Data from: D quantification of tumor vasculature in lymphoma xenografts in NOD/SCID mice allows to detect differences among vascular-targeted therapies

Righi M, Giacomini A, Cleris L, Carlo-Stella C

Date Published: May 20, 2013

DOI: http://dx.doi.org/10.5061/dryad.6c44q

 

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Title 3DFilter
Downloaded 155 times
Description Text of an ImageJ macro used to remove small unconnected particles from samples before voxel classification.
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Title Macro_VesselCalibrometry
Downloaded 95 times
Description ext of an ImageJ macro used to classify voxels in a binary stack according to the minimal Cartesian surface to which they belong (i.e., the approximated vessel cross-section).
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Title Spatial_Dispersion plugin
Downloaded 33 times
Description Source code for the ImageJ plug-in used in the reference paper to calculate the 3D spatial dispersion of vessels in binary stacks. Expansion was performed by rhombicuboctahedral dilation after volume normalization according to the total number of vessel voxels.
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Title FilteredStacks
Downloaded 17 times
Description The filteredStacks.zip file carries a compressed folder containing 32 binary stacks representative of vascular trees ready to be splitted in substacks according to vessel caliber. The stacks have already been filtered in order to remove particles less than 1 µm3 but their voxels should still be classified by vessel masking as reported in the paper. BEWARE ! upon expansion this file will occupy 1.45 GB (gigabytes) of space.
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Title OriSect_x_Paper
Downloaded 18 times
Description The OriSect.zip file carries a compressed folder containing 32 subfolders each containing 6 stacks representative of vascular maps of vessels showing specific projected cross-sections (values in Table I of the paper). In order to correctly normalize all of the stacks against a common reference, the stack with the highest percent Volume of signal (black pixels) should be added to the other 31 folders. BEWARE ! upon expansion this file will occupy 9.3 GB (gigabytes) of space.
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Title DataForFigure_4
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Download DataForFigure_4.txt (16.09 Kb)
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Title DataForFigures_5&6
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Title Graph_1
Downloaded 22 times
Description Graph obtained using data archived in file DataForFigures_5&6.txt. Explanation on the meaning of the graph can be found in the readMe associated to that file.
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Title Graph_2
Downloaded 27 times
Description Graph obtained using data archived in file DataForFigures_5&6.txt. Explanation on the meaning of the graph can be found in the readMe associated to that file.
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Title Graph_3
Downloaded 21 times
Description Graph obtained using data archived in file DataForFigures_5&6.txt. Explanation on the meaning of the graph can be found in the readMe associated to that file.
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Title Graph_4
Downloaded 28 times
Description Graph obtained using data archived in file DataForFigures_5&6.txt. Explanation on the meaning of the graph can be found in the readMe associated to that file.
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Title Graph_5
Downloaded 21 times
Description Graph obtained using data archived in file DataForFigures_5&6.txt. Explanation on the meaning of the graph can be found in the readMe associated to that file.
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Title Graph_6
Downloaded 23 times
Description Graph obtained using data archived in file DataForFigures_5&6.txt. Explanation on the meaning of the graph can be found in the readMe associated to that file.
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Title Graph_7
Downloaded 25 times
Description Graph obtained using data archived in file DataForFigures_5&6.txt. Explanation on the meaning of the graph can be found in the readMe associated to that file.
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Title Graph_8
Downloaded 25 times
Description Graph obtained using data archived in file DataForFigures_5&6.txt. Explanation on the meaning of the graph can be found in the readMe associated to that file.
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Title Graph_9
Downloaded 21 times
Description Graph obtained using data archived in file DataForFigures_5&6.txt. Explanation on the meaning of the graph can be found in the readMe associated to that file.
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Title Graph_10
Downloaded 22 times
Description Graph obtained using data archived in file DataForFigures_5&6.txt. Explanation on the meaning of the graph can be found in the readMe associated to that file.
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Title Graph_11
Downloaded 20 times
Description Graph obtained using data archived in file DataForFigures_5&6.txt. Explanation on the meaning of the graph can be found in the readMe associated to that file.
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Title Graph_12
Downloaded 30 times
Description Graph obtained using data archived in file DataForFigures_5&6.txt. Explanation on the meaning of the graph can be found in the readMe associated to that file.
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Title Graph_13
Downloaded 22 times
Description Graph obtained using data archived in file DataForFigures_5&6.txt. Explanation on the meaning of the graph can be found in the readMe associated to that file.
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Title Graph_14
Downloaded 23 times
Description Graph obtained using data archived in file DataForFigures_5&6.txt. Explanation on the meaning of the graph can be found in the readMe associated to that file.
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Title Graph_15
Downloaded 25 times
Description Graph obtained using data archived in file DataForFigures_5&6.txt. Explanation on the meaning of the graph can be found in the readMe associated to that file.
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Title Macro_Spatial_Dispersion
Downloaded 18 times
Description Given a set of isotropic, equidimensional binary stacks of squared images, this ImageJ macro calculates the number of cycles of rhombicubocthedric dilation necessary to fill 90%, 95% and 99% of each volume on the basis of the distribution of the black pixels. The macro asks for a source folder containing a set of subfolders (mandatory) containing binary image stacks (.tif files) with equal dimensions. The procedure is iterated over the nested folders for all the images present in every folder. The results are saved in a target location, choosed by the operator, as a number of .txt result files - one for each subfolder - named after the source subfolders. Results are expressed as raw values (Hv) which are normalized, subfolder after subfolder, according to the highest percentual volume observed in each subfolder to give nHv results. To normalize all subfolders in a single run, the image presenting the highest percentual volume should be present in all subfolders. This macro has been validated against simple images manually dilated. This version analyzes all .tif stacks present in nested folders. It behaves alike the accompanying ImageJ plugin but it is at least an order of magnitude slower. Its function was essentially that of validating the results obtained with the plugin.
Download S11_Macro_Spatial_Dispersion.txt (11.63 Kb)
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When using this data, please cite the original publication:

Righi M, Giacomini A, Cleris L, Carlo-Stella C (2013) Data from: D quantification of tumor vasculature in lymphoma xenografts in NOD/SCID mice allows to detect differences among vascular-targeted therapies. PLoS One 8(3): e59691. http://dx.doi.org/10.1371/journal.pone.0059691

Additionally, please cite the Dryad data package:

Righi M, Giacomini A, Cleris L, Carlo-Stella C (2013) Data from: D quantification of tumor vasculature in lymphoma xenografts in NOD/SCID mice allows to detect differences among vascular-targeted therapies. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.6c44q
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