a b c d e f g h i j k l m n o p q r s t u v w x y z

#s

• 2 photon Olympus and Zeiss 710
• 3D rendering using ImageJ
• 710 NLO, Zeiss This microscope has been dissassembled. Link still here for historical info.
• 880

A

• absolute intensity quantification of cell membranes
• actin staining, typical
• AI (artificial intelligence) -- Oct 2022 assessment of de novo image generation
• art analysis using ImageJ - local contrast in Paul Signac painting
• AiryScan (on Zeiss 880)
• AmScope camera (now obsolete, but here as history)
• Archiving data for massive public access
• AxioCam field of view, comparison AxioCam and Zyla 5.5
• AxioObserver microscope (Zeiss)

B

• BAB solvent imaging on inverted confocal
• bead tests of a few microscopes -- 4um beads
• Best Fitted Ellipses
• biosensor (FRET)

C

• CLAHE
• colocalization and spots simulation
  Colocalization Thresholding Fiji did not work late 2019
  Coloc2 in Fiji did not work in early 2020
  Colocalization_finder appeared to be a great tool in late 2019 but revisiting in early 2020 with neuron data it failed
• confocal pinhole, what it does practically
• confocal Zeiss 710 ACLSW
• confocal Zeiss 700 ACLSE
• confocal Zeiss 700 MSB694
• confocal Zeiss 700 SK5
• confocal Zeiss 800 SK5
• confocal Zeiss 880 SK2
• counting nuclei, cells, or other features in 3D manually
• coverslips
• CrestOptics Spinning Disk with Kinetix camera on Nikon Ti2 microscope
• Cut region of interest into equal parts (IJ macro)

D

• data naming
• data storage using the server
• data storage for massive public access
• date format for naming data
• DIC (cool images not by me)
• drawing stars
• dynamic range

E

• educational resources
• Elyra 7
• Expansion microscopy, one example
• Evos
• Exposure time setting with Zen Blue

F

• FFT filtering to remove periodic noise example here and older version here
• FFT on stacks (see macros)
• field of view, comparison AxioCam and Zyla 5.5
• figures, simple way to make with ImageJ
• figures, general tips -
• figures, about rasters vs vectors, RGB vs CMYK, resolution, etc. Website recommended by a colleague: https://b.nanes.org/figures/
• flatfield correction
• fluorescent probes
• FRAP fluorescence recovery after photobleaching

 G

• gamma
• Glenwood Lake
• GP120-GFP intensity quantification at cell membranes using spinning disk confocal
• grid - drawing spots in a grid pattern
• grid - overlaying a grid on an image for counting

H

• History - Nature Cell Biology has a great timeline of milestones

I

• iLab general instructions for staff - how to add new user - sign in - for users to register
• Images: What is an image?
• ImageJ
• My how to get started instructions
• Instructions how to use ImageJ. https://imagej.nih.gov/ij/docs/menus/image.html
• Official web site home page
• Excellent How To guide
• Image macros (mine)
• ImageJ macros (ImageJ official website) and ImageJ functions
• ImageJ best fitted ellipses
• ImageJ tables
• Imaris getting started
• Imaris crashing due to memory
• immunofluorescence prep
• intensity measurements not always in agreement with your perception
• intensity primer
• intensity quantification of cell membranes
• Interactive slope of line and example of live running macros and "is" command.
• interleaving stacks, ImageJ macro
• intepolating slices, ImageJ macro
• IRM in collagen matrix and on coverslip using confocal
• iSIM VT-iSIM demonstration February 2016

J

• J is for ?

