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algorithm imaris bitplane rrid scr 007370 software  (Oxford Instruments)


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    Oxford Instruments algorithm imaris bitplane rrid scr 007370 software
    Algorithm Imaris Bitplane Rrid Scr 007370 Software, supplied by Oxford Instruments, used in various techniques. Bioz Stars score: 99/100, based on 44453 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/algorithm+imaris+bitplane+rrid+scr+007370+software/Imaris/10__7554_slash_elife__93326-401-110-111
    Average 99 stars, based on 44453 article reviews
    algorithm imaris bitplane rrid scr 007370 software - by Bioz Stars, 2026-10
    99/100 stars

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    Virus:

    Article Title: Mesenchyme instructs growth while epithelium directs branching in the mouse mammary gland
    Article Snippet: DOI: https://doi.org/10.7554/eLife.93326 20 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Strain, strain background (Mus musculus,) Eda-/- The Jackson Laboratory Strain #:000314; RRID:IMSR_JAX:000314 Strain, strain background (Mus musculus, C57/Bl6) Rosa26Fucci2a flox/Fucci2a flox EMMA EMMA:08395; RRID:IMSR_EM:08395 The original strain was bred with Pgk1- cre before using in this study. .. Strain, strain background (Mus musculus, C57/Bl6) Pgk1- cre The Jackson Laboratory Strain #:020811; RRID:IMSR_JAX:020811 Strain, strain background (Mus musculus, ICR) Rosa26mTmG The Jackson Laboratory Strain #:007576; RRID:IMSR_JAX:007576 Strain, strain background (Mus musculus, mix) Rosa26mGFP/mTmG This paper Obtained by breeding mTmG mouse with Pgk1- cre Strain, strain background (Mus musculus, C57/Bl6) Ctnnb1lox(ex3)/lox(ex3) PMID:10545105 RRID: MGI:2673882 Strain, strain background (Mus musculus, 129S2/SvPasCrl) Igf1r +/- PMID:12483226 RRID: MGI:3775301 Strain, strain background (Mus musculus, C57/Bl6) TCF/LEF:H2B- GFP PMID: 21176145 Strain #:013752; RRID:IMSR_JAX:013752 Chemical compound, drug Hoechst 33342 Invitrogen H3570 1:1000 Other Adeno- Associated Virus (AAV8- Cre) Gene Transfer and Cell Therapy Core Facility, Faculty of Medicine, University of Helsinki 1:100 (stock: 1.13×109 vg/μl) Software, algorithm Imaris Bitplane RRID:SCR_007370 Software, algorithm Fiji http://fiji.sc RRID:SCR_002285 Software, algorithm AfterQc PMID:28361673 RRID:SCR_016390 Software, algorithm SortMeRNA PMID:23071270 RRID:SCR_014402 Software, algorithm DEseq2 PMID;25516281 RRID:SCR_015687 Software, algorithm Limma PMID:25605792 RRID:SCR_010943 Software, algorithm biomaRt PMID:16082012; 19617889 RRID:SCR_019214 Software, algorithm Salmon PMID:28263959 RRID:SCR_017036 Software, algorithm Mfuzz PMID:28263959;16078370 RRID:SCR_000523 Software, algorithm GraphPad Prism GraphPad Software RRID:SCR_002798 Software, algorithm R Project for Statistical Computing http://www.r-project.org/ RRID:SCR_001905 Continued .. To obtain mice constitutively expressing the Fucci2a cell cycle reporters (Rosa26Fucci2a del/Fucci2a del), the conditional Rosa26Fucci2a flox/Fucci2a flox mice (Mort et al., 2014) were first bred with Pgk1- cre mice (Lallemand et al., 1998) ubiquitously expressing Cre.

