Image processing was performed using either the Fiji upgrade of ImageJ (58 (link)) or Imaris software v9.2 (Bitplane, Oxford Instruments). Quantifications for colocalization measurements were performed using Imaris software v9.2 (Bitplane, Oxford Instruments). Statistical analyses were performed with Microsoft Excel 2016 and Prism v7.04 (GraphPad). Flow cytometry analysis was done using FlowJo software v10.4.2 (FlowJo LLC). Raw MS data were first analyzed using MaxQuant v1.6.0.16. Differential proteomics data analysis was performed using DAPAR v1.10.3 and ProStaR v1.10.4.
Bitplane
Manufactured by Oxford Instruments
Sourced in United Kingdom
Bitplane is a powerful and versatile image processing and analysis software suite developed by Oxford Instruments. It provides a comprehensive set of tools for visualizing, analyzing, and processing 2D, 3D, and 4D images from a wide range of microscopy and imaging techniques.
Automatically generated - may contain errors
Lab products found in correlation
Prism v7, by GraphPad (1 mentions)
Microsoft excel 2016, by GraphPad (1 mentions)
Imaris software v9, by Oxford Instruments (1 mentions)
Lsm800 upright confocal microscope, by Zeiss (1 mentions)
Thunder imaging system, by Leica (1 mentions)
Ms 222, by Merck Group (1 mentions)
Femtojet 5247, by Eppendorf (1 mentions)
Lsm 700 confocal microscope, by Zeiss (1 mentions)
Axio observer z1 inverted microscope, by Zeiss (1 mentions)
Fluoromount g mounting medium, by Interchim (1 mentions)
Elyra ps 1, by Zeiss (1 mentions)
A1r confocal microscope, by Nikon (1 mentions)
11 protocols using bitplane
1
Image Analysis and Proteomics Workflow
2
3D Reconstruction of Mouse Liver
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Overview of mouse livers was established on a side view of a 3D reconstruction (IMARIS v8.4.2 software, Bitplane, Oxford Instruments, Abingdon, UK) of a series of optical cross-sections (z stacks). In brief, a series of z stacks through the liver was performed with a z-step of 1 µm approximately through 50 z planes. Then, liver structure was reconstructed with IMARIS v8.4.2 software with DAPI and RFP channels, for neutrophils and platelets, respectively
3
Immunofluorescent Staining of Organoids
4
Human NK Cell Engraftment in Zebrafish
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
MEL270 cells that were pre-labelled with red fluorescent DIL (Thermo Fisher) and human NK cells were mixed at a 1:3 ratio (MEL270: NK). Zebrafish embryos at the age of 24 hpf (hours post fertilization) were incubated in water containing 0.2 mmol/L 1-phenyl-2-thio-urea (PTU, Sigma). At 48-hpf prior to microinjection, zebrafish embryos were dechorionated and anesthetized with 0.04 mg/mL of tricaine (MS-222, Sigma). The microinjection of human cell mixture was performed by infusing 5nL (approximately 500 cells in total) into the perivitelline space of each larvaes using an Eppendorf microinjector (FemtoJet 5247, Eppendorf and Manipulator MM33-Right, Märzhäuser Wetziar). Successfully injected larvae were transferred into PTU aquarium water at 33°C for 48 h incubation before fixation with 4% paraformaldehyde (PFA) for image acquisition. 3D Images of zebrafish larvaes were acquired on Thunder Imaging System (Leica Microsystems) under 4X objectives. Batch quantification of different treatment groups were done using IMARIS software. (Bitplane, Oxford Instruments).
5
Quantitative Analysis of Huntingtin Aggregates
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
For Htt ISH, images of sections were taken with a Zeiss Axio A1/D1 microscope (Zeiss, Oberkochen, Germany) and deconvoluted using Huygens software (Scientific Volume Imaging (SVI), Hilversum, Netherlands). For quantitative analysis of Htt aggregates, Htt RNA staining, and HTT/DAPI colocalization, particle counting was done using IMARIS with default settings (Bitplane, Oxford Instrument, England). For Ppp1r1b ISH integrated density was measured in FIJI. Ccnd1 ISH quantification was performed on matched HD and control sections from the same cassette, and imaged using a Zeiss LSM700 confocal microscope with identical settings. For quantification, a sum projection of Z-stacks was performed in FIJI and mean fluorescence intensity was measured in the granular layer right and left of arbor vita after background correction.
