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Indica Labs cytonuclear v1 5 image analysis algorithm
Cytonuclear V1 5 Image Analysis Algorithm, supplied by Indica Labs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/analysis+algorithms/algorithm+deconvolution+halo/pm41933194-250-13-11
Average 86 stars, based on 1 article reviews
cytonuclear v1 5 image analysis algorithm - by Bioz Stars, 2026-09
86/100 stars

Images

Related Articles

Software:

Article Title: Alternatively activated macrophages cause DNA damage through an arginase 1-mediated bystander effect and promote epithelial cell transformation.
Article Snippet: Files were analyzed using HALO Image Analysis (Version 3.10, Indica Labs). .. Image analysis algorithms were designed using Indica Labs High-Plex FL software (Version 4.2.14, Supplemental Table 2). ..

Article Title: Alternatively activated macrophages cause DNA damage through an arginase 1-mediated bystander effect and promote epithelial cell transformation
Article Snippet: .. Image analysis algorithms were designed using Indica Labs High-Plex FL software (Version 4.2.14, Supplementary Table ). ..

Article Title: Species-specific cleavage of the autophagy adaptor p62 dictates responses to TNF.
Article Snippet: Protein lysates were mixed with 6x loading buffer (125 mM TRIS-HCl pH 6.8, 6% SDS, 5% β-mercaptoethanol, 30% Glycerol, 0.1% bromophenol blue), proteins were separated on NuPAGE 4-12% Polyacrylamide, Bis-Tris Gels (Thermo Fisher Scientific, Cat# NW04125) and proteins were blotted onto polyvinylidene difluoride .. REAGENT or RESOURCE SOURCE IDENTIFIER HALO image analysis platform v3.6.4134.263 Indica Labs https://indicalab.com/halo/ Area Quantification v2.4.2 algorithm Indica Labs https://indicalab.com/halo/ CytoNuclear v2.0.9 algorithm (HALO) Indica Labs https://indicalab.com/halo/ CRISPOR Concordet et al.59 https://crispor.gi.ucsc.edu Image Lab Touch Software v. 2.4.0.03 BioRad https://www.bio-rad.com ImageJ64 software ImageJ https://imagej.net/ij/ Incucyte Software v. 2024B Sartorius https://www.sartorius.com/en/products/ live-cell-imaging-analysis/live-cellanalysis-software/incucyte-softwarev2024b Other Orbitrap FusionTM LumosTM TribridTM Mass Spectrometer Thermo Fisher Scientific Cat# IQLAAEGAAPFADBMBHQ Easy-nLC 1200 LC System Thermo Fisher Scientific Cat# LC140 50 cm Emitters CoAnn Technologies Cat# ICT36007508-50 ABIRD - The Active Background Ion Reduction Device for nanospray LC/MS ESI Solutions Cat# ABIRD ll OPEN ACCESS Article e5 Molecular Cell 86, 1–13.e1–e11, April 16, 2026 membranes (Merck). .. Membranes were blocked with BSA 5% in TBST for 30 min and incubated with the following primary antibodies overnight (all 1:1000 dilution): ATG7 (Cell Signaling, Cat# 8558; RRID:AB_11179039), BiP (Cell Signaling, Cat# 3177; RRID:AB_2119845), β actin (Cell Signaling, Cat# 4970; RRID:AB_2223172), Caspase-2 (BD Transduction Laboratories, Cat# 611023; RRID:AB_397606), Caspase-8 (Cell Signaling, Cat# 4790; RRID:AB_10545723), Caspase-9 (Cell Signaling, Cat# 9502; RRID:AB_2228052), CHOP (Cell Signaling, Cat# 2895; RRID:AB_2089254), Cleaved caspase-3 (Asp175) (Cell Signaling, Cat# 9664; RRID:AB_2070042), Cleaved caspase 7 (Asp198) (Cell Signaling, Cat# 9491; RRID:AB_2068261), Cleaved caspase-8 (Cell Signaling, Cat# 9429; RRID:AB_2062634), Cleaved caspase-8 (Asp374) (for human samples) (Cell Signaling, Cat# 9496S; RRID:AB_561378), Cleaved caspase-8 (mouse specific) (Cell Signaling, Cat# 8592S; RRID:AB_10999739), Cleaved PARP (Asp214) (rodent specific) (Cell Signaling, Cat# 94885; RRID:AB_2800237), FADD (Abcam, Cat# 124812; RRID:AB_11155370), FADD (Merck, Cat# 05-486; RRID:AB_309984), FLAG (Sigma-Aldrich, Cat# F7425; RRID:AB_439687), FLAG (M2) mAb (Merck, Cat# F3165; RRID:AB_2209044), GAPDH (Abcam, Cat# ab9484; RRID:AB_307274), GFP (Santa Cruz Biotechnology, Cat# sc-9996; RRID:AB_627695), HA-tag (Merck, Cat# 11867423001; RRID:AB_390918), HSP90 (Santa Cruz, Cat# sc-1057; RRID:AB_675714), LC3B (Cell Signaling, Cat# 3868; RRID:AB_2137707), MLKL (Cell Signaling, Cat# 14993; RRID:AB_2687572), p62 in human cells (BD Transduction Laboratories, Cat# 610833; RRID:AB_398152), p62 in mouse cells (Sigma-Aldrich, Cat# P0067; RRID:AB_1841028), p-MLKL (Cell Signaling, Cat# 91689; RRID:AB_2732034), pRIPK1 S166 (rodent specific) (Cell Signaling, Cat# 31122; RRID:AB_2799000), p-RIPK1 (Ser166) (Cell Signaling, Cat# 65746; RRID:AB_2799693), RIPK1 (BD Transduction Laboratories, Cat# 610459; RRID:AB_398668), TRADD (Abcam, Cat# ab319029; RRID: AB_3741122), TRADD (Cell Signaling, Cat# 3694; RRID:AB_2209044).

