How to use the OMERO web viewer
Shift + mouse drag to rotate, scroll wheel to zoom in/out.
Right-click and select "Save view port as PNG" to save the view area as a PNG.
How to view the samples
Each sample is a glass slide of 10 micrometer-thick serial sections
from the olfactory bulb to near the medulla oblongata.
The sections are placed in the order shown by the arrows in the photo.
The order of the sections may have been switched due to circumstances at the time of sectioning.
When viewing the sections, note that the left and right sides of the sections are inverted.
For a reference atlas of each section, please refer to the following paper.
Neuropeptide gene expression atlas in the adult zebrafish forebrain. XXXX
How to view downloaded .ndpi data
The downloaded .ndpi data can be viewed by installing the free software NDPview.2 (Hamamatsu Photonics).
NDPview.2 can be downloaded from
Hamamatsu HP
.
Details of metadata
File set name
The file is named as follows: Gene symbol-Sex-Presence of counters stain-Date of scanning.
Number of files
When scanning with the Nanozoomer, the focus may shift in some areas, resulting in a blurry image. In such cases, the area is re-scanned and multiple files are uploaded for each glass slide.
Gene symbol
Gene symbols are based on ZFIN nomenclature.
Gene name
Gene names are based on ZFIN nomenclature.
Synonym
If a gene is also called by other names or has a previous name, it is described here.
NCBI gene ID
Gene ID in NCBI database.
mRNA NCBI reference sequence
NCBI reference sequence, which was used for ISH probe synthesis.
Sex
Sex of the sample fish.
Age (month)
Age of the sample fish.
Sampling time
Time of day when sampling was conducted.
Antibody dilution ratio
Antibody dilution ratio of alkaline phosphatase-conjugated anti-DIG antibody (1:10000 for oxt, 1:1000 for other genes, Sigma-Aldrich).
Color development duration (h)
Duration of color development in 5-bromo-4-chloro-3-indolyl phosphate/nitro blue tetrazolium (BCIP/NBT) solution.
Counter stain
Presence or absence of nuclear counter stain with 1% methyl green stain solution (Muto Pure Chemicals)
Mounting media
Glass slide mounting media. Aqua-Poly/Mount (Polysciences) or Immu-mount (Thermo Fisher Scientific).
Background intensity
Background intensity of the result.
Scanning date
Date of scanning.
