Indica
Backed by cutting edge technology, an uncompromising focus on ease-of-use and dedicated customer service, Indica Labs’ software and services are being used to make vital discoveries in pathology labs and research organizations around the world.

Backed by cutting edge technology, an uncompromising focus on ease-of-use and dedicated customer service, Indica Labs’ software and services are being used to make vital discoveries in pathology labs and research organizations around the world. Discover how our solutions can help you.

Backed by cutting edge technology, an uncompromising focus on ease-of-use and dedicated customer service, Indica Labs’ software and services are being used to make vital discoveries in pathology labs and research organizations around the world. Discover how our solutions can help you.

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With uncompromising ease-of-use and flexibility, the HALO IMAGE ANALYSIS PLATFORM can adapt to any image analysis application.

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HALO AI2

HALO-AI, the first of its kind intuitive interface for deep learning in digital pathology, is putting the power of AI in the hands of the pathologist.

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Share images and analysis data with remote collaborators using HALO LINK, our browser-based image management system.

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services

If you are overwhelmed with your image analysis workload or need help with more complex analysis, our PHARMA SERVICES team can help.

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Explore our Integrated Platforms

Explore the functionality of each of our platform individually and how they work together to form one integrated solution.  Simply click on the platforms and the integration points between them in the image to the right.  

Platforms

HALO is the image analysis workhorse of the HALO solution.

Within the user-friendly, modular HALO interface, users can tune algorithms to address their image analysis questions, create classifiers, segment TMAs, annotate images, export image analysis results, create figures from markup images, and more.

HALO modules make it easy to accomplish specific image analysis tasks without any image analysis expertise. New modules can be added anytime, so the platform can be scaled according to budget and need.


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HALO Link allows secure remote access to images and image analysis data generated by the HALO platform.

Data generated by HALO can be viewed and explored remotely via the browser-based HALO Link interface.  Importantly, HALO alone is not user aware. HALO Link provides secure access control to images and data stored in the HALO database.

Click on HALO and HALO Link to learn more about each of these platforms individually.

HALO Link is the sharing and management arm of the HALO solution.

Within the browser-based HALO Link interface, digital slides are organized into studies and can be shared with invited users. HALO Link is tied directly to the HALO database so analysis data, markups, and annotations generated by HALO and HALO-AI can be viewed by remote users and collaborators via HALO Link without any need for HALO at remote sites - the perfect solution for CROs and core facilities!


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HALO Link provides the collaborative interface for HALO-AI.

Neural networks need to be trained with more examples compared to other machine learning classifiers, so collaboration is an important part of HALO-AI. To facilitate this collaboration, HALO-AI is integrated with HALO Link. Using the browser-based HALO Link viewer and intuitive annotation tools, remote pathologists can train HALO-AI without any requirement for HALO or HALO-AI at the remote site.

Learn more about HALO-AI and HALO Link by clicking on the respective sections to the left and right.

HALO-AI enables deep learning tissue classification within the HALO solution.

HALO-AI is used for advanced tissue classification and segmentation. Using a state-of-the-art GPU-driven neural network, HALO-AI can handle stain and morphological variability better than other machine learning algorithms.

The difference between HALO-AI and other deep learning platforms can be summed up in one word - usability. Designed to be used by pathologists not computer scientists, HALO-AI is tightly integrated with HALO and HALO Link platforms providing an intuitive, visual interface for pathologists to use.


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The HALO platform is the primary user interface for HALO-AI.

HALO-AI is integrated within the user-friendly HALO interface. Pathologists can add classes in one click and train the neural network that underlies HALO-AI by annotating slides using HALO's intuitive annotation tools. Importantly, classifiers created through HALO-AI can then be used for region-of-interest (ROI) detection in any HALO algorithm module.

Learn more about HALO and HALO-AI by clicking on the respective sections above and below.

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Application Notes & White Papers

Follow the links below to explore a few of our most popular applications.

HALO Application Note

Measure immune cell density and spatial distance to tumor cells within the tumor and invasive margin

Using our multiplex IHC module, we quantify immune cells and tumor cell markers across whole slide images.  The tissue classifier add-on is employed to segment tumor and stroma and the spatial analysis module is used for proximity and invasive margin analysis.  

