3dmorph automatic analysis software Search Results


3dmorph  (Oxford Instruments)
99
Oxford Instruments 3dmorph
(A) Segmentation of microglia from light microscopy data produced by PrestoCell, user-edited PrestoCell, <t>3DMorph,</t> and the LABKIT extension in Imaris (top row). The mask generated by each tool is then compared visually to the ground state (bottom row, white), and image math is performed to identify false positives (“FP”, red) and false negatives (“FN”, cyan). Quantitative analysis comparing each segmentation to the ground state truth was performed using (B) F1 score, (C) Jaccard score, the (D) percent of false positive and (E) false negative pixels. Data are presented as mean ± SD, with each segmented cell as a data point. All files are compared to the ground truth, thus the percentage of false positives or negatives can be higher than 100. Scale bar: 10 μm.
3dmorph, supplied by Oxford Instruments, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/3dmorph/product/Oxford Instruments
Average 99 stars, based on 1 article reviews
3dmorph - by Bioz Stars, 2026-03
99/100 stars
  Buy from Supplier
3dmorph processing pipeline for  (MathWorks Inc)
90
MathWorks Inc 3dmorph processing pipeline for
(A) Segmentation of microglia from light microscopy data produced by PrestoCell, user-edited PrestoCell, <t>3DMorph,</t> and the LABKIT extension in Imaris (top row). The mask generated by each tool is then compared visually to the ground state (bottom row, white), and image math is performed to identify false positives (“FP”, red) and false negatives (“FN”, cyan). Quantitative analysis comparing each segmentation to the ground state truth was performed using (B) F1 score, (C) Jaccard score, the (D) percent of false positive and (E) false negative pixels. Data are presented as mean ± SD, with each segmented cell as a data point. All files are compared to the ground truth, thus the percentage of false positives or negatives can be higher than 100. Scale bar: 10 μm.
3dmorph Processing Pipeline For, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/3dmorph processing pipeline for/product/MathWorks Inc
Average 90 stars, based on 1 article reviews
3dmorph processing pipeline for - by Bioz Stars, 2026-03
90/100 stars
  Buy from Supplier
lsm 700 confocal microscope  (Carl Zeiss)
90
Carl Zeiss lsm 700 confocal microscope
(A) Segmentation of microglia from light microscopy data produced by PrestoCell, user-edited PrestoCell, <t>3DMorph,</t> and the LABKIT extension in Imaris (top row). The mask generated by each tool is then compared visually to the ground state (bottom row, white), and image math is performed to identify false positives (“FP”, red) and false negatives (“FN”, cyan). Quantitative analysis comparing each segmentation to the ground state truth was performed using (B) F1 score, (C) Jaccard score, the (D) percent of false positive and (E) false negative pixels. Data are presented as mean ± SD, with each segmented cell as a data point. All files are compared to the ground truth, thus the percentage of false positives or negatives can be higher than 100. Scale bar: 10 μm.
Lsm 700 Confocal Microscope, supplied by Carl Zeiss, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/lsm 700 confocal microscope/product/Carl Zeiss
Average 90 stars, based on 1 article reviews
lsm 700 confocal microscope - by Bioz Stars, 2026-03
90/100 stars
  Buy from Supplier
matlab code 3dmorph  (MathWorks Inc)
90
MathWorks Inc matlab code 3dmorph
(A) Segmentation of microglia from light microscopy data produced by PrestoCell, user-edited PrestoCell, <t>3DMorph,</t> and the LABKIT extension in Imaris (top row). The mask generated by each tool is then compared visually to the ground state (bottom row, white), and image math is performed to identify false positives (“FP”, red) and false negatives (“FN”, cyan). Quantitative analysis comparing each segmentation to the ground state truth was performed using (B) F1 score, (C) Jaccard score, the (D) percent of false positive and (E) false negative pixels. Data are presented as mean ± SD, with each segmented cell as a data point. All files are compared to the ground truth, thus the percentage of false positives or negatives can be higher than 100. Scale bar: 10 μm.
Matlab Code 3dmorph, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/matlab code 3dmorph/product/MathWorks Inc
Average 90 stars, based on 1 article reviews
matlab code 3dmorph - by Bioz Stars, 2026-03
90/100 stars
  Buy from Supplier
3dmorph automatic analysis software  (MathWorks Inc)
90
MathWorks Inc 3dmorph automatic analysis software
Quantitative analysis of microglial-cell morphology in the rostral ventrolateral region of the medulla. (A,D) Axioscan images of whole brainstem (AxioScan.Z1scanner, Carl Zeiss, Zaventem, Belgium) showing targeted areas from the rostral ventrolateral region of the medulla (white boxes) in one control (left) and one LPS-injected (right) lamb. Scale bar: 1000 μm. (B,E) Example of a 3D confocal image stack with full-cell segmentation automatically generated by <t>3DMorph</t> MATLAB-based script showing how quantitative morphological analysis of microglial cells (Iba1-positive cells, green) is performed. The full-cell segmentation shows remaining microglial cells after exclusion of partial cells and small processes not related to a cell body. Scale bar: 35 μm. (C,F) High magnification of the same medullary areas allows for appreciation of the morphological changes of the activated microglial cells in the LPS-injected lamb compared to the resting state in the control lamb. Qualitative analysis thus reveals a higher number of microglial cells with a larger cell-body surface, a larger total territory occupied by microglial cells, and shorter branch length in the LPS-injected lamb. Meanwhile, qualitative assessment of astrogliosis (GFAP-positive cells, red) does not suggest differences between the LPS-injected and the control lamb over the same medullary regions. Scale bar: 10 μm. (G) 3DMorph quantitative analysis of microglial-cell morphology from the above images (C,F) shows an increased average cell volume and territorial volume, as well as smaller branch length in the LPS-injected compared to the control lamb.
3dmorph Automatic Analysis Software, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/3dmorph automatic analysis software/product/MathWorks Inc
Average 90 stars, based on 1 article reviews
3dmorph automatic analysis software - by Bioz Stars, 2026-03
90/100 stars
  Buy from Supplier

