Quick Definitions Archives | Page 2 of 32 | Expert Cytometry | Flow Cytometry Training Quick Definitions Archives | Page 2 of 32 | Expert Cytometry | Flow Cytometry Training

Blog

How To Perform A SPICE Analysis With FlowJo

Pin It

Flow cytometry data analysis is getting more complex. Gone is the rule of 2-3 color experiments. Even beginners are starting with 5+ color assays, and the adoption of mass cytometry has the potential to increase our headaches even more. Current data analysis methods are good for single tubes or small cohort studies.  What do you do when you have a large dataset, with multiple sampling conditions, and multiple outcome measurements? With data complexity of this nature, one can export the numerical data to a third party analysis package, but even then the analysis can be difficult to perform. To overcome this limitation, and to allow for better discovery science, Mario Roederer and his colleagues have developed a solution. SPICE was developed in order to make sense of the increasingly complex data sets that modern flow cytometric methods can produce. You can read the paper about the design and math behind SPICE here. SPICE is an acronym for Simplified Presentation of Incredibly Complex Evaluations, and it is designed to look at these complex multidimensional data sets. Take, for example, research interested in CD34+ cell counts.  At the individual level, that’s easy and what standard data analysis packages can do. Now take that same dataset, add comparison of a couple of conditions (smoker vs non-smoker), age and gender with over 100 different patients. This is where SPICE assist your analysis without being tied to large spreadsheets and endless meeting with biostatisticians. With SPICE you can escape endless spreadsheets and their less-than-intuitive graphing and […]

Read More

Logicle Scaling

Pin It

An implementation of biexponential scaling published by the Herzenberg lab at Stanford. The biexonential scale is a combination of linear and log scaling on a single axis using an arcsine function as its backbone. The “logicle” implementation of biexponential was implemented in many popular software packages like FACSDiva and FlowJo. Other types of biexponential scaling exist, including Hyperlog. Biexponential scales are more generally referred to as hybrid scales and include other variations like lin/log or log with negative. More information on logicle sclaing can be found here: Parks DR, Roederer M, Moore WA. (2006). A new “Logicle” display method avoids deceptive effects of logarithmic scaling for low signals and compensated data. Cytometry. 69: 541-545

Read More

Yellow Laser

Pin It

A laser type in a flow cytometer with a wavelength of about 560nm. The green and yellow laser are more effective at exciting PE and its tandems than the traditional blue laser. The yellow laser is also often used to excite the “fruit” dyes like mCherry. For more information, please review this journal article: Telford  W,  Murga  M,  Hawley  T, et.al. (2005). DPSS yellow-green 561-nm lasers for improved fluorochrome detection by flow cytometry. Cytometry. 68A: 36-44

Read More

Green Laser

Pin It

The laser type in flow cytometers with a wavelength of around 530nm. Standard “green” lasers are about 532nm, but vary between 530nm and 535nm usually. The green and yellow laser are more effective at exciting PE and its tandems than the traditional blue laser.

Read More

UV Laser

Pin It

A laser with a wavelength in the UV range. Typically in flow cytometers, the UV laser has a wavelength of 350nm or 355nm. Some have a wavelength of 375nm.

Read More
Flow Cytometry Education And Consulting - Affordable. Effective. Leading Edge.