embryos of each treatment group were placed on a dissecting microscope (Olympus SZ61, Olympus Canada, Richmond Hill, ON, Canada) and an image obtained using a Lumenera Infinity 2 camera and Infinity Capture software (Teledyne Lumenera, Ottawa, ON, Canada) to measure animal surface. A subsequent second picture of the eleutheroembryos was taken immediately afterwards using two perpendicularly placed 77 mm circular polarizing lenses (77 mm circular polarizing lens (Amazon Basics, Amazon, Seattle, USA) to visualize and image birefringence created by sarcomeres. Care was taken to maintain eleutheroembryo position. Birefringence intensity was quantified using ImageJ software and normalized by larval surface area.
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10

Quantifying Larval Lipid Deposition via Nile Red

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Neutral lipid deposition was measured in 7 dpf larvae using Nile Red (9-Diethylamino-5H-benzo [alpha]phenoxazine-5-one, Sigma-Aldrich), a lipophilic fluorescent stain (Jones et al., 2008 (link); Minchin and Rawls, 2017 (link)). Nile Red stock was diluted in analytical grade acetone to a concentration of 500 μg/ml. This was then diluted 1:100 in system water and larvae were maintained in 10 ml of this solution for 30 min in the dark at 27°C. Larvae were then rinsed twice in system water and anesthetized with tricaine. Each larva was imaged under a fluorescent stereomicroscope with a super high-pressure mercury lamp (Nikon SMZ 1500). Images were captured with a Lumenera Infinity 2 camera using a Texas Red filter and processed using the Infinity Capture software (Teledyne Lumenera, Ottawa, ON, Canada). All images were taken at the same exposure settings and magnification. Fluorescence was quantified using ImageJ and Nile Red stains were normalized to the lateral body area of the fish. A total of three cohorts were analyzed reaching a combined sample size of n = 18–22 per treatment group. All images were renamed prior to analysis to assure the experimenter was blind to specific treatment groups during analysis.
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