Image Search Results


(A) Segmentation of microglia from light microscopy data produced by PrestoCell, user-edited PrestoCell, 3DMorph, and the LABKIT extension in Imaris (top row). The mask generated by each tool is then compared visually to the ground state (bottom row, white), and image math is performed to identify false positives (“FP”, red) and false negatives (“FN”, cyan). Quantitative analysis comparing each segmentation to the ground state truth was performed using (B) F1 score, (C) Jaccard score, the (D) percent of false positive and (E) false negative pixels. Data are presented as mean ± SD, with each segmented cell as a data point. All files are compared to the ground truth, thus the percentage of false positives or negatives can be higher than 100. Scale bar: 10 μm.

Journal: PLOS ONE

Article Title: PrestoCell: A persistence-based clustering approach for rapid and robust segmentation of cellular morphology in three-dimensional data

doi: 10.1371/journal.pone.0299006

Figure Lengend Snippet: (A) Segmentation of microglia from light microscopy data produced by PrestoCell, user-edited PrestoCell, 3DMorph, and the LABKIT extension in Imaris (top row). The mask generated by each tool is then compared visually to the ground state (bottom row, white), and image math is performed to identify false positives (“FP”, red) and false negatives (“FN”, cyan). Quantitative analysis comparing each segmentation to the ground state truth was performed using (B) F1 score, (C) Jaccard score, the (D) percent of false positive and (E) false negative pixels. Data are presented as mean ± SD, with each segmented cell as a data point. All files are compared to the ground truth, thus the percentage of false positives or negatives can be higher than 100. Scale bar: 10 μm.

Article Snippet: As expected from the graphical visualization, unedited PrestoCell segmentations have a lower F1 and Jaccard score, compared to either 3DMorph or Imaris ( ) .

Techniques: Light Microscopy, Produced, Generated

Interacting microglia were segmented and identified as single cells by 3DMorph (left white). The unedited PrestoCell output demonstrates the power of using nuclear identification, allowing the interacting cells to be resolved (right, pseudo-colored purple, and cyan). Scale bar: 10 μm, representative image of 41 interacting cells identified in 245 discrete masked microglia.