K

• Koehler illumination
• kymograms: neuron example - mitochondria example

L

• lambda scan 880 confocal, Opal example
• LEDs
• Leica - old upright scope with color camera in microbiology dept.
• Local contrast enhancement (CLAHE)
• Local contrast in painting (Signac example)

M

• macrophage spectral timelapse with Zeiss 880 - movie from Nikon widefield
• magnification doesnt show more
• manual counting nuclei, cells, or other features in 3D
• metadata - bit of code to stamp metadata info on ImageJ images
• mitochondria live using Nikon TI widefield and using iSIM
• mitochondria potential, physiologic measurements
• mitochondria kymogram
• mitochondria movie
• multiphoton Olympus and Zeiss 710
• myelin with polarized light

N

• Naming data
• Nikon A1 demonstration 2017
• Nikon Ti widefield microscope with Zyla 5.5 camera
• Nikon W1 demonstration 2018
• Nomarski (cool images not by me)
• Numerical Aperture

O

• offset -- example why should be at zero
• Olympus Multiphoton
• Opal fluorescent probes
• organic solvent imaging on inverted confocal

P

• PALM (localization microscopy with Zeiss Elyra 7)
• Particle tracking simulations to challenge Volocity, Trackmate, and Imaris in 2011
  particle_tracking_simulation_v100.ijm
  particle_tracking_speed_and_wiggle_change_with_no_backup.ijm
  particle_tracking_speed_and_wiggle_change_with_speedvariation_no_backup.ijm
  
• permeabilization
• phagocytosis, LR5 cells eating beads, Nikon widefield
• phase separation assay
• photon counting not required for linear response
• pinhole, confocal
• plaques inside vessels Measure plaques inside blood vessels
• Plexiglas slides
• plot profiles multiple colors, ImageJ
• polarized light with myelin and skin and plaques inside vessels
• poly-L-lysine coverslips
• poster, retreat 2019
• PowerPoint to publication trick (old method, but still works)
• Prairie 2Photon (now obsolete, but here as history)
• prep notes
• Probes, fluorescent
• pseudocolor LUT and conversion for presentations
• pumpkin pollen

Q

• Quantification of intensities better than by eye

R

• radial plot coded for ImageJ
• radial reslice - one plane grayscale
• radial reslice - composite color hyperstacks
• ratio LUT
• ratio imaging cyan-yellow Zeiss880
• ratio imaging of mitochondria
• retreat 2019 poster
• reflection microscopy in collagen matrix and on coverslip using confocal
• registration Stackreg
• registration using multilabeled bead references bUnwarpJ
• resolution
• RRIDs - e.g. proper citation: New York University Grossman School of Medicine, Langone Health Microscopy Laboratory Core Facility (RRID:SCR_017934)

S

• sample prep
• Saturation
• Science fiction of all data searchable
• Shared resources, what do you need to do to run one? Job interview talk from 2002.
• spatial resolution
• spectral imaging with Zeiss 880
  • spectral timelapse movie
  • spectral quantification
  • measurement of Opal probes
• spinning disk confocal, CrestOptics with Kinetix camera on Nikon Ti2 microscope
• spinning disk confocal, Yokogawa and Nikon W1 overview and instructions and demonstration data 2018
• Simulation of colocalization
• Stageplates
• Stamp metadata info on ImageJ images
• stars, drawing with ImageJ
• STORM (localization microscopy with Zeiss Elyra 7)
• straighten function ImageJ
• super resolution
• syringe pump

T

• tables example code in ImageJ (also see https://imagej.nih.gov/ij/developer/macro/functions.html#T)
• TIRF (Total Internal Reflectance Microscopy) start at slide #16 (skip first 15 slides)
• TIRF Zeiss microscope
• Tool, F key, pull down menus example in ImageJ using selective Z projection macros-functions
• Training resources
• Transmitted light imaging with confocal - phase separation assay - with 880
• transwell imaging
• tunneling nanotubes (TNTs), of historical note

U  

V  

• Vessels with plaque occulsions. Measure plaques inside blood vessels.
• Videos, training on setting exposures with Zen Blue
• Volume rendering using ImageJ
• VT-iSIM demonstration February 2016

W  

Z  

• Z projection tool for ImageJ, set first and last slices easier
• Zeiss, if not below, see specific instruments above...
• Zeiss 710 NLO confocal/multiphoton This microscope has been dissassembled. Link still here for historical info.
• Zeiss 880 confocal
• Zeiss AxioObserver
• Zeiss AxioZoom
• Zeiss Elyra 7
• Zeiss Imager.Z2 Pathology research only
• Zyla 5.5 field of view, comparison AxioCam and Zyla 5.5