Data from: Ellipsoid segmentation model for analyzing light-attenuated 3D confocal image stacks of fluorescent multi-cellular spheroids

Barbier M, Jaensch S, Cornelissen F, Vidic S, Gjerde K, De Hoogt R, Graeser R, Gustin E, Chong YT

Date Published: June 20, 2016

DOI: http://dx.doi.org/10.5061/dryad.0m9n7

 

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Title S2_File: tiff image stack of the example 3D spheroid culture used in figures 1-4 and figure 6
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of LNCaP human prostate cancer cells (ATCC, Rockville, USA) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S3_File: ground truth manual segmentation data on 2D MIP images
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Description This is a zip-file containing manually segmented 2D ground truth labeled masks of 3D spheroid cultures. The cultures are LNCaP cancer spheroids in co-culture with CAF stromal cells (untreated, DMSO samples). For the manual segmentation 2D maximum intensity projections (MIPs) were used of the original 3D stacks. The spheroids are labeled in five distinct classes: (1) well separated, (2) overlapping with brighter spheroids in the MIP (rendering it non-separable), (3) overlapping with less bright spheroids in the MIP (rendering it well separable), (4) merely touching other spheroids, and (5) touching the border of the 2D projection of the image. Opening of the images in FIJI (ImageJ) with the ROI Manager allows visual inspection of the data. For this purpose the cases (1) to (5) are color-coded in red, green, magenta, cyan, and blue, respectively.
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Title S5_File: 3D image stack of PC346c cancer spheroids in co-culture with CAFs, control sample (DMSO), well A06, field 1
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of PC346c prostate cancer cells (a cell line obtained from the Erasmus Medical Center, via the PREDECT consortium) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S5_File: 3D image stack of PC346c cancer spheroids in co-culture with CAFs, control sample (DMSO), well A06, field 2
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of PC346c prostate cancer cells (a cell line obtained from the Erasmus Medical Center, via the PREDECT consortium) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S5_File: 3D image stack of PC346c cancer spheroids in co-culture with CAFs, control sample (DMSO), well A06, field 3
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of PC346c prostate cancer cells (a cell line obtained from the Erasmus Medical Center, via the PREDECT consortium) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S5_File: 3D image stack of PC346c cancer spheroids in co-culture with CAFs, control sample (DMSO), well A06, field 4
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of PC346c prostate cancer cells (a cell line obtained from the Erasmus Medical Center, via the PREDECT consortium) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S5_File: 3D image stack of PC346c cancer spheroids in co-culture with CAFs, control sample (DMSO), well A08, field 1
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of PC346c prostate cancer cells (a cell line obtained from the Erasmus Medical Center, via the PREDECT consortium) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S5_File: 3D image stack of PC346c cancer spheroids in co-culture with CAFs, control sample (DMSO), well A08, field 2
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of PC346c prostate cancer cells (a cell line obtained from the Erasmus Medical Center, via the PREDECT consortium) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S5_File: 3D image stack of PC346c cancer spheroids in co-culture with CAFs, control sample (DMSO), well A08, field 3
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of PC346c prostate cancer cells (a cell line obtained from the Erasmus Medical Center, via the PREDECT consortium) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S5_File: 3D image stack of PC346c cancer spheroids in co-culture with CAFs, control sample (DMSO), well A08, field 4
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of PC346c prostate cancer cells (a cell line obtained from the Erasmus Medical Center, via the PREDECT consortium) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S5_File: 3D image stack of PC346c cancer spheroids in co-culture with CAFs, treated with docetaxel, well E08, field 1
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of PC346c prostate cancer cells (a cell line obtained from the Erasmus Medical Center, via the PREDECT consortium) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S5_File: 3D image stack of PC346c cancer spheroids in co-culture with CAFs, treated with docetaxel, well E08, field 2
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of PC346c prostate cancer cells (a cell line obtained from the Erasmus Medical Center, via the PREDECT consortium) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S5_File: 3D image stack of PC346c cancer spheroids in co-culture with CAFs, treated with docetaxel, well E08, field 3
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of PC346c prostate cancer cells (a cell line obtained from the Erasmus Medical Center, via the PREDECT consortium) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S5_File: 3D image stack of PC346c cancer spheroids in co-culture with CAFs, treated with docetaxel, well E08, field 4
Downloaded 2 times
Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of PC346c prostate cancer cells (a cell line obtained from the Erasmus Medical Center, via the PREDECT consortium) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S5_File: 3D image stack of PC346c cancer spheroids in co-culture with CAFs, treated with MDV, well F05, field 1
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of PC346c prostate cancer cells (a cell line obtained from the Erasmus Medical Center, via the PREDECT consortium) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S5_File: 3D image stack of PC346c cancer spheroids in co-culture with CAFs, treated with MDV, well F05, field 2
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of PC346c prostate cancer cells (a cell line obtained from the Erasmus Medical Center, via the PREDECT consortium) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S5_File: 3D image stack of PC346c cancer spheroids in co-culture with CAFs, treated with MDV, well F05, field 3
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of PC346c prostate cancer cells (a cell line obtained from the Erasmus Medical Center, via the PREDECT consortium) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S5_File: 3D image stack of PC346c cancer spheroids in co-culture with CAFs, treated with MDV, well F05, field 4
Downloaded 2 times
Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of PC346c prostate cancer cells (a cell line obtained from the Erasmus Medical Center, via the PREDECT consortium) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S4_File: 3D image stack, LNCaP cancer spheroids in co-culture with CAFs, control sample (DMSO), well A05, field 1, stack 333
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of LNCaP human prostate cancer cells (ATCC, Rockville, USA) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S4_File: 3D image stack, LNCaP cancer spheroids in co-culture with CAFs, control sample (DMSO), well A05, field 2, stack 334
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of LNCaP human prostate cancer cells (ATCC, Rockville, USA) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S4_File: 3D image stack, LNCaP cancer spheroids in co-culture with CAFs, control sample (DMSO), well A05, field 3, stack 335
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of LNCaP human prostate cancer cells (ATCC, Rockville, USA) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S4_File: 3D image stack, LNCaP cancer spheroids in co-culture with CAFs, control sample (DMSO), well A05, field 4, stack 336
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of LNCaP human prostate cancer cells (ATCC, Rockville, USA) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S4_File: 3D image stack, LNCaP cancer spheroids in co-culture with CAFs, control sample (DMSO), well A07, field 1, stack 337
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of LNCaP human prostate cancer cells (ATCC, Rockville, USA) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S4_File: 3D image stack, LNCaP cancer spheroids in co-culture with CAFs, control sample (DMSO), well A07, field 2, stack 338
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of LNCaP human prostate cancer cells (ATCC, Rockville, USA) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S4_File: 3D image stack, LNCaP cancer spheroids in co-culture with CAFs, control sample (DMSO), well A07, field 3, stack 339
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of LNCaP human prostate cancer cells (ATCC, Rockville, USA) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title S4_File: 3D image stack, LNCaP cancer spheroids in co-culture with CAFs, control sample (DMSO), well A07, field 4, stack 340
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Description 3D image stack of 3D fluorescent multi-cellular spheroid culture existing out of LNCaP human prostate cancer cells (ATCC, Rockville, USA) and CAF-PF179T human cancer associated fibroblasts (a cell line obtained from the Weizmann Institute, via the PREDECT consortium).
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Title ReadMe
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Description The ReadMe file describes the 3D image data contained in this data repository.
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Title S6 File. Spot detection algorithm illustrated on the 3D image stack in S2 File.
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Description This is a multi-page tiff file which shows the EdU channel of the 3D image stack in the supplement S2 File, with the EdU positive cells annotated by small spheres. This image can serve as an example result of the spot detection algorithm (3D version). Similar to the image stack in the supplement S2 File, this image stack can be opened with an application such as ImageJ.
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When using this data, please cite the original publication:

Barbier M, Jaensch S, Cornelissen F, Vidic S, Gjerde K, De Hoogt R, Graeser R, Gustin E, Chong YT (2016) Ellipsoid segmentation model for analyzing light-attenuated 3D confocal image stacks of fluorescent multi-cellular spheroids. PLOS ONE 11(6): e0156942. http://dx.doi.org/10.1371/journal.pone.0156942

Additionally, please cite the Dryad data package:

Barbier M, Jaensch S, Cornelissen F, Vidic S, Gjerde K, De Hoogt R, Graeser R, Gustin E, Chong YT (2016) Data from: Ellipsoid segmentation model for analyzing light-attenuated 3D confocal image stacks of fluorescent multi-cellular spheroids. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.0m9n7
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