Journal: PLOS ONE

Article Title: PrestoCell: A persistence-based clustering approach for rapid and robust segmentation of cellular morphology in three-dimensional data

doi: 10.1371/journal.pone.0299006

Figure Lengend Snippet: Interacting microglia were segmented and identified as single cells by 3DMorph (left white). The unedited PrestoCell output demonstrates the power of using nuclear identification, allowing the interacting cells to be resolved (right, pseudo-colored purple, and cyan). Scale bar: 10 μm, representative image of 41 interacting cells identified in 245 discrete masked microglia.

Article Snippet: As expected from the graphical visualization, unedited PrestoCell segmentations have a lower F1 and Jaccard score, compared to either 3DMorph or Imaris ( ) .

Techniques:

Quantitative analysis of microglial-cell morphology in the rostral ventrolateral region of the medulla. (A,D) Axioscan images of whole brainstem (AxioScan.Z1scanner, Carl Zeiss, Zaventem, Belgium) showing targeted areas from the rostral ventrolateral region of the medulla (white boxes) in one control (left) and one LPS-injected (right) lamb. Scale bar: 1000 μm. (B,E) Example of a 3D confocal image stack with full-cell segmentation automatically generated by 3DMorph MATLAB-based script showing how quantitative morphological analysis of microglial cells (Iba1-positive cells, green) is performed. The full-cell segmentation shows remaining microglial cells after exclusion of partial cells and small processes not related to a cell body. Scale bar: 35 μm. (C,F) High magnification of the same medullary areas allows for appreciation of the morphological changes of the activated microglial cells in the LPS-injected lamb compared to the resting state in the control lamb. Qualitative analysis thus reveals a higher number of microglial cells with a larger cell-body surface, a larger total territory occupied by microglial cells, and shorter branch length in the LPS-injected lamb. Meanwhile, qualitative assessment of astrogliosis (GFAP-positive cells, red) does not suggest differences between the LPS-injected and the control lamb over the same medullary regions. Scale bar: 10 μm. (G) 3DMorph quantitative analysis of microglial-cell morphology from the above images (C,F) shows an increased average cell volume and territorial volume, as well as smaller branch length in the LPS-injected compared to the control lamb.

Journal: Frontiers in Physiology

Article Title: Cardiorespiratory Alterations in a Newborn Ovine Model of Systemic Inflammation Induced by Lipopolysaccharide Injection

doi: 10.3389/fphys.2020.00585

Figure Lengend Snippet: Quantitative analysis of microglial-cell morphology in the rostral ventrolateral region of the medulla. (A,D) Axioscan images of whole brainstem (AxioScan.Z1scanner, Carl Zeiss, Zaventem, Belgium) showing targeted areas from the rostral ventrolateral region of the medulla (white boxes) in one control (left) and one LPS-injected (right) lamb. Scale bar: 1000 μm. (B,E) Example of a 3D confocal image stack with full-cell segmentation automatically generated by 3DMorph MATLAB-based script showing how quantitative morphological analysis of microglial cells (Iba1-positive cells, green) is performed. The full-cell segmentation shows remaining microglial cells after exclusion of partial cells and small processes not related to a cell body. Scale bar: 35 μm. (C,F) High magnification of the same medullary areas allows for appreciation of the morphological changes of the activated microglial cells in the LPS-injected lamb compared to the resting state in the control lamb. Qualitative analysis thus reveals a higher number of microglial cells with a larger cell-body surface, a larger total territory occupied by microglial cells, and shorter branch length in the LPS-injected lamb. Meanwhile, qualitative assessment of astrogliosis (GFAP-positive cells, red) does not suggest differences between the LPS-injected and the control lamb over the same medullary regions. Scale bar: 10 μm. (G) 3DMorph quantitative analysis of microglial-cell morphology from the above images (C,F) shows an increased average cell volume and territorial volume, as well as smaller branch length in the LPS-injected compared to the control lamb.

Article Snippet: Following qualitative assessment of the number and morphology of microglial cells, a quantitative 3D-morphological analysis of microglial cells using the 3DMorph Automatic Analysis Software, a MATLAB-based script (MathWorks, Natick, MA, United States) was performed.

Techniques: Injection, Generated