Lattice Light-Sheet Microscopy data from Developing Zebrafish Embryo

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Data DOI: 10.15785/SBGRID/187 | ID: 187

Kirchhausen Laboratory, Children's Hospital Boston

Release Date: 16 Oct 2015

Data Access Instructions

1. If this dataset is locally available, it should be accessable at /programs/datagrid/187

2. To download this dataset, please run the following command from your Terminal on a Linux or OS X workstation:

'rsync -av rsync:// .' (Harvard Medical School, USA)

Depending on your location, faster access may be available from a Tier 1 site closer to your location

'rsync -av rsync:// .' (Uppsala University, Sweden)

'rsync -av rsync:// .' (Institut Pasteur de Montevideo, Uruguay)

'rsync -av rsync:// .' (Shanghai Institutes for Biological Sciences, China)

3. After the transfer is completed, please issue the following command to verify data integrity:

'cd 187 ; shasum -c files.sha'

Storage requirements: 26G

Biological Sample:

Developing Zebrafish Embryo

Dataset Type:

Lattice Light-Sheet Microscopy

Subject Composition:

DNA, Ligand, Protein, RNA

Collection Facility:

Harvard Medical School - mSlice 1 - Kirchhausen Lab

Data Creation Date:

18 Dec 2014

Related Datasets:


Cite this Dataset

Upadhyayula, S; Kirchhausen, T. 2015. "Lattice Light-Sheet Microscopy data for: Developing Zebrafish Embryo.", SBGrid Data Bank, V1,

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Dataset Description

mSlice Conditions: Waveform type : Linear X Galvo Offset, Interval (um), # of Pixels for Excitation (0) : 0 0.1 51 Z Galvo Offset, Interval (um), # of Pixels for Excitation (0) : -0.599257 0 251 Z PZT Offset, Interval (um), # of Pixels for Excitation (0) : 26 0 251 S PZT Offset, Interval (um), # of Pixels for Excitation (0) : 50 0.398406 251 # of stacks (0) : 200 Excitation Filter, Laser, Power (%), Exp(ms) (0) : N/A 488 20 40 Cycle lasers : per Z Z motion : Sample piezo

Project Members

Name Additional Roles Affiliation While Working on the Project
Srigokul UpadhyayulaData Collector, DepositorHarvard Medical School / BCH
Tom KirchhausenPIChildren's Hospital Boston

Reprocessing Instructions

Deskew: 31.5 degrees geometric transformation to convert raw data into real space. Segmentation Software: ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes; DOI: 10.1371/journal.pcbi.1002780

License and Terms of use

License: CC0

Terms: Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation, as generated by the SBGrid Data Bank.