These are the datasets used for the analysis of the zebra fish gills.
From the original scans Dea and Matthias delineated volumes of interest containing only the gills.
These VOIs were saved into a `VOI` subfolder for each of the samples.
Since [OSF is better used with large files](https://github.com/osfclient/osfclient/issues/155#issuecomment-440458992), we zipped each of the folders prior to uploading them here (even though we load each of the single reconstructions into one big image stack in the analysis notebook).
This was done in the root folder of the analysis files with these commands:
# All the log files
for i in *; do zip $i\_VOI.zip $i/*/*.log -9; done
# All slices of the VOI (some PNG, some BMP)
# The overview images are also BMP...
for i in *; do zip $i\_VOI.zip $i/VOI/*.* -9; done
for i in *; do zip $i\_VOI.zip $i/*/*.bmp -9; done
# The delineated ROIs exported from CTAn
for i in *; do zip $i\_VOI.zip $i/*.roi -9; done
# Scan support files
for i in *; do zip $i\_VOI.zip $i/proj/*.csv -9; done
This iterates through every sample folder and compresses the whole contents of the `VOI` folder inside every one of these folders into one `.zip`-file with the correct name in the root folder.
And then adds some more files, too.
The zip files were then uploaded using the [OSF client](https://github.com/osfclient/osfclient) with the command
for i in *.zip; do osf upload $i $i;done
To reproduce our results, you can download all zip files to one folder and unpack them.
Since every single zip files contains the folder structure for its sample, the unzipping should result in a folder for each fish containing a `proj`, `rec` and `VOI` subfolder each.
The `proj` and `rec` folders contain the log and supporting files, while the `VOI` folder contains all slices of the delineated gill volumes.
These are the input files to the analysis
To fully reproduce our results all you then need to do is then to adapt cell 15 of the analysis notebook ([linked in this project here on OSF](https://osf.io/bxtd6/) or available [directly on GitHub](https://github.com/habi/Zebra-Fish-Gills/blob/master/Gills-Analysis.ipynb)) to point `RootFolder` to where you saved the folders.
(Of course you need a working installation of [Jupyter](http://jupyter.org/) with all the dependencies met...)