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HALO Application Note

Quantify Single and Multiplexed RNAscope® probes across whole slide tissues

Using our ISH module for brightfield and our FISH module for fluorescence, we demonstrate how to quantify ISH signal from RNAScope® assays on a per cell or per unit area basis and output an overall expression score based on ACD Bio’s recommended scoring guidelines.  

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HALO AI White Paper

Moving deep learning out of the computer lab and into the hands of the pathologist with HALO AI™

If you’ve been to any digital pathology meetings recently you have heard artificial intelligence or deep learning mentioned at least once. In this white paper, we will introduce some of the basics about this emerging technology and explain how HALO AI™  is making artificial intelligence accessible to the pathology community.

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Read what our customers are publishing

Our customers are making vital discoveries in oncology, neuroscience, and diabetes research.  Check out some of the research our customers are publishing using the HALO Image Analysis Platform and Indica analysis modules.

Peroxisome Proliferator-Activated Receptor g2 Controls the Rate of Adipose Tissue Lipid Storage and Determines Metabolic Flexibility

Sam Virtue, Kasparas Petkevicius, Jose Maria Moreno-Navarrete, Benjamin Jenkins, Daniel Hart, Martin Dale, Albert Koulman, Jose Manuel Fernandez-Real, and Antonio Vidal-Puig Cell Reports| Published August 21st, 2018 | DOI https://doi.org/10.1073/pnas.1721418115 One understudied function of white adipose tissue (AT) is its role...

Diet-Induced Growth Is Regulated via Acquired Leptin Resistance and Engages a Pomc-Somatostatin-Growth Hormone Circuit

Heiko Löhr, Simon Hess, Mafalda M.A. Pereira, Philip Reinoß, Sandra Leibold, Christel Schenkel, Claudia M. Wunderlich, Peter Kloppenburg, Jens C. Brüning, Matthias Hammerschmidt5,'Correspondence information about the author Matthias Hammerschmidt Cell Reports , 2018 DOI: https://doi.org/10.1016/j.celrep.2018.04.018 Abstract Anorexigenic pro-opiomelanocortin (Pomc)/alpha-melanocyte stimulating hormone...

Plant-based vaccines for oral delivery of type 1 diabetes-related autoantigens: Evaluating oral tolerance mechanisms and disease prevention in NOD mice

Amanda L. Posgai, Clive H. Wasserfall, Kwang-Chul Kwon, Henry Daniell, Desmond A. Schatz, & Mark A. Atkinson Scientific Reports, February 2017 doi:10.1038/srep42372 Abstract Autoantigen-specific immunological tolerance represents a central objective for prevention of type 1 diabetes (T1D). Previous studies demonstrated...

High levels of tumor-associated neutrophils are associated with improved overall survival in patients with stage II colorectal cancer

Ryan S. Berry, Meng-Jun Xiong, Alissa Greenbaum, Parisa Mortaji, Robert A. Nofchissey, Fred Schultz, Cathleen Martinez, Li Luo, Katherine T. Morris, & Joshua A. Hanson PLoS ONE, December 2017 https://doi.org/10.1371/journal.pone.0188799 Abstract Conflicting reports regarding whether high tumor-associated neutrophils (TAN) are...

ANGPTL8/betatrophin does not control pancreatic beta cell expansion

Gusarova V, Alexa CA, Na E, Stevis PE, Xin Y, Bonner-Weir S, Cohen JC, Hobbs HH, Murphy AJ, Yancopoulos GD, Gromada J. Cell. 2014 Oct 23;159(3):691-6. Recently, it was reported that angiopoietin-like protein 8 (ANGPTL8) was the long-sought "betatrophin" that...

FOXM1 contributes to treatment failure in acute myeloid leukemia

Irum Khan, Marianna Halasi, Anand Patel, Rachael Schultz, Nandini Kalakota, Yi-Hua Chen, Nathan Aardsma, Li Liu, John D. Crispino, Nadim Mahmud, Olga Frankfurt, and Andrei L. Gartel JCI Insight | Published August 9th, 2018 | DOI https://doi.org/10.1172/jci.insight.121583 Acute myeloid leukemia (AML) patients...