    Software:

    Article Title: Mesenchyme instructs growth while epithelium directs branching in the mouse mammary gland
    Article Snippet: DOI: https://doi.org/10.7554/eLife.93326 20 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Strain, strain background (Mus musculus,) Eda-/- The Jackson Laboratory Strain #:000314; RRID:IMSR_JAX:000314 Strain, strain background (Mus musculus, C57/Bl6) Rosa26Fucci2a flox/Fucci2a flox EMMA EMMA:08395; RRID:IMSR_EM:08395 The original strain was bred with Pgk1- cre before using in this study. .. Strain, strain background (Mus musculus, C57/Bl6) Pgk1- cre The Jackson Laboratory Strain #:020811; RRID:IMSR_JAX:020811 Strain, strain background (Mus musculus, ICR) Rosa26mTmG The Jackson Laboratory Strain #:007576; RRID:IMSR_JAX:007576 Strain, strain background (Mus musculus, mix) Rosa26mGFP/mTmG This paper Obtained by breeding mTmG mouse with Pgk1- cre Strain, strain background (Mus musculus, C57/Bl6) Ctnnb1lox(ex3)/lox(ex3) PMID:10545105 RRID: MGI:2673882 Strain, strain background (Mus musculus, 129S2/SvPasCrl) Igf1r +/- PMID:12483226 RRID: MGI:3775301 Strain, strain background (Mus musculus, C57/Bl6) TCF/LEF:H2B- GFP PMID: 21176145 Strain #:013752; RRID:IMSR_JAX:013752 Chemical compound, drug Hoechst 33342 Invitrogen H3570 1:1000 Other Adeno- Associated Virus (AAV8- Cre) Gene Transfer and Cell Therapy Core Facility, Faculty of Medicine, University of Helsinki 1:100 (stock: 1.13×109 vg/μl) Software, algorithm Imaris Bitplane RRID:SCR_007370 Software, algorithm Fiji http://fiji.sc RRID:SCR_002285 Software, algorithm AfterQc PMID:28361673 RRID:SCR_016390 Software, algorithm SortMeRNA PMID:23071270 RRID:SCR_014402 Software, algorithm DEseq2 PMID;25516281 RRID:SCR_015687 Software, algorithm Limma PMID:25605792 RRID:SCR_010943 Software, algorithm biomaRt PMID:16082012; 19617889 RRID:SCR_019214 Software, algorithm Salmon PMID:28263959 RRID:SCR_017036 Software, algorithm Mfuzz PMID:28263959;16078370 RRID:SCR_000523 Software, algorithm GraphPad Prism GraphPad Software RRID:SCR_002798 Software, algorithm R Project for Statistical Computing http://www.r-project.org/ RRID:SCR_001905 Continued .. To obtain mice constitutively expressing the Fucci2a cell cycle reporters (Rosa26Fucci2a del/Fucci2a del), the conditional Rosa26Fucci2a flox/Fucci2a flox mice (Mort et al., 2014) were first bred with Pgk1- cre mice (Lallemand et al., 1998) ubiquitously expressing Cre.

    Article Title: Phagocytic ‘teeth’ and myosin-II ‘jaw’ power target constriction during phagocytosis
    Article Snippet: .. 68627 22 of 31 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Software, algorithm Fiji (ImageJ) NIH RRID:SCR_002285 Software, algorithm Imaris Bitplane RRID:SCR_007370 Software, algorithm MATLAB Mathworks RRID:SCR_001622 Software, algorithm Python Python Software foundation RRID:SCR_008394 Software, algorithm Custom MATLAB code Other https:// gitlab. com/ dvorselen/ DAAMparticle_ Shape_ Analysis Software, algorithm Custom Python code Other https:// gitlab. com/ micronano_ public/ ShElastic Other VECTASHIELD Antifade Mounting Medium Vector Laboratories H- 1000 Continued .. The RAW 264.7 and HL- 60 cell lines were obtained directly from the ATCC and used within passages 3–15.

