Note that OpenJDK 15 doesn't yet work with build script

docs/intro/citing.md

@@ -26,7 +26,7 @@ The following key indicates what, if anything, was cited in the main references
 
 ### Contents
 
-* [2020](#2020) (201)
+* [2020](#2020) (216)
 * [2019](#2019) (144)
 * [2018](#2018) (48)
 * [2017](#2017) (5)
@@ -35,6 +35,8 @@ The following key indicates what, if anything, was cited in the main references
 
 1. Abengozar-Muela, M. et al. (2020). Diverse immune environments in human lung tuberculosis granulomas assessed by quantitative multiplexed immunofluorescence. **Modern Pathology**. https://doi.org/10.1038/s41379-020-0600-6 📗
 
+1. Aguanno, D. et al. (2020). The intestinal quorum sensing 3-oxo-C12:2 Acyl homoserine lactone limits cytokine-induced tight junction disruption. **Tissue Barriers**. https://doi.org/10.1080/21688370.2020.1832877 📗
+
 1. Ansermet, C. et al. (2020). Renal tubular Arginase‐2 participates in the formation of the corticomedullary urea gradient and attenuates kidney damage in ischemia‐reperfusion injury in mice. **Acta Physiologica**. https://doi.org/10.1111/apha.13457 😞
 
 1. April-Monn, S. L. et al. (2020). 3D Primary Cell Culture: A Novel Preclinical Model For Pancreatic Neuroendocrine Tumors (PanNETs). **Neuroendocrinology**. https://doi.org/10.1159/000507669 📗
@@ -133,10 +135,14 @@ The following key indicates what, if anything, was cited in the main references
 
 1. Fahr, L. et al. (2020). Expression of the _EWSR1-FLI1_ fusion oncogene in pancreas cells drives pancreatic atrophy and lipomatosis. **Pancreatology**. https://doi.org/10.1016/j.pan.2020.10.033 😞
 
+1. Frangež, Ž. et al. (2020). Loss of Concurrent Regulation of the Expression of BIF-1, BAX, and Beclin-1 in Primary and Metastatic Melanoma. **Biochemistry (Moscow)**. https://doi.org/10.1134/S0006297920100107 📗
+
 1. Friedman, G. et al. (2020). Cancer-associated fibroblast compositions change with breast cancer progression linking the ratio of S100A4+ and PDPN+ CAFs to clinical outcome. **Nature Cancer**. https://doi.org/10.1038/s43018-020-0082-y 📗
 
 1. Frangež, Z. et al. (2020). BIF-1 inhibits both mitochondrial and glycolytic ATP production: its downregulation promotes melanoma growth. **Oncogene**. https://doi.org/10.1038/s41388-020-1339-8 📗
 
+1. Gao, W. et al. (2020). Targeting SKA3 suppresses the proliferation and chemoresistance of laryngeal squamous cell carcinoma via impairing PLK1–AKT axis-mediated glycolysis. **Cell Death & Disease**. https://doi.org/10.1038/s41419-020-03104-6 😞
+
 1. Ghasemi, F. et al. (2020). High MHC-II expression in Epstein–Barr virus-associated gastric cancers suggests that tumor cells serve an important role in antigen presentation. **Scientific Reports**. https://doi.org/10.1038/s41598-020-71775-4 📗
 
 1. Gil, K. N. et al. (2020). Rorqual whale nasal plugs: protecting the respiratory tract against water entry and barotrauma. **Journal of Experimental Biology**. https://doi.org/10.1242/jeb.219691 📗
@@ -175,10 +181,14 @@ The following key indicates what, if anything, was cited in the main references
 
 1. Herrspiegel, C. et al. (2020). Digital morphometry of tumor nuclei correlates to BAP-1 status, monosomy 3, gene expression class and survival in uveal melanoma. **Experimental Eye Research**. https://doi.org/10.1016/j.exer.2020.107987 📗
 
+1. Holczer, M. et al. (2020). Fine-tuning of AMPK–ULK1–mTORC1 regulatory triangle is crucial for autophagy oscillation. **Scientific Reports**. https://doi.org/10.1038/s41598-020-75030-8 😞
+
 1. Huang, A. Y-S. et al. (2020). Region-Specific Transcriptional Control of Astrocyte Function Oversees Local Circuit Activities. **Neuron**. https://doi.org/10.1016/j.neuron.2020.03.025 📗
 
 1. Hodgson, A. et al. (2020). Suppression of ovarian hormones in adolescent rats has no effect on anxiety‐like behaviour or c‐fos activation in the amygdala. **Journal of Endocrinology**. https://doi.org/10.1111/jne.12897 📗
 