Nerve fibers infiltrate the tumor microenvironment and are associated with nerve growth factor production and lymph node invasion in breast cancer

Pundavela J, Roselli S1, Faulkner S, Attia J, Scott RJ, Thorne RF, Forbes JF, Bradshaw RA, Walker MM, Jobling P, Hondermarck H. Mol Oncol. 2015 May 14. pii: S1574-7891(15)00115-5. Infiltration of the tumor microenvironment by nerve fibers is an understudied...

Islet-1 is essential for pancreatic beta cell function

Ediger BN, Du A, Liu J, Hunter CS, Walp ER, Schug J, Kaestner KH, Stein R, Stoffers DA, May CL. Diabetes. 2014 Dec;63(12):4206-17. Islet-1 (Isl-1) is essential for the survival and ensuing differentiation of pancreatic endocrine progenitors. Isl-1 remains expressed...

Digital image analysis improves precision of PD‐L1 scoring in cutaneous melanoma

Viktor H. Koelzer, Aline Gisler, Jonathan C. Hanhart, Johannes Griss, Stephan N. Wagner, Niels Willi, Gieri Cathomas, Melanie Sachs, Werner Kempf, Daniela S. Thommen, Kirsten D. Mertz Nature Medicine | First published April 16th, 2018 | DOI https://doi.org/10.1111/his.13528 Abstract Aims Immune checkpoint...

The neurotrophic tyrosine kinase receptor TrkA and its ligand NGF are increased in squamous cell carcinomas of the lung

Fangfang Gao, Nathan Griffin, Sam Faulkner, Christopher W. Rowe, Lily Williams, Severine Roselli, Rick F. Thorne, Aysha Ferdoushi, Phillip Jobling, Marjorie M. Walker & Hubert Hondermarck Scientific Reports | Published May 25th, 2018 | DOI https://doi.org/10.1038/s41598-018-26408-2 Abstract The neurotrophic tyrosine kinase...

Mice harboring the human SLC30A8 R138X loss-of-function mutation have increased insulin secretory capacity

Sandra Kleiner, Daniel Gomez, Bezawit Megra, Erqian Na, Ramandeep Bhavsar, Katie Cavino, Yurong Xin, Jose Rojas, Giselle Dominguez-Gutierrez, Brian Zambrowicz, Gaelle Carrat, Pauline Chabosseau, Ming Hu, Andrew J. Murphy, George D. Yancopoulos, Guy A. Rutter, and Jesper Gromada PNAS | Published July 23rd, 2018 | DOI https://doi.org/10.1073/pnas.1721418115 SLC30A8 encodes a zinc transporter that is primarily expressed in the pancreatic...

A single dose of peripherally infused EGFRvIII-directed CAR T cells mediates antigen loss and induces adaptive resistance in patients with recurrent glioblastoma

Donald M. O’Rourke, MacLean P. Nasrallah, Arati Desai, Jan J. Melenhorst, Keith Mansfield, Jennifer J. D. Morrissette, Maria Martinez-Lage, Steven Brem, Eileen Maloney, Angela Shen, Randi Isaacs, Suyash Mohan, Gabriela Plesa, Simon F. Lacey, Jean-Marc Navenot, Zhaohui Zheng, Bruce L....

T-cell Localization, Activation, and Clonal Expansion in Human Pancreatic Ductal Adenocarcinoma

Ingunn M. Stromnes, Ayaka Hulbert, Robert H. Pierce, Philip D. Greenberg and Sunil R. Hingorani Cancer Immunology Research , 2017 DOI: 10.1158/2326-6066.CIR-16-0322 Abstract Pancreatic ductal adenocarcinoma (PDA) is a lethal malignancy resistant to most therapies, including immune checkpoint blockade. To elucidate mechanisms of immunotherapy resistance, we assessed immune parameters in...

Angptl4 does not control hyperglucagonemia or α-cell hyperplasia following glucagon receptor inhibition

Haruka Okamotoa, Katie Cavinoa, Erqian Naa, Elizabeth Krumma, Steven Kima, Panayiotis E. Stevisa, Joyce Harpa, Andrew J. Murphya, George D. Yancopoulosa, and Jesper Gromadaa PNAS January 31, 2017, doi:10.1073/pnas.1620989114  Abstract Genetic disruption or pharmacologic inhibition of glucagon signaling effectively lowers...

Differential Cytokine Gene Expression in Granulomas from Lungs and Lymph Nodes of Cattle Experimentally Infected with Aerosolized Mycobacterium bovis

Mitchell V. Palmer , Tyler C. Thacker ,W. Ray Waters Abstract The hallmark lesion of tuberculosis in humans and animals is the granuloma. The granuloma represents a distinct host cellular immune response composed of epithelioid macrophages, lymphocytes, and multinucleated giant cells,...

G-protein-independent coupling of MC4R to Kir7.1 in hypothalamic neurons

Ghamari-Langroudi M, Digby GJ, Sebag JA, Millhauser GL, Palomino R, Matthews R, Gillyard T, Panaro BL, Tough IR, Cox HM, Denton JS, Cone RD. Nature. 2015 Apr 2;520(7545):94-8. The regulated release of anorexigenic α-melanocyte stimulating hormone (α-MSH) and orexigenic Agouti-related...

Use of the Fluidigm C1 platform for RNA sequencing of single mouse pancreatic islet cells

Yurong Xin, Jinrang Kim, Min Ni, Yi Wei, Haruka Okamoto, Joseph Lee, Christina Adler, Katie Cavino, Andrew J. Murphy, George D. Yancopoulos, Hsin Chieh Lin, and Jesper Gromada PNAS March 2016 vol. 113 no. 12 Abstract This study provides an assessment of the Fluidigm C1 platform for RNA sequencing of...

PD-1 Blockade Induces Responses by Inhibiting Adaptive Immune Resistance

Tumeh PC, Harview CL, Yearley JH, Shintaku IP, Taylor EJ, Robert L, Chmielowski B, Spasic M, Henry G, Ciobanu V, West AN, Carmona M, Kivork C, Seja E, Cherry G, Gutierrez AJ, Grogan TR, Mateus C, Tomasic G, Glaspy JA, Emerson...

Cross-Platform Comparison of Computer-assisted Image Analysis Quantification of In Situ mRNA Hybridization in Investigative Pathology.

Timothy R. Holzer, Jeffrey C. Hanson, Erin M. Wray, Jason A. Bailey, Kim R. Kennedy, Patrick R. Finnegan, Aejaz Nasir, & Kelly M. Credille Applied Immunohistochemistry &  Molecular Morphology, July 2017 doi: 10.1097/PAI.0000000000000542 Abstract Although availability of automated platforms has...

Phosphorylation of calcium/calmodulin-stimulated protein kinase II at T286 enhances invasion and migration of human breast cancer cells

Mengna Chi, Hamish Evans, Jackson Gilchrist, Jack Mayhew, Alexander Hoffman, Elizabeth Ann Pearsall, Helen Jankowski, Joshua Stephen Brzozowski & Kathryn Anne Skelding Scientific Reports | Published September 8th, 2016 | DOI: 10.1038/srep33132 Calcium/calmodulin-stimulated protein kinase II (CaMKII) is a multi-functional...

Acetate Recapturing by Nuclear Acetyl-CoA Synthetase 2 Prevents Loss of Histone Acetylation during Oxygen and Serum Limitation

Vinay Bulusu, Sergey Tumanov, Evdokia Michalopoulou, Niels J. van den Broek, Gillian MacKay, Colin Nixon, Sandeep Dhayade, Zachary T. Schug, Johan Vande Voorde, Karen Blyth, Eyal Gottlieb, Alexei Vazquez, Jurre J. Kamphorst Cell Reports January 2017 Volume 18, Issue 3 ...

Cutaneous wound healing through paradoxical MAPK activation by BRAF inhibitors

Helena Escuin-Ordinas, Shuoran Li, Michael W. Xie, Lu Sun, Willy Hugo, Rong Rong Huang, Jiang Jiao, Felipe Meira de-Faria, Susan Realegeno, Paige Krystofinski, Ariel Azhdam, Sara Marie D. Komenan, Mohammad Atefi, Begona Comin-Aunduix, Matteo Pellegrini, Alistar J Cochran, Robert Modlin,...

Association of HIV Status With Local Immune Response to Anal Squamous Cell Carcinoma

Elizabeth L. Yanik, Genevieve J. Kaunitz, Tricia R. Cottrell, Farah Succaria, Tracee L. McMiller, Maria L. Ascierto, Jessica Esandrio, Haiying Xu, Aleksandra Ogurtsova, Toby Cornish, Evan J. Lipson, Suzanne L. Topalian, Eric A. Engels, & Janis M. Taube JAMA Oncology,...

The R-enantiomer of ketorolac delays mammary tumor development in mouse mammary tumor virus-polyoma middle T antigen (MMTV-PyMT) mice

Amanda S. Peretti, Dayna Dominguez, Martha M. Grimes, Helen J. Hathaway, Eric R. Prossnitz, Melanie R. Rivera, Angela Wandinger-Ness, Donna F. Kusewitt, & Laurie G. Hudson The American Journal of Pathology, 2017 https://doi.org/10.1016/j.ajpath.2017.10.018 Abstract Epidemiologic studies report improved breast cancer...

Neutrophils dominate the immune cell composition in non-small cell lung cancer

Julia Kargl, Stephanie E. Busch, Grace H. Y. Yang, Kyoung-Hee Kim, Mark L. Hanke, Heather E. Metz, Jesse J. Hubbard, Sylvia M. Lee, David K. Madtes, Martin W. McIntosh & A. McGarry Houghton Nature Communications 8, Article number: 14381, February 2017 Abstract...

Weight Perturbation Alters Leptin Signal Transduction in a Region-Specific Manner throughout the Brain

Michael V. Morabito, Yann Ravussin, Bridget R. Mueller, Alicja A. Skowronski, Kazuhisa Watanabe, Kylie S. Foo, Samuel X. Lee, Anders Lehmann, Stephan Hjorth, Lori M. Zeltser, Charles A. LeDuc, Rudolph L. Leibel PLOS One, January 20, 2017 Abstract Diet-induced obesity (DIO) resulting...

Glucagon receptor inhibition normalizes blood glucose in severe insulin-resistant mice

Haruka Okamotoa, Katie Cavinoa, Erqian Naa, Elizabeth Krumma, Sun Y. Kima, Xiping Chenga, Andrew J. Murphya, George D. Yancopoulosa, and Jesper Gromadaa PNAS January 23, 2017, doi:10.1073/pnas.1621069114 Abstract Inactivating mutations in the insulin receptor results in extreme insulin resistance. The resulting...

Molecular Pathways: Mucins and Drug Delivery in Cancer

Chinthalapally V. Rao, Naveena B. Janakiram, and Altaf Mohammed Clinical Cancer Research, February 2017 DOI: 10.1158/1078-0432.CCR-16-0862 Abstract Over the past few decades, clinical and preclinical studies have clearly demonstrated the role of mucins in tumor development. It is well established...

Glucagon Receptor Blockade With a Human Antibody Normalizes Blood Glucose in Diabetic Mice and Monkeys

Okamoto H, Kim J, Aglione J1, Lee J, Cavino K, Na E1, Rafique A, Kim JH, Harp J, Valenzuela DM, Yancopoulos GD, Murphy AJ, Gromada J. Endocrinology. 2015 Aug;156(8):2781-94. Antagonizing glucagon action represents an attractive therapeutic option for reducing hepatic...

Exacerbated Experimental Colitis in TNFAIP8-Deficient Mice

Sun H, Lou Y, Porturas T, Morrissey S, Luo G, Qi J, Ruan Q, Shi S, Chen YH. J Immunol. 2015 Jun 15;194(12):5736-42. The TNF-α-induced protein 8 (TNFAIP8 or TIPE) is a risk factor for cancer and bacterial infection, and...

LATEST NEWS

Catch up on the latest press releases, event announcements and other news from Indica Labs.