    Article Title: Localization of KRAS downstream target ARL4C to invasive pseudopods accelerates pancreatic cancer cell invasion
    Article Snippet: Software, algorithm UCSC Xena browser http:// xena. ucsc. edu RRID:SCR_018938 Software, algorithm Kaplan–Meier plotter http://www. kmplot. com RID:SCR_018753 Software, algorithm GraphPad Prism 8 GraphPad Software. .. RRID:SCR_002798 Software, algorithm Excel Toukei ESUMI Co., Ltd. Software, algorithm Imaris Bitplane RRID:SCR_007370 Software, algorithm Image J National Institutes of Health RRID:SCR_003070 Software, algorithm Living Image 4.3.1 Software Caliper Life Sciences RRID:SCR_014247 Software, algorithm ikra v1.2.2 https:// zenodo. org/ record/ 3606888 (Yu et al., 2019) Software, algorithm iDEP.90 http:// bioinformatics. sdstate. edu/ idep90/ (Ge et al., 2020) Software, algorithm Ingenuity Pathway Analysis IPA; Qiagen RRID:SCR_008653 Other LSM880 laser scanning microscope Carl Zeiss Other BZ- 9000 Keyence Other IVIS imaging system Xenogen Corp. Other Hoechst33342 Invitrogen H1399 Other Alexa Fluor 488 Phalloidin Invitrogen A12379 Other Alexa Fluor 546 Phalloidin Invitrogen A22283 Other Alexa Fluor 647 Phalloidin Invitrogen A22287 Continued ..

    other:

    Article Title: Retinoic acid-induced protein 14 controls dendritic spine dynamics associated with depressive-like behaviors
    Article Snippet: DOI: https://doi.org/10.7554/eLife.77755 17 of 30 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Commercial assay or kit FD Rapid GolgiStainTM Kit FD Neurotechnologies Cat# PK401 Commercial assay or kit MAX Efficiency DH5α Competent Cells Invitrogen Cat# 18258012 Chemical compound, drug Ara- C (Cytosine β-D- arabinofuranoside) Sigma- Aldrich C1768 Chemical compound, drug B27 supplement Gibco Cat# 17504044 Chemical compound, drug Clarity Western ECL Substrate Bio- Rad Cat# 1705061 Chemical compound, drug Complete Protease Inhibitor Cocktail Roche Cat# 11697498001 Chemical compound, drug DNase I Sigma- Aldrich Cat# DN25 Chemical compound, drug fetal bovine serum (FBS) Gibco Cat# 10082147 Chemical compound, drug Fluoxetine hydrochloride Sigma- Aldrich Cat# 1279804 Chemical compound, drug Ketamine hydrochloride Yuhan Corporation N/A Chemical compound, drug Laminin Corning Cat# 354,239 Chemical compound, drug Latrunculin A Cayman Chemical Cat# CAY- 10010630–2 Chemical compound, drug Lipofectamine 2000 Invitrogen Cat# 11668019 Chemical compound, drug penicillin/streptomycin Gibco Cat# 15140122 Chemical compound, drug Poly- D- lysine hydrobromide Sigma- Aldrich Cat# P6407 Chemical compound, drug Polyethylenimine Polysciences Cat# 23,966 Chemical compound, drug RNAlaterTM Solution Invitrogen Cat# AM7020 Chemical compound, drug Surgipath FSC22 Clear OCT solution Leica Biosystems Cat# FSC22 Chemical compound, drug Vivamagic Vivagen Cat# VM001 Chemical compound, drug Xylazine Bayer AG N/A Software, algorithm ImageJ (Fiji) Schindelin et al., 2012 RRID:SCR_002285 Software, algorithm Imaris Bitplane RRID:SCR_007370 Software, algorithm Olympus cellSens Software Olympus RRID:SCR_016238 Software, algorithm GraphPad Prism GraphPad RRID:SCR_002798 Other ECM 830 Square Wave Electroporation System Harvard Apparatus Cat# W3 45–0052 Materials and methods – In utero electroporation Other Leica VT1000S vibrating blade microtome Leica Microsystems N/A Materials and methods – GolgiCox impregnation Other Olympus Confocal Laser Scanning Microscope Fluoview FV3000 Olympus RRID:SCR_017015 Materials and methods – Microscopy, Time- lapse imaging of live neurons Continued Kim et al. eLife 2022;11:e77755.