+1. Hornsby, A. K. E. et al. (2020). Unacylated-Ghrelin Impairs Hippocampal Neurogenesis and Memory in Mice and Is Altered in Parkinson’s Dementia in Humans. **Cell Reports Medicine**. https://doi.org/10.1016/j.xcrm.2020.100120 📗
+
 1. Hudeček, J. et al. (2020). Application of a risk-management framework for integration of stromal tumor-infiltrating lymphocytes in clinical trials. **npj Breast Cancer**. https://doi.org/10.1038/s41523-020-0155-1 📗
 
 1. Hughes, K. et al. (2020). Proliferation of HIV-infected renal epithelial cells following virus acquisition from infected macrophages. **AIDS**. https://doi.org/10.1097/QAD.0000000000002589 📗
@@ -193,6 +203,8 @@ The following key indicates what, if anything, was cited in the main references
 
 1. Jung, M. et al. (2020). CK14 Expression Identifies a Basal/Squamous-Like Type of Papillary Non-Muscle-Invasive Upper Tract Urothelial Carcinoma. **Frontiers in Oncology**. https://doi.org/10.3389/fonc.2020.00623 📗
 
+1. Jung, M. et al. (2020). Non-Muscle-Invasive Bladder Carcinoma with Respect to Basal Versus Luminal Keratin Expression. **International Journal of Molecular Sciences**. https://doi.org/10.3390/ijms21207726 📗
+
 1. Jung, S. et al. (2020). Seizure-induced neuronal apoptosis is related to dysregulation of the RNA-edited GluR2 subunit in the developing mouse brain. **Brain Research**. https://doi.org/10.1016/j.brainres.2020.146760 😞
 
 1. Junttila, A. et al. (2020). Immunophenotype based on inflammatory cells, PD-1/PD-L1 signalling pathway and M2 macrophages predicts survival in gastric cancer. **British Journal of Cancer**. https://doi.org/10.1038/s41416-020-01053-7 😞
@@ -205,6 +217,8 @@ The following key indicates what, if anything, was cited in the main references
 
 1. Kather, J. et al. (2020). Pan-cancer image-based detection of clinically actionable genetic alterations. **Nature Cancer**. https://doi.org/10.1038/s43018-020-0087-6 📗
 
+1. Kenney, H. M. et al. (2020). Lineage tracing reveals evidence of a popliteal lymphatic muscle progenitor cell that is distinct from skeletal and vascular muscle progenitors. **Scientific Reports**. https://doi.org/10.1038/s41598-020-75190-7 📗
+
 1. Kerby, A. et al. (2020). Placental Morphology and Cellular Characteristics in Stillbirths in Women With Diabetes and Unexplained Stillbirths. **Archives of Pathology & Laboratory Medicine**. https://doi.org/10.5858/arpa.2019-0524-OA 📗
 
 1. Kelly, L. et al. (2020). Increased Hypothalamic Projections to the Lateral Hypothalamus and Responses to Leptin in Rat Neonates From High Fat Fed Mothers. **Frontiers in Neuroscience**. https://doi.org/10.3389/fnins.2019.01454 📗
@@ -237,6 +251,8 @@ The following key indicates what, if anything, was cited in the main references
 
 1. Lee, J.A. et al. (2020). Differential immune microenvironmental features of microsatellite-unstable colorectal cancers according to Fusobacterium nucleatum status. **Cancer Immunology, Immunotherapy**. https://doi.org/10.1007/s00262-020-02657-x 📗
 
+1. Lee, K. et al. (2020). _Proline rich 11 (PRR11)_ overexpression amplifies PI3K signaling and promotes antiestrogen resistance in breast cancer. **Nature Communications**. https://doi.org/10.1038/s41467-020-19291-x 📗
+
 1. Liot, S. et al. (2020). Loss of Tenascin-X expression during tumor progression: A new pan-cancer marker. **Matrix Biology Plus**. https://doi.org/10.1016/j.mbplus.2020.100021 😞
 
 1. Liu, B. et al. (2020). Mutant SF3B1 promotes AKT and NF-kB driven mammary tumorigenesis. **Journal of Clinical Investigation**. https://doi.org/10.1172/JCI138315 📗
@@ -267,6 +283,8 @@ The following key indicates what, if anything, was cited in the main references
 
 1. Martino, F. et al. (2020). A Machine-learning Approach for the Assessment of the Proliferative Compartment of Solid Tumors on Hematoxylin-Eosin-Stained Sections. **Cancers**. https://doi.org/10.3390/cancers12051344 📗
 
