[Work Log] Diadem dataset investigation
Software
ImageJ
ImageJ has great image stack tools (slicing, manipulation, analysis). Has the "tubeness" measure from the diadem challenge.
ImageJ Cookbook
The "cookbook" plugin for microscopy seems to be very useful in particular.
MBF Plugin Collection
The original software associated with the "ImageJ for Microscopy" reference (see below). It seems defunct now, and is supplanted by the ImageJ Cookbook plugin suite.
link;
Neuromantic
Need to look into this tool. Was mentioned in Diadem data documentation.
count: 3
Xvoxtrace
Manual segmentation tool
Synu
Surface reconstruct tool (used with Xvoxtrace?)
Neurolucida
Segmentation tool. Provides nice single-line segmentations, rather than the volumetric ones from other tools.
Extension: *.asc (ascii)
Count: 5
Analyze (7.5)
Image stack tool? Compressed image stacks
extension: .img, .hdr
Amira
Semi-automatic segmentation
BioRadPIC
microscopy image data format
extension: *.PIC
flNeuronTool
Neuron Tracing tool (C++)
cvapp - Duke / Southampton Morphology editor
Neuron tracing, labelling. Can read neurolucida files.
Vaa3D
NeuronStudio
Rayburst
Algorithm used in at least one tracing algorithm.
Neurozoom
TBD
NeuronML
open format for representing neurons, neuron networks, and others.
NeuronLand
convert between over 20 difference neuron morphology formats
Other
- autoneuron
- neuronj
- neuronmetrics
- Raveler
- tablet
- TRAKA
References
- ImageJ for Microscopy
- Sezgin & Sankur. 2004. Survey over image thresholding techniques and quantitative performance evaluation. Journal of Electronic Imaging, 2004
- For reconstruction and analysis of dendritic spines: Rodriguez A., Ehlenberger D.B., Dickstein D.L., Hof P.R., Wearne S.L. Automated Three-Dimensional Detection and Shape Classification of Dendritic Spines from Fluorescence Microscopy Images. PLoS ONE 3(4): e1997
- For reconstruction and analysis of dendritic arbors: Wearne, S.L., Rodriguez, A., Ehlenberger, D.B., Rocher, A.B., Hendersion, S.C., and Hof, P.R. New Techniques for imaging, digitization and analysis of three-dimensional neural morphology on multiple scales.
Neuron Datasets
NeuroMorpho
Seems to be an open neuron reconstruction dataset. They don't appear to have the original images, unfortunatley. I could try to contact the labs
Duke Southampton Archive of Neuronal Morphology
Cell-centered database
General database of cell images.
Useful search terms:
- Neuron (obviously)
- Dendritic tree
- Spiny Dendrite
- Purkinje
- neurolucida (ground truth tool)
- vascular?
- protoplasmic astrocyte
- cerebellar basket cell
Examined datasets
- dendritic tree - could be good for "tracking" through slices. Ground truth segmentation isn't clear
- spiny dendrite -
- Purkinje neuron (dendritic tree) - very complex branching structure, with ground truth
- Purkinje neuron (spiny dendrite) - nice electron microscopy image
- Purkinje neuron (multiphoton) Nice but no ground truth
- (http://ccdb.ucsd.edu/sand/main?mpid=3380&event=displaySeg) - confocal data seems in the seetspot between clean and noisy. Nice 3d ground truth
- medium spiny neuron (transmitted light - has a nice looking ground-truth
- neocortex pyramidal neuron - different-looking neuron, different lab, could be an easier dataset
Datasets to look into
- Maryann Martone - at least 4 very complex dendritic tree stacks w/ ground truth.
- Mark Ellisman, Stephen Larson - at least 1 full neuron w/ semi-auto segmentation
Data types
- confocal
- IVEM / UHVEM - {intermediate, ultra high} voltage electron microscopy)
- transmitted light
- multiphoton - very clean images
Miscellaneous
- Lucifer yellow - cell stain
- Golgi - staining method
- genesis modelling package?
To Try
- Decovolution with synthetic and emperical point spread functions.
- using duke/southampton format - swc
- use neuromorpho for training ** experimental condition: "Control"