Multiplex Assay:

Article Title: Neoadjuvant immunotherapy in mismatch-repair-proficient colon cancers.
Article Snippet: Immune checkpoint blockade has led to paradigm shifts in the treatment of various tumour types, yet limited efficacy has been observed in patients with metastatic mismatch-repair-proficient (pMMR) colorectal cancer.. Here we report clinical results and in-depth analysis of patients with early-stage pMMR colon cancer from the phase II NICHE study (ClinicalTrials.gov: NCT03026140).. A total of 31 patients received neoadjuvant treatment of nivolumab plus ipilimumab followed by surgery.

Article Title: Bone-derived Osterix+ osteolineage cells are a source of tumor-promoting myofibroblastic cancer-associated fibroblasts in breast cancer.
Article Snippet: Immunostaining was chromogenically visualized using the Bond Polymer Refine Detection (#DS9800, Leica Biosystems) or the Bond Polymer Refine Red Detection (#DS9390, Leica Biosystems). .. Slides were mounted using Xylene-based Cytoseal (Thermo Fisher) or Vectamount (Vector Labs), as appropriate, scanned with a Zeiss AxioScan 7 microscope, and IHC analyses performed using the HALO image analysis platform (Indica Labs; Deconvolution v1.1.1, Multiplex IHC v.3.2.3 algorithms). ..

Immunohistochemistry:

Article Title: Neoadjuvant immunotherapy in mismatch-repair-proficient colon cancers.
Article Snippet: Immune checkpoint blockade has led to paradigm shifts in the treatment of various tumour types, yet limited efficacy has been observed in patients with metastatic mismatch-repair-proficient (pMMR) colorectal cancer.. Here we report clinical results and in-depth analysis of patients with early-stage pMMR colon cancer from the phase II NICHE study (ClinicalTrials.gov: NCT03026140).. A total of 31 patients received neoadjuvant treatment of nivolumab plus ipilimumab followed by surgery.