6
Quantifying Bacterial Membrane Depolarization
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Cocultures were prepared as indicated previously. The dye DiBAC4(3) was added to the BHI medium (final concentration 2.5 μM) when the cocultures were prepared. Nisin was used as a positive control (final concentration 5 μM). After 3, 4, and 6 h of coculture, bacteria were washed once and resuspended in PBS, mounted on a glass coverslip with Fluoromount-G mounting medium (Interchim), and dried in the dark at 37 °C for 30 min. Slides were observed with an AxioObserver.Z1 inverted microscope (Carl Zeiss) equipped with a high-speed CSU-X1 spinning-disk confocal system (Yokogawa) and an Evolve EM-CCD camera (Photometrics). Images were acquired through a Plan-Apochromat 100× oil objective, using MetaMorph software (version 7.7.9.0). Stacks of 20 images were acquired every 200 nm in the z axis. Three-dimensional reconstruction was performed on stacks with IMARIS software (Bitplane; Oxford Instruments). Icy was used for image processing and analysis. For each condition tested, at least 150 cells were marked as regions of interest (ROIs) manually by using only one image of the Z stacks (better focused image). To quantify the effects of depolarization, ROI mean pixel intensities of the GFP channel were obtained and normalized to the background mean pixel intensities of the GFP channel.
7
3D Reconstruction of Mouse Liver
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Overview of mouse livers was established on a side view of a 3D reconstruction (IMARIS software, Bitplane, Oxford Instruments) of a series of optical cross-sections (z stacks). In brief, a series of z stacks through the liver was performed with a z-step of 1 μm approximately through 50 z planes. Then, liver structure was reconstructed with IMARIS software with DAPI, RFP, and Cy5 channels, for neutrophils, KCs, and neutrophil elastase, respectively. Additionally, on some acquired z stacks, red signal (KC staining) was made semi-transparent to expose the blue signal (neutrophil staining) present inside.
8
In Vitro Tumor Cell Migration Assay
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
In vitro migration assays were performed with GFP-expressing OCM-3 cells with or without 41BBL-KO. 3 × 105 tumor cells were seeded in a transwell inserts of 8μm pore size (Corning) in serum-free RPMI media before the addition of 1 × 105 NK cells in suspension. The transwell inserts containing both NK and tumor cells were then transferred into a 24 well plate containing 10% FBS in RPMI media cultured in 37°C, 5% CO2 incubator for 48 h. Subsequently, the transwell inserts with media removed, rinsed with PBS and then fixed with 4% paraformaldehyde (PFA) solution. Using a cotton swab, cells on the inner side of the transwell inserts were physically removed prior to imaging of the outer transwell membrane under 5 × magnification on ZIESS LSM 800 confocal system. Quantification of GFP positive tumor cells on the outer membrane was done on IMARIS software (Bitplane, Oxford Instruments).
9
3D Super-Resolution Imaging with SIM
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Structured Illumination microscopy (3D‐SIM) was performed using a Zeiss Elyra PS.1 super‐resolution microscope (Carl Zeiss, Germany). A plan‐Apochromat 63×/1.4 Oil lens was used, and Z‐steps of 0.2 µm were acquired (total thickness between 5 and 7 µm) in five rotations using the ZEN Black Edition Imaging software. For 3D modeling, acquired images were analyzed and processed by IMARIS software (Bitplane, Oxford Instruments).
10
Confocal Imaging of Synaptic Density
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Sections were imaged using a Nikon A1R Confocal microscope and NiS elements software. Z-stack images were taken using a x63 oil immersion objective and the Z-stack controlled using a Piezo drive. The settings for laser power, gain and offset were set on ‘no primary’ and single stained controls (whereby one primary was applied followed by the cocktail of secondary antibodies), for each staining run. These settings were then used to image all cases. Image capture and analysis was done blind to disease status. Based on power calculations, six Z stack images were captured per case ensuring the capture of a number of synapses or at least two axons per image. Images were then analysed using IMARIS software (Bitplane, Oxford Instruments).
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!