    Article Title: Subventricular zone/white matter microglia reconstitute the empty adult microglial niche in a dynamic wave
    Article Snippet: DOI: https://doi.org/10.7554/eLife.66738 26 of 39 Continued Reagent type (species) or resource Designation Source or reference Identifiers Additional information Antibody Anti-Nestin (Mouse monoclonal) Abcam Cat# ab6142, RRID:AB_305313 IF(1:200) Antibody Anti-MASH1 (Mouse monoclonal) BD Biosciences Cat# 556604, RRID:AB_396479 IF(1:200) Antibody Anti-TIE2 (Mouse monoclonal) Abcam Cat# ab24859, RRID:AB_2255983 IF(1:100) Antibody Anti-GFAP (Chicken polyclonal) Abcam Cat# ab4674, RRID:AB_304558 IF(1:3000) Antibody Anti-doublecortin (DCX) (Goat polyclonal) Santa Cruz Biotechnology Cat# sc-8066, RRID:AB_2088494 IF(1:200) Antibody Anti-Olig2 (Rabbit monoclonal) Abcam Cat# ab109186, RRID:AB_10861310 IF(1:200) Antibody Anti-SOX2 (Goat polyclonal) R and D Systems Cat# AF2018, RRID:AB_355110 IF(1:200) Antibody Anti-GFP (Rabbit polyclonal) Abcam Cat# ab6556, RRID:AB_305564 IF(1:200) Antibody Anti-GFP (Chicken polyclonal) Abcam Cat# ab13970, RRID:AB_300798 IF(1:200) Antibody Anti-PU.1 (Rabbit monoclonal) Cell Signaling Technology Cat# 2258, RRID:AB_2186909 IF(1:200) Antibody Anti-Collagen IV (Rabbit polyclonal) Abcam Cat# ab6586, RRID:AB_305584 IF(1:200) Antibody Anti-Parvalbumin (Mouse monoclonal) Millipore Cat# MAB1572, RRID:AB_2174013 IF(1:200) Antibody Anti-Wisteria floribunda lectin (WFA) (Biotinylated) Vector Laboratories Cat# B-1355, RRID:AB_2336874 IF(1:1000) Antibody Anti-PDGF Receptor alpha (PDGFRa) (Rabbit polyclonal) Abcam Cat# ab124392, RRID:AB_10978090 IF(1:200) Antibody Anti-Myelin Basic Protein (MBP) (Rat monoclonal) Millipore Cat# MAB386, RRID:AB_94975 IF(1:200) Antibody Anti-NeuN (Mouse monoclonal) Millipore Cat# MAB377, RRID:AB_2298772 IF(1:1000) Software, algorithm Leica Application Suite X (LASX) Leica RRID:SCR_013673 Software, algorithm Imaris Bitplane RRID:SCR_007370 Software, algorithm Image J Image J RRID:SCR_003070 Software, algorithm Fiji Fiji RRID:SCR_002285 Software, algorithm Weighted Gene Co-expression Network Analysis Software R package RRID:SCR_003302 Software, algorithm EdgeR Bioconductor software package RRID:SCR_012802 Software, algorithm DESeq Bioconductor software package RRID:SCR_000154 Continued on next page Hohsfield et al. eLife 2021;10:e66738.

    Article Title: Parallel evolution between genomic segments of seasonal human influenza viruses reveals RNA-RNA relationships
    Article Snippet: (species) or resource Designation Source or reference Identifiers Additional information Antibody Anti- Mouse IgG Alexa Fluor 594 (goat polyclonal) Invitrogen Cat# A- 11005, RRID:AB_2534073 IF (1:2000) Recombinant DNA reagent A/Perth/16/2009 (H3N2) reverse genetics plasmids PMID:33919124 Bidirectional pHW2000 backbone Peptide, recombinant protein Trypsin, TPCKtreated Worthington Biochemical Cat# LS003750 1:1000 Cell line (Homo sapiens) A549 cells ATCC Cat# CCL- 185, RRID:CVCL_0023 Validation performed by U. of Arizona Genetics Core Sequence- based reagent H3N2 PB2 FISH probes conjugated to Quasar 670 This paper FISH probes Oligo sequences provided in Supplementary file 6 Sequence- based reagent H3N2 NA FISH probes conjugated to Quasar 570 This paper FISH probes Oligo sequences provided in Supplementary file 6 Sequence- based reagent Amine- labeled H3N2 NS FISH probes This paper FISH probes Oligo sequences provided in Supplementary file 6 Commercial assay or kit Alexa Fluor 488 Oligonucleotide Amine Labeling Kit Invitrogen Cat# A20191 Other DAPI Sigma Cat# D9542 0.2 μg/ml Chemical compound, drug ProLong Diamond antifade mountant Thermo Fisher Cat# P36965 Software, algorithm R CRAN RRID:SCR_001905 Software, algorithm Parallel Evolution Of Influenza Viral RNA (custom script) This paper See Materials and methods, Code availability section Software, algorithm Huygens Scientific Volume Imaging B.V. RRID:SCR_014237 Software, algorithm Imaris Bitplane RRID:SCR_007370 Software, algorithm Matlab MathWorks RRID:SCR_001622 Software, algorithm Matlab extension PMID:28724771 See Materials and methods, Validation of vRNA relationships section Continued

    Article Title: Activity-dependent modulation of synapse-regulating genes in astrocytes
    Article Snippet: or resource Designation Source or reference Identifiers Additional information Sequence- based reagent RNAscope probe: Chrdl1 ACDbio CAT# 442811 Sequence- based reagent RNAscope probe: Thbs1 ACDbio CAT# 457891 Sequence- based reagent RNAscope probe: Thbs2 ACDbio CAT# 492681 Sequence- based reagent RNAscope probe: Thbs4 ACDbio CAT# 526821 Sequence- based reagent RNAscope probe: Slc1a3 (Glast) channel 2 ACDbio CAT# 430781- C2 Sequence- based reagent RNAscope probe: Tubb3 channel 3 ACDbio CAT# 423398- C3 Software, algorithm Imaris Bitplane RRID:SCR_007370 Software, algorithm ImageJ (Fiji) NIH RRID:SCR_003070 Software, algorithm Zen Zeiss RRID:SCR_013672 Software, algorithm AxioVision Zeiss RRID:SCR_002677 Software, algorithm Odyssey Image Studio LI- COR RRID:SCR_014211 Software, algorithm InteractiVenn Heberle et al., 2015 N/A Software, algorithm GraphPad Prism Prism RRID:SCR_002798 Software, algorithm Python RRID:SCR_008394 Software, algorithm RStudio RRID:SCR_000036 Other Cell culture inserts Thermo Fisher CAT# 353102 Other Vivaspin centrifugal concentrator Sartorius CAT# 14558502 Other 4–12% bolt gels Thermo Fisher CAT# NW04120 Other PVDF membranes, Immobilon- FL Millipore CAT# IPFL00005 Other Odyssey Infrared Imager LI- COR N/A Other Fluorescence microscope with apotome Zeiss Axio Imager.Z2 Other Cryostat Hacker Industries OTF5000 Other Confocal microscope Zeiss LSM710 Other Confocal microscope Zeiss LSM880 Other FACS Aria Fusion sorter BD N/A Other HybEZ hybridization system ACDbio N/A Other Illumina HiSeq 2500 Illumina N/A Other NovaSeq 6000 Illumina N/A Contact for reagent and resource sharing Further information and requests for resources and reagents should be directed to and will be fulfilled by the lead contact, Nicola J. Allen ( nallen@ salk. edu).

    Indirect Immunoperoxidase Assay:

