2-photon cross-section plotter
Easily view a range of 2-p cross sections with this simple web app
AMF Blog
We maintain a blog of things we find useful or interesting. This page lists our posts chronologically. You can also view our posts organised by tag, or by category.
2023
2021
Multi-Scale Light-Sheet Fluorescence Microscopy for Fast Whole Brain Imaging
Combined serial-sectioning plus lightsheet imaging
2020
Multi-focal serial-section 2-photon imaging
Super-fast serial section imaging by multiplexing
Allen Reference Atlas
Creation of the Allen template brain and reference atlas
2019
Reconstruction of 1000 projection neurons
Janelia trace 1000 neurons and provide more details about their imaging system
Python-based image registration
Fast Python-based image registration
On-line optical clearing method for whole-brain imaging in mice
On-line clearing during serial section imaging
ChroMS Multicolor Imaging
4 channel serial-section 2-photon and brainbow
FAST Spinning Disk Confical Protocol
Detailed protocol for FAST serial section imaging
Embedding without covalent agarose bonding
How to cut thin sections without the covalent bonding protocol
Imaging multiple samples at once
BakingTray and StitchIt can now handle multiple samples at once
Registering widefield functional imaging data to the Allen Atlas
Using blood vessel patterns to register in vivo data
2017
Stopping the TissueCyte on laser modelock failure
Code and instructions for stopping the TissueCyte upon laser modelock failure
Covalent Agarose Cross-Linking Protocol
Our protocol for covalently cross-linking the brain to the agar
Stage alignment to imaging plane
How to ensure the imaging plane is aligned with the stage axes
2016
Adjustable stage tilt on TissueCyte
How to add fine tip/tilt adjusters to the TissueCyte X/Y/Z stage
Changing the dichroics on the TissueCyte
How to change the dichroics on the TissueCyte
ScanImage on the TissueCyte
How to run ScanImage on the TissueCyte
Adding bandpass filters in front of the PMTs
How to add band pass filters on the TissueCyte
TissueCyte Beam Alignment: Primary Dichroic
How to align the excitation path dichroic on the TissueCyte
TissueCyte Beam Alignment: LCVR
Safely aligning the beam through the LCVR
Handy consumables
List of useful consumables
Quick front/left routine for TissueCyte
Protocol for quickly finding the front/left position when imaging brains on a TissueCyte