Article Title: Bone-derived Osterix+ osteolineage cells are a source of tumor-promoting myofibroblastic cancer-associated fibroblasts in breast cancer.
Article Snippet: Immunostaining was chromogenically visualized using the Bond Polymer Refine Detection (#DS9800, Leica Biosystems) or the Bond Polymer Refine Red Detection (#DS9390, Leica Biosystems). .. Slides were mounted using Xylene-based Cytoseal (Thermo Fisher) or Vectamount (Vector Labs), as appropriate, scanned with a Zeiss AxioScan 7 microscope, and IHC analyses performed using the HALO image analysis platform (Indica Labs; Deconvolution v1.1.1, Multiplex IHC v.3.2.3 algorithms). ..

Mass Spectrometry:

Article Title: Species-specific cleavage of the autophagy adaptor p62 dictates responses to TNF.
Article Snippet: Protein lysates were mixed with 6x loading buffer (125 mM TRIS-HCl pH 6.8, 6% SDS, 5% β-mercaptoethanol, 30% Glycerol, 0.1% bromophenol blue), proteins were separated on NuPAGE 4-12% Polyacrylamide, Bis-Tris Gels (Thermo Fisher Scientific, Cat# NW04125) and proteins were blotted onto polyvinylidene difluoride .. REAGENT or RESOURCE SOURCE IDENTIFIER HALO image analysis platform v3.6.4134.263 Indica Labs https://indicalab.com/halo/ Area Quantification v2.4.2 algorithm Indica Labs https://indicalab.com/halo/ CytoNuclear v2.0.9 algorithm (HALO) Indica Labs https://indicalab.com/halo/ CRISPOR Concordet et al.59 https://crispor.gi.ucsc.edu Image Lab Touch Software v. 2.4.0.03 BioRad https://www.bio-rad.com ImageJ64 software ImageJ https://imagej.net/ij/ Incucyte Software v. 2024B Sartorius https://www.sartorius.com/en/products/ live-cell-imaging-analysis/live-cellanalysis-software/incucyte-softwarev2024b Other Orbitrap FusionTM LumosTM TribridTM Mass Spectrometer Thermo Fisher Scientific Cat# IQLAAEGAAPFADBMBHQ Easy-nLC 1200 LC System Thermo Fisher Scientific Cat# LC140 50 cm Emitters CoAnn Technologies Cat# ICT36007508-50 ABIRD - The Active Background Ion Reduction Device for nanospray LC/MS ESI Solutions Cat# ABIRD ll OPEN ACCESS Article e5 Molecular Cell 86, 1–13.e1–e11, April 16, 2026 membranes (Merck). .. Membranes were blocked with BSA 5% in TBST for 30 min and incubated with the following primary antibodies overnight (all 1:1000 dilution): ATG7 (Cell Signaling, Cat# 8558; RRID:AB_11179039), BiP (Cell Signaling, Cat# 3177; RRID:AB_2119845), β actin (Cell Signaling, Cat# 4970; RRID:AB_2223172), Caspase-2 (BD Transduction Laboratories, Cat# 611023; RRID:AB_397606), Caspase-8 (Cell Signaling, Cat# 4790; RRID:AB_10545723), Caspase-9 (Cell Signaling, Cat# 9502; RRID:AB_2228052), CHOP (Cell Signaling, Cat# 2895; RRID:AB_2089254), Cleaved caspase-3 (Asp175) (Cell Signaling, Cat# 9664; RRID:AB_2070042), Cleaved caspase 7 (Asp198) (Cell Signaling, Cat# 9491; RRID:AB_2068261), Cleaved caspase-8 (Cell Signaling, Cat# 9429; RRID:AB_2062634), Cleaved caspase-8 (Asp374) (for human samples) (Cell Signaling, Cat# 9496S; RRID:AB_561378), Cleaved caspase-8 (mouse specific) (Cell Signaling, Cat# 8592S; RRID:AB_10999739), Cleaved PARP (Asp214) (rodent specific) (Cell Signaling, Cat# 94885; RRID:AB_2800237), FADD (Abcam, Cat# 124812; RRID:AB_11155370), FADD (Merck, Cat# 05-486; RRID:AB_309984), FLAG (Sigma-Aldrich, Cat# F7425; RRID:AB_439687), FLAG (M2) mAb (Merck, Cat# F3165; RRID:AB_2209044), GAPDH (Abcam, Cat# ab9484; RRID:AB_307274), GFP (Santa Cruz Biotechnology, Cat# sc-9996; RRID:AB_627695), HA-tag (Merck, Cat# 11867423001; RRID:AB_390918), HSP90 (Santa Cruz, Cat# sc-1057; RRID:AB_675714), LC3B (Cell Signaling, Cat# 3868; RRID:AB_2137707), MLKL (Cell Signaling, Cat# 14993; RRID:AB_2687572), p62 in human cells (BD Transduction Laboratories, Cat# 610833; RRID:AB_398152), p62 in mouse cells (Sigma-Aldrich, Cat# P0067; RRID:AB_1841028), p-MLKL (Cell Signaling, Cat# 91689; RRID:AB_2732034), pRIPK1 S166 (rodent specific) (Cell Signaling, Cat# 31122; RRID:AB_2799000), p-RIPK1 (Ser166) (Cell Signaling, Cat# 65746; RRID:AB_2799693), RIPK1 (BD Transduction Laboratories, Cat# 610459; RRID:AB_398668), TRADD (Abcam, Cat# ab319029; RRID: AB_3741122), TRADD (Cell Signaling, Cat# 3694; RRID:AB_2209044).