    Article Title: Localization of KRAS downstream target ARL4C to invasive pseudopods accelerates pancreatic cancer cell invasion
    Article Snippet: Software, algorithm UCSC Xena browser http:// xena. ucsc. edu RRID:SCR_018938 Software, algorithm Kaplan–Meier plotter http://www. kmplot. com RID:SCR_018753 Software, algorithm GraphPad Prism 8 GraphPad Software. .. RRID:SCR_002798 Software, algorithm Excel Toukei ESUMI Co., Ltd. Software, algorithm Imaris Bitplane RRID:SCR_007370 Software, algorithm Image J National Institutes of Health RRID:SCR_003070 Software, algorithm Living Image 4.3.1 Software Caliper Life Sciences RRID:SCR_014247 Software, algorithm ikra v1.2.2 https:// zenodo. org/ record/ 3606888 (Yu et al., 2019) Software, algorithm iDEP.90 http:// bioinformatics. sdstate. edu/ idep90/ (Ge et al., 2020) Software, algorithm Ingenuity Pathway Analysis IPA; Qiagen RRID:SCR_008653 Other LSM880 laser scanning microscope Carl Zeiss Other BZ- 9000 Keyence Other IVIS imaging system Xenogen Corp. Other Hoechst33342 Invitrogen H1399 Other Alexa Fluor 488 Phalloidin Invitrogen A12379 Other Alexa Fluor 546 Phalloidin Invitrogen A22283 Other Alexa Fluor 647 Phalloidin Invitrogen A22287 Continued ..

    Laser-Scanning Microscopy:

    Article Title: Localization of KRAS downstream target ARL4C to invasive pseudopods accelerates pancreatic cancer cell invasion
    Article Snippet: Software, algorithm UCSC Xena browser http:// xena. ucsc. edu RRID:SCR_018938 Software, algorithm Kaplan–Meier plotter http://www. kmplot. com RID:SCR_018753 Software, algorithm GraphPad Prism 8 GraphPad Software. .. RRID:SCR_002798 Software, algorithm Excel Toukei ESUMI Co., Ltd. Software, algorithm Imaris Bitplane RRID:SCR_007370 Software, algorithm Image J National Institutes of Health RRID:SCR_003070 Software, algorithm Living Image 4.3.1 Software Caliper Life Sciences RRID:SCR_014247 Software, algorithm ikra v1.2.2 https:// zenodo. org/ record/ 3606888 (Yu et al., 2019) Software, algorithm iDEP.90 http:// bioinformatics. sdstate. edu/ idep90/ (Ge et al., 2020) Software, algorithm Ingenuity Pathway Analysis IPA; Qiagen RRID:SCR_008653 Other LSM880 laser scanning microscope Carl Zeiss Other BZ- 9000 Keyence Other IVIS imaging system Xenogen Corp. Other Hoechst33342 Invitrogen H1399 Other Alexa Fluor 488 Phalloidin Invitrogen A12379 Other Alexa Fluor 546 Phalloidin Invitrogen A22283 Other Alexa Fluor 647 Phalloidin Invitrogen A22287 Continued ..

    Imaging:

    Article Title: Localization of KRAS downstream target ARL4C to invasive pseudopods accelerates pancreatic cancer cell invasion
    Article Snippet: Software, algorithm UCSC Xena browser http:// xena. ucsc. edu RRID:SCR_018938 Software, algorithm Kaplan–Meier plotter http://www. kmplot. com RID:SCR_018753 Software, algorithm GraphPad Prism 8 GraphPad Software. .. RRID:SCR_002798 Software, algorithm Excel Toukei ESUMI Co., Ltd. Software, algorithm Imaris Bitplane RRID:SCR_007370 Software, algorithm Image J National Institutes of Health RRID:SCR_003070 Software, algorithm Living Image 4.3.1 Software Caliper Life Sciences RRID:SCR_014247 Software, algorithm ikra v1.2.2 https:// zenodo. org/ record/ 3606888 (Yu et al., 2019) Software, algorithm iDEP.90 http:// bioinformatics. sdstate. edu/ idep90/ (Ge et al., 2020) Software, algorithm Ingenuity Pathway Analysis IPA; Qiagen RRID:SCR_008653 Other LSM880 laser scanning microscope Carl Zeiss Other BZ- 9000 Keyence Other IVIS imaging system Xenogen Corp. Other Hoechst33342 Invitrogen H1399 Other Alexa Fluor 488 Phalloidin Invitrogen A12379 Other Alexa Fluor 546 Phalloidin Invitrogen A22283 Other Alexa Fluor 647 Phalloidin Invitrogen A22287 Continued ..



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