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NEUBIAS / bioimage-analysis-training-standards

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Example data for image formation #6

Open tischi opened 1 year ago

tischi commented 1 year ago

Zebrafish embryo (broken link, see below)

https://oc.embl.de/index.php/s/gRckFAfkkbrRGQh

Useful to demonstrate image formation issues in confocal microscopy:

  1. membranes appear with more contrast if they run along the optical axis
  2. signal decays within the specimen, due to scattering and absorption
haesleinhuepf commented 1 year ago

Hi @tischi ,

that link is broken :-)

image

tischi commented 1 year ago

Thanks for checking @haesleinhuepf !

Here another attempt:

Zebrafish embryo

Data

https://oc.embl.de/index.php/s/8SngHDn9SulwLnx

Description

It was taken with a 20X water immersion objective (upright set up LSM 980, confocal setting, it says W Pen Apo 20X/1 W DICIII on our display)

Channel 1: histone Channel 2: membrane

Sample: zebrafish embryo blastula (7th division) of a zebrafish embryo with transgenes expressing histone-gfp (channel 1, ref: Stegmaier et al., 2016) and membrane marker lyn-tdtomato (channel 2, ref: Compagnon et al., 2014) everywhere (both actin b promoter). The histone at these early stages is very cytoplasmic still, as you can see.

Teaching examples

Useful to demonstrate image formation issues in confocal microscopy:

  1. membranes appear with more contrast if they run along the optical axis
  2. signal decays within the specimen, due to scattering and absorption
image