Data from: Whole-organism 3D quantitative characterization of zebrafish melanin by silver deposition micro-CT

A ReadMe file has been included to describe the dataset organization.

DATA & FILE OVERVIEW

1. Folder List

Unstained wild-type samples:

.\wt_5dpf_unstained_1_(AAA406).7z

Silver-stained wild-type samples:

.\wt_5dpf_silver_1_(AAA411).7z

.\wt_5dpf_silver_2_(AAA412).7z

.\wt_5dpf_silver_3_(AAA413).7z

Silver-stained golden mutant samples:

.\gol_5dpf_silver_1_(AAA421).7z

.\gol_5dpf_silver_2_(AAA422).7z

.\gol_5dpf_silver_3_(AAA423).7z

Silver-stained nacre/casper mutant samples:

.\nac_5dpf_silver_1_(AAA431).7z

.\nac_5dpf_silver_2_(AAA432).7z

.\nac_5dpf_silver_3_(AAA433).7z

Source Code:

.\Source_Code.7z

2. Folder Architecture

All sample folders* are organized in the following organization:

.\Sample_name_(ID)\

ID_Avizo_Source_Files\ --> contains necessary files to open the Avizo Project File for each sample

ID_colormap.am

ID_final_mask.labels.am --> segmented label file after all morphological operators have been applied

ID_final_mask.MaterialStatistics.am --> extracted intensity statistics for segmented regions

<recon_name>.tif.am --> Merged reconstruction used for intensity analysis

<recon_name>.tif.labels --> manually segmented label file

<recon_name>.tif.labels.closing --> segmented label file after Closing morhphological operator has been applied

ID_head\

rotated and cropped 32-bit reconstruction folder --> contains image sequence of 32-bit tiffs with nominal 0.52 um voxel resolution

cleaned and normalized 16-bit reconstruction folder --> contains image sequence of 16-bit tiffs with nominal 0.52 um voxel resolution

ID_tail\

rotated and cropped 32-bit reconstruction folder

cleaned and normalized 16-bit reconstruction folder

Avizo_Project_File.hx --> Avizo projects used to analyze each merged zebrafish sample

*NOTE: nacre/casper samples only contain head reconstructions

3. Additional Data: Raw projection and micro-CT reconstructions (~100 Gb per scan) are available upon request from the authors as digital download or physical media.

 

METHODOLOGICAL INFORMATION

1. Description of Methods for Collection and Processing of Data: Available at https://doi.org/10.1101/2021.03.11.434673

2. Software Information for Data:

These folders (.7z) were compressed using the LZMA2 Ultra algorithm of 7-Zip, a free, open-source software available here: https://www.7-zip.org/

We recommend opening 32- or 16-bit reconstructions (as .tif series) in the free, open-source software Fiji (Fiji is Just ImageJ, https://imagej.net/Fiji)

Avizo Project Files (.hx) were generated in Avizo 2020.1 and 2020.2 (ThermoFisher Scientific)

Avizo source files (.am) were generated in Avizo 2020.1 and 2020.2, but may also be opened using Fiji using the File > Import > Amira

 

SOURCE CODE

We have included example scripts for our reconstruction and data processing pipeline:

hdf5_extractor.py --> Python script for extracting projection images from hdf5 database

allinwonderful_v1.1.py --> Python script for reconstruction from raw projections in hdf5 database format

allinwonderful_v1.1_center_find.py --> Python script for automatically estimating reconstruction center used for reconstruction script above

clear_outside.ijm --> Fiji/ImageJ script used to manually clean up reconstruction data by removing data outside a designated selection and moving to the next slice in an image series

measure_all.ijm --> Fiji/ImageJ script used to take measurements throughout an entire image series

Funding provided by: NIH Office of the Director
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000052
Award Number: R24-OD018559

Funding provided by: National Institutes of Health
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000002
Award Number: R24-RR017441

Funding provided by: Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine*
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Funding provided by: Zebrafish Functional Genomics Core, Penn State College of Medicine*
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Funding provided by: Huck Institutes of the Life Sciences, Pennsylvania State University*
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Funding provided by: Institute for Cyber Science, Pennsylvania State University*
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Funding provided by: Pennsylvania Department of Health
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100004897
Award Number: Tobacco CURE Funds

Funding provided by: Institute for Cyber Science, Pennsylvania State University*
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Funding provided by: Huck Institutes of the Life Sciences, Pennsylvania State University*
Crossref Funder Registry ID:
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Funding provided by: Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine
Crossref Funder Registry ID:

Funding provided by: Zebrafish Functional Genomics Core, Penn State College of Medicine
Crossref Funder Registry ID:

Funding provided by: Huck Institutes of the Life Sciences, Pennsylvania State University
Crossref Funder Registry ID:

Funding provided by: Institute for Cyber Science, Pennsylvania State University
Crossref Funder Registry ID: