Spike-in Normalization
Spike-in Normalization - Related Videos
02:19
Triggering a Closed-Loop Stimulation by Neuron Spiking Activity
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2025
This video demonstrates the operation of closed-loop stimulation in a rat with a surgically implanted device to record neural activity. Neuronal signals are first recorded and analyzed. Template waveforms are then uploaded, and parameters are defined to trigger closed-loop stimulation.
07:34
A Simple Stimulatory Device for Evoking Point-like Tactile Stimuli: A Searchlight for LFP to Spike Transitions
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Cited by 4 •
2014
To elucidate the complex transition from Local Field Potentials (LFPs) to spikes a suitable stimulator for light mechanical peripheral stimuli was built. As an application, the spiking activities recorded from somatosensory cortex were analyzed by a multi-objective optimization strategy. The results demonstrated that the proposed stimulator was able to deliver tactile stimuli with millisecond and millimeter precisions.
02:46
Visualizing Dose-Dependent Spike Protein Uptake with Quantum Dot Conjugates
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2026
Source: Tran, B. N., et. al. High-throughput Confocal Imaging of Quantum Dot-Conjugated SARS-CoV-2 Spike Trimers to Track Binding and Endocytosis in HEK293T Cells. J. Vis. Exp. (2022)This video demonstrates the use of quantum dot–conjugated spike protein (QD-Spike) to visualize dose-dependent viral entry in ACE2-GFP–expressing cells. Confocal imaging captures the internalization of QD-Spike via receptor-mediated endocytosis, modeling early coronavirus entry.
08:29
Averaging of Viral Envelope Glycoprotein Spikes from Electron Cryotomography Reconstructions using Jsubtomo
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Cited by 23 •
2014
An approach is presented for determining structures of viral membrane glycoprotein complexes using a combination of electron cryo-tomography and sub-tomogram averaging with the computational package Jsubtomo.
08:48
Optical Recording of Suprathreshold Neural Activity with Single-cell and Single-spike Resolution
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Cited by 1 •
2012
Understanding the function of the vertebrate central nervous system requires recordings from many neurons because cortical function arises on the level of populations of neurons. Here we describe an optical method to record suprathreshold neural activity with single-cell and single-spike resolution, dithered random-access scanning. This method records somatic fluorescence calcium signals from up to 100 neurons with high temporal resolution. A maximum-likelihood algorithm deconvolves the...
FAQs
An external reference creates a measurement baseline that is processed alongside the biological sample. Researchers compare the reference signal with the target signal, then use differences in that reference signal to account for technical effects such as unequal recovery, sequencing depth, or assay efficiency. Remaining differences in the target measurement can therefore be interpreted more confidently as biological variation.
Spike-ins are particularly informative when a condition may alter molecular quantities broadly across a sample. In that situation, comparisons based only on the target material can make a widespread biological shift difficult to distinguish from a measurement-scale difference. The external baseline helps preserve a point of reference, improving interpretation of changes in overall or relative abundance.
Suitable reference material depends on the measurement system and can include standardized cells, organisms, nucleic acids, or other externally supplied material. The essential features are that its amount is known and that it is introduced before sample processing. Its measured signal then provides a basis for evaluating how consistently samples moved through the assay.
Across samples, the spike-in signal indicates whether differences in target signal could reflect processing rather than biology. A sample with altered recovery, sequencing depth, or assay efficiency may show a corresponding change in reference signal, allowing the target measurement to be adjusted. This makes cross-sample comparisons more reliable and can strengthen reproducibility between experiments.
A practical workflow begins by adding a known amount of standardized reference material to each sample before processing. Samples are then processed and measured, and the reference and target signals are compared. Researchers use the spike-in measurement to adjust for detected differences in recovery, sequencing depth, or assay efficiency before interpreting changes in the target measurement.
Adding the reference before processing allows the spike-in to experience the experimental steps that may introduce technical variation. If it is measured only after those steps, it would not provide the same information about recovery or assay performance. Early incorporation therefore connects the reference signal to the conditions affecting the target measurement.
Researchers apply this strategy in RNA sequencing, chromatin profiling, and gene-expression analysis. In each setting, the external signal supplies an experimental baseline for comparing target measurements across samples. This is especially useful when the biological system may undergo broad molecular changes, because the analysis is not forced to rely solely on variation within the target material.
After adjustment, differences in target signal can be evaluated with greater separation between biological effects and technical variation. The resulting comparisons address relative abundance more reliably across samples and can make patterns easier to reproduce across experiments. Spike-in normalization does not replace the target measurement; it provides the reference needed to interpret that measurement against an experimental baseline.