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.
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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 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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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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The HALO AP platform brings case-centric automation, collaboration and quantification to your Anatomic Pathology lab.

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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.  


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.


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, infectious disease, and diabetes research.  Check out some of the research our customers are publishing using the HALO Image Analysis Platform and Indica analysis modules.

Immunogradient Indicators for Antitumor Response Assessment by Automated Tumor-Stroma Interface Zone Detection

Allan Rasmusson, Dovile Zilenaite, Ausrine Nestarenkaite, Renaldas Augulis, Aida Laurinaviciene, Valerijus Ostapenko, Tomas Poskus, and Arvydas Laurinavicius The American Journal of Pathology, Vol. 190, No. 6, June 2020 | DOI: The distribution of tumor-infiltrating lymphocytes (TILs) within the tumor...

Prognostic significance of mesothelin expression in colorectal cancer disclosed by area-specific four-point tissue microarrays

Takehiro Shiraishi, Eiji Shinto, Ines P. Nearchou, Hitoshi Tsuda, Yoshiki Kajiwara, Takahiro Einama, Peter D. Caie, Yoji Kishi & Hideki Ueno Virchows Archiv | February 2020 | DOI: 10.1007/s00428-020-02775-y Mesothelin (MSLN) is a cell surface glycoprotein present in many cancer...

Detection of Lung Cancer Lymph Node Metastases from Whole-Slide Histopathologic Images Using a Two-Step Deep Learning Approach

Hoa Hoang Ngoc Pham, Mitsuru Futakuchi, Andrey Bychkov, Tomoi Furukawa, Kishio Kuroda, Junya Fukuoka The American Journal of Pathology | Volume 189, Issue 12, December 2019 | DOI: 10.5858/arpa.2019-0004-OA The application of deep learning for the detection of lymph node metastases...

A Deep Learning Convolutional Neural Network Can Recognize Common Patterns of Injury in Gastric Pathology

Martin, D.R., Hanson, J.A., Gullapalli, R.R., Schultz, F.A., Sethi, A. and Clark, D.P. Archives of Pathology & Laboratory Medicine In-Press | Published April 5, 2019 | DOI: 10.5858/arpa.2019-0004-OA Context.— Most deep learning (DL) studies have focused on neoplastic pathology, with...

Automated Analysis of Lymphocytic Infiltration, Tumor Budding, and Their Spatial Relationship Improves Prognostic Accuracy in Colorectal Cancer

Ines P. Nearchou, Kate Lillard, Christos G. Gavriel, Hideki Ueno, David J. Harrison, and Peter D. Caie Cancer Immunology Research| Published March 7, 2019 | DOI 10.1158/2326-6066.CIR-18-0377 Both immune profiling and tumor budding significantly correlate with colorectal cancer patient outcome...

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 One understudied function of white adipose tissue (AT) is its role...

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 Acute myeloid leukemia (AML) patients...

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 SLC30A8 encodes a zinc transporter that is primarily expressed in the pancreatic...

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 Abstract Aims Immune checkpoint...

A transcriptionally and functionally distinct PD-1+ CD8+ T cell pool with predictive potential in non-small-cell lung cancer treated with PD-1 blockade

Daniela S. Thommen, Viktor H. Koelzer, Petra Herzig, Andreas Roller, Marcel Trefny, Sarah Dimeloe, Anna Kiialainen, Jonathan Hanhart, Catherine Schill, Christoph Hess, Spasenija Savic Prince, Mark Wiese, Didier Lardinois, Ping-Chih Ho, Christian Klein, Vaios Karanikas, Kirsten D. Mertz, Ton N....

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 Abstract The neurotrophic tyrosine kinase...

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: Abstract Anorexigenic pro-opiomelanocortin (Pomc)/alpha-melanocyte stimulating hormone...

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...

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...

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 Abstract Epidemiologic studies report improved breast cancer...

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 Abstract Conflicting reports regarding whether high tumor-associated neutrophils (TAN) are...

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,...

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...

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....

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...

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 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...

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...

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...

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 ...

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,...

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...

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...

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,...

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...

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...

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...

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...

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...

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...

Spotlight on Covid-19 Research

Follow the links below to learn how our customers are using HALO, HALO AI and HALO Link to advance our understanding of the novel coronavirus.

Covid-19 Collaborations

Indica Labs works with NIH to launch a global COVID-19 digital pathology repository

Indica Labs announce the launch of the online COVID Digital Pathology Repository (COVID-DPR), a virtual collection of high resolution microscopic COVID-related human tissue images hosted at the National Institutes of Health.

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Covid-19 Publications

Cutting edge investigations into Covid-19 published by HALO and HALO AI customers

Read about the exciting research being performed by our HALO and HALO AI customers to elucidate the biological mechanisms of novel coronavirus infection and Covid-19 disease progression.

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Covid-19 Presentations

Digital Pathology in the New Normal: Leveraging HALO to Investigate a Global Pandemic

This workshop will present some insight on how HALO and HALO AI has been used by researchers at three different global institutions to study and characterize the novel coronavirus.

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Read independent reviews on HALO® and learn how these customers are using Indica Labs’ solutions to streamline their workflows.

Simply use the scroll bar on the right to read more.


Read full reviews or write your own


Read independent reviews on HALO® and learn how these customers are using Indica Labs’ solutions to streamline their workflows.

Simply use the scroll bar on the right to read more.


Read full reviews or write your own


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