+1. Mast, N. et al. (2020). CYP46A1-dependent and independent effects of efavirenz treatment. **Brain Communications**. https://doi.org/10.1093/braincomms/fcaa180 📗
+
 1. McBurney-Lin, J. et al. (2020). Bidirectional pharmacological perturbations of the noradrenergic system differentially affect tactile detection. **Neuropharmacology**. https://doi.org/10.1016/j.neuropharm.2020.108151 📗
 
 1. McLeod, R. et al. (2020). First-in-human study of AT13148, a dual ROCK-AKT inhibitor in patients with solid tumors. **Clinical Cancer Research**. https://doi.org/10.1158/1078-0432.CCR-20-0700 📗
@@ -281,6 +299,8 @@ The following key indicates what, if anything, was cited in the main references
 
 1. Mohanty, A. et al. (2020). A Non-genetic Mechanism Involving the Integrin β4/Paxillin Axis Contributes to Chemoresistance in Lung Cancer. **iScience**. https://doi.org/10.1016/j.isci.2020.101496 📗
 
+1. Molitor, D. C. A. et al. (2020). Macrophage frequency in the bone marrow correlates with morphologic subtype of myeloproliferative neoplasm. **Annals of Hematology**. https://doi.org/10.1007/s00277-020-04304-y 📗
+
 1. Morral, C. et al. (2020). Zonation of Ribosomal DNA Transcription Defines a Stem Cell Hierarchy in Colorectal Cancer. **Cell Stem Cell**. https://doi.org/10.1016/j.stem.2020.04.012 😞
 
 1. Morriss, N. J. et al. (2020). Automated quantification of immunohistochemical staining of large animal brain tissue using QuPath software. **Neuroscience**. https://doi.org/10.1016/j.neuroscience.2020.01.006 📗
@@ -289,6 +309,8 @@ The following key indicates what, if anything, was cited in the main references
 
 1. Mulvaney, E. et al. (2020). NTP42, a novel antagonist of the thromboxane receptor, attenuates experimentally induced pulmonary arterial hypertension. **BMC Pulmonary Medicine**. https://dx.doi.org/10.21203/rs.2.18445/v4 📗
 
+1. Mulvaney, E. P. et al. (2020). Efficacy of the thromboxane receptor antagonist _NTP42_ alone, or in combination with sildenafil, in the sugen/hypoxia-induced model of pulmonary arterial hypertension. **European Journal of Pharmacology**. https://doi.org/10.1016/j.ejphar.2020.173658 📗
+
 1. Muthalagu, N. et al. (2020). Repression of the Type I Interferon pathway underlies MYC & KRAS-dependent evasion of NK & B cells in Pancreatic Ductal Adenocarcinoma. **Cancer Discovery**. http://doi.org/10.1158/2159-8290.CD-19-0620 😞
 
 1. Mysona, B. A. et al. (2020). QuPath Automated Analysis of Optic Nerve Degeneration in Brown Norway Rats. **Translational Vision Science & Technology**. https://doi.org/10.1167/tvst.9.3.22 📗
@@ -317,6 +339,8 @@ The following key indicates what, if anything, was cited in the main references
 
 1. Ottley, E. C. et al. (2020). Greater utility of molecular subtype rather than epithelial‐to‐mesenchymal transition (EMT) markers for prognosis in high‐risk non‐muscle‐invasive (HGT1) bladder cancer. **Journal of Pathology: Clinical Research**. https://doi.org/10.1002/cjp2.167 📗
 
+1. Oulès, B. et al. (2020). Contribution of GATA6 to homeostasis of the human upper pilosebaceous unit and acne pathogenesis. **Nature Communications**. https://doi.org/10.1038/s41467-020-18784-z 😞
+
 1. Owens, R. et al. (2020). Comparison of different anti‐Ki67 antibody clones and hot‐spot sizes for assessing proliferative index and grading in pancreatic neuroendocrine tumours using manual and image analysis. **Histopathology**. https://doi.org/10.1111/his.14200 📗
 
 1. Patel, K. S. et al. (2020). Decorin expression is associated with predictive diffusion MR phenotypes of anti-VEGF efficacy in glioblastoma. **Scientific Reports**. https://doi.org/10.1038/s41598-020-71799-w 📗
@@ -351,6 +375,8 @@ The following key indicates what, if anything, was cited in the main references
 
 1. Robertson, S. et al. (2020). Prognostic potential of automated Ki67 evaluation in