Document Type
Dataset
Publication Date
6-2019
Digital Object Identifier
https://doi.org/10.35482/bld.003.2019
Data Directories
[ 22hpf, 24hpf, 26hpf, 28hpf, 30hpf ] | -- Raw …..| -- AT …..| -- *.h5 …..| -- ilastik.ilp | -- Gfap …..| -- *.h5 …..| -- ilastik.ilp | -- Probability …..| -- AT ………| -- *_Probabilities.h5 …..| -- Gfap ………| -- *_Probabilities.h5 | -- PSI …..| -- AT_*.psi …..| -- Gfap_*.psi …..| -- model.csv | -- landmarks.csv
Experiment Description
The post optic commissure (POC) is a parabolic ribbon like structure which connects the two halves of the ventral anterior nervous system. It develops in concert with a host of glial cells, called a glial bridge, which has been proposed by us and others to perform the region for POC development. We have built ΔSCOPE as a computational analytical tool to quantify POC and glial bridge development. We have used ΔSCOPE to probe the developmental course of POC development, and leveraging the analytical power of ΔSCOPE, elucidate the relationship the glial bridge has with the developing POC. We show that the glial bridge has solidified its position prior to the formation of the POC, and that the POC is established in dorsal-ventral extent earlier than has been previously observed.
Data Description
Raw: After collection on a Leica LSCM, data from each sample and each channel were saved individually to hdf5 files. The files are saved in a subdirectory for each channel as appropriate. Additionally, the ilastik file that was used to process the raw data is included in the subdirectory for each channel. Probability: Raw data files were processed using the ilastik training file saved in each raw channel subdirectory. The output from ilastik is a two channel hdf5 file saved to the appropriate channel subdirectory. PSI: After processing through ΔSCOPE, the resulting data is saved to a single directory as a psi file. The model file contains the coefficients that specified the quadratic function fit to each sample.
Collection Method
Wild type background embryos (20 per time point) from 22-30 hpf in 2 hour intervals were fixed in 4% PFA for 3 hrs (or o/n 4 deg C). Immunocytochemistry using mouse IgG2b anti-acetylated tubulin and mouse IgG1 anti-ZRF1 (ZIRC) (anti-Gfap) made up in PBStx (2% triton x100) with 5% BSA and 10% normal goat serum. Secondaries used were alexafluor goat anti-mouse IgG2b 594 and goat anti-mouse IgG1 647 (invitrogen). Heads were dissected and mounted for coronal collection of z-stacks imaging from most anterior of the POC to the the start of the ventral rostral cluster. Images were collected on a leica scanning confocal microscope (LSCM) SP5, using a 594 laser and a 633 laser. Care is taken to ensure that dichroic mirrors do not pick up signal from adjacent channels. Imaging is performed at 63x with a 1.5x digital zoom with a pixel setting of 1024 x 1024 (for time points <26 hpf 1024 x 512 to limit bleaching of>signal), yielding a 0.128 x 0.128 um xy dimension, and a z thickness of 0.21 um is selected. Post collection, images are imported into Fiji/Imagej, and collections are cropped to select only the immediate surrounding of the POC, approximately from the luminal junction of the telencephalon and diencephalon to a corresponding distance in the ventral direction on the other side of the POC. Care is taken to eliminate any AT signal contributions of the telencephalic anterior commissure. After cropping, any associated channels are then split, and saved separately as HDF5 files for Ilastik processing.
File Formats
HDF5: Image-based data are saved as hdf5 files, which are compatible with Ilastik. The file format is described here https://portal.hdfgroup.org/display/support. Hdf5 files can be easily viewed using the plugin for Fiji https://github.com/fiji/HDF5_Vibez/. ILP: These files are generated by the open source machine learning program ilastik https://github.com/fiji/HDF5_Vibez/. They contain the training data used to generate the probability files. PSI: Text based file format similar to a csv with space delimiters. The first twenty lines of the file specify details about the file including the columns: x, y, z, alpha, theta, r.
Recommended Citation
Barresi Lab, Smith College, "Glial Bridge Development: 22 hpf" (2019). Dataset, Smith College, Northampton, MA.
https://scholarworks.smith.edu/bl_ds_gbr/1
Comments
This is file contains the zipped folder, 22 hpf, with Probability, Psi, and Raw folders within.
All files in the Glial Bridge Experiment include the experiment's .json and .csv files as additional files.