FAQs
- What is the Field of View (FOV) limit per well for this platform?
- What is the size of the imaging area?
- Can Pyxa 3D data be analyzed without cell segmentation? (LDA and SM3DD segmentation-free workflows)
- How well do Pyxa 3D cell types agree with scRNA-seq reference data (235-plex Mouse Neuron Cell Typing panel)?
- What are your sensitivity and specificity?
- How do probes penetrate thick tissue? How do you know they reach the center?
- Can I change pipeline parameters (for example, cell segmentation)?
- What is the false detection rate and how is it validated?
- Does Pyxa need extra compute for analysis and visualization?
- How many base-pair differences are needed for probe specificity?
- What is the minimum target region to consider?
- How many genes can be analyzed per number of imaging rounds?
- Are reading probes universal? Can different probe sets be used in different wells?
- How much does the protocol change tissue structure? How do we know transcripts stay in place?
- What does SEDAL-seq give that other approaches do not?
- How long can samples be stored after sample prep?
- How long are the SNAIL probes used in STARmap assays?
- Do you support sequential SEDAL sequencing?
- Pyxa Optical System and Compute Specifications
- Is there a maximum allowable number of Fields of View (FOVs) per sample or well?
- Tissue Transfer RING
- how to ship Fully Processed, Gelled and Cleared Sample Plates
- How is cell body-based segmentation done
- do mouse brains need to be perfused for Pyxa?
- What is the concentration of the probe?
- What is DAPI used for?
- What images are saved during a run?
- Run Time
- What is the size of a Field of View (FOV) at 10x magnification?
- What is the Field of View (FOV) size at 60x?
- What are the data outputs from a Pyxa run?
- How many probes per target
- Size of the images saved
- Can I start another run before data transfer finishes?
- What is the instrument-workstation setup?
- How sensitive is Pyxa? How many genes in the panel can be reliably detected?
System Software
Assay
- is the plate treated
- What are the optimization points for a new tissue type?
- Where to buy the tissue transfer rings?
- Can I restrip and reprobe a sequenced plate?
- Can you process my [new tissue type]?
- Can you do higher plex than 235 genes now?
- What is your tissue thickness?
- When will you support FFPE?
- Does amplification bias your assay?
- What type of hydrogel do you use?
- Why true 3D vs. 3D reconstruction using cheaper 2D sections?
- What does Pyxa chemistry give you that other approaches don’t?
data
Instrument
- What is the allowed Z-axis imaging range (depth capacity) for the Pyxa platform?
- What is the spatial resolution of the system (60x)?
- What is the maximum imaging depth/thickness limit for the system?
- How does 3D segmentation differ from 2D?
- What makes your imaging better than your competitors?
- What are the dimensions of the instrument?
- What objectives are used for verification and sequencing scans?
- How many lasers do you have in the system?