Microscopy:

Article Title: Bone-derived Osterix+ osteolineage cells are a source of tumor-promoting myofibroblastic cancer-associated fibroblasts in breast cancer.
Article Snippet: Immunostaining was chromogenically visualized using the Bond Polymer Refine Detection (#DS9800, Leica Biosystems) or the Bond Polymer Refine Red Detection (#DS9390, Leica Biosystems). .. Slides were mounted using Xylene-based Cytoseal (Thermo Fisher) or Vectamount (Vector Labs), as appropriate, scanned with a Zeiss AxioScan 7 microscope, and IHC analyses performed using the HALO image analysis platform (Indica Labs; Deconvolution v1.1.1, Multiplex IHC v.3.2.3 algorithms). ..



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Image Search Results


Angiogenesis induced by VEGF secreted from VEGF-MSCs. Human umbilical vein endothelial cells labelled by CytoLight Green (GFP-HUVECs) were used for the development of angiogenic networks, and the length of networks was determined by the IncuCyte live-cell analysis system. ( A ) VEGF effectively induced the formation of vascular networks, which was able to be inhibited by suramin, a VEGF signaling inhibitor. Data shown as mean (SD) ( n = 6). ( B ) A concentration-dependent effect was shown in the angiogenesis assay using CCM-VEGF with different VEGF concentrations (1, 2, 4, and 8 ng/mL). Blank control, without any VEGF supplement added; suramin group, 4 ng/mL VEGF and 100 µM suramin added. Data shown as mean (SD) ( n = 4); ns, not significant; **** p < 0.05.

Journal: Cells

Article Title: Extracellular Vesicles Derived from VEGF mRNA-Engineered Mesenchymal Stem Cells Promote Endothelial Cell Survival

doi: 10.3390/cells15080717

Figure Lengend Snippet: Angiogenesis induced by VEGF secreted from VEGF-MSCs. Human umbilical vein endothelial cells labelled by CytoLight Green (GFP-HUVECs) were used for the development of angiogenic networks, and the length of networks was determined by the IncuCyte live-cell analysis system. ( A ) VEGF effectively induced the formation of vascular networks, which was able to be inhibited by suramin, a VEGF signaling inhibitor. Data shown as mean (SD) ( n = 6). ( B ) A concentration-dependent effect was shown in the angiogenesis assay using CCM-VEGF with different VEGF concentrations (1, 2, 4, and 8 ng/mL). Blank control, without any VEGF supplement added; suramin group, 4 ng/mL VEGF and 100 µM suramin added. Data shown as mean (SD) ( n = 4); ns, not significant; **** p < 0.05.

Article Snippet: Image analysis was performed using the IncuCyte automated angiogenesis algorithm (Incucyte software, v2024B, Sartorius).

Techniques: Cell Analysis, Concentration Assay, Angiogenesis Assay, Control