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Image 2D
Display image description
Wide field fluorescent image of cultured neuroblastoma cells labeled with phalloidn FITC (green) and DAPI (blue) nuclear stain.
Full resolution image description
Zip file containing full resolution single channel 12 bit images. For each image, F01_*w1.TIF corresponds to the phalloidin channel and F01_*w2.TIF to the DAPI channel.

Segmentation
Display image description
Manual segmentation of cell and nuclear boundaries of double labeled cultured neurons, generated using Adobe Photoshop
Segmentation file description
Manually segmented files in tiff format. The name of the binary files indicates the corresponding original image, available for download through the 2D Image panel, e.g., F01_120_GT_01.tiff contains the "ground truth (GT)" masks for image file F01_120.tiff. Each image may have more than one mask file generated for it, indicated by the final number, e.g., F01_120_Gt_02.tiff is the second mask generated for F01_120.tiff.

License
Attribution Only: This image is licensed under a Creative Commons Attribution License. View License Deed | View Legal Code

CCDB:6843*
Project: P2043
Project name
Autosegmentation of cultured neurons
Description
To develop automated algorithms for analysis of neurite outgrowth in high content screens of cultured neurons. This data set consists of wide field epifluorescent images of cultured neurons with both cytoplasmic (phalloidin) and nuclear stains (DAPI) and a set of manual segmentations of neuronal and nuclear boundaries that can be used as benchmarking data sets for the development of segmentation algorithms.
Leader(s)
Weimiao Yu
Collaborator(s)
Hwee Kuan Lee
Srivats Hariharan
Wen Yu Bu and Sohail Ahmed
Start date
unspecified
End date
unspecified
 
Experiment
Experiment ID
6835
Title
High throughput image acquisition and segmentation
Purpose
To generate a set of ground truth image data sets for development of automated segmentation routines for neurite outgrowth
Experimenter(s)
Weimiao Yu
Microscopy product
Microscopy product ID
6843
Instrument
Zeiss
Microscopy type
EPIFLUORESCENT
Product type
SURVEY
Image basename
F01
Spatial Axis Image Size Pixel Size
X 1392px 0.31 nm/pixels
Y 1040px 0.31 nm/pixels
Y 1px
Subject
Species
mouse
Scientific name
mus musculus
Strain
unknown
Group by
not applicable
Treatment
The data sets actually are derived from 4 different culture conditions: (i) serum starvation with 50,000 cells/slide, (ii) serum starvation with 30,000 cells/ slide, (iii) Toca-1 transfected with 50,000 cells/slide, and (iv) Toca-1 transfected with 30,000 cells/slide. However, as these culture conditions are not relevant for the purpose of this study, we have collapsed all data into a single data set.
Age class
not applicable
Specimen description
System
central nervous system
Cell type
Neuroblastoma
Imaging parameters
Type
Light microscopy product
Lens magnification
X
Notes
mmartone
Specimen preparation
Protocol used
Cells are grown on 18 X 18 lamin coated glass coverslips maintained at 37 deg C in 5% CO2. Culture medium is Dulbecoo's Modified Eagle's medium supllemented with 4500 mg/ml glucose and 1% penicillin-streptomycin as an antibiotic. Cells were serum starged for 48 hrs and then fixed with 4% Paraformaldehyde, then counterstained with DAPI and FITC-phalloidin
Imaging product type
Type
Survey
Description
Automated acquisition of survey images of cultured neurons for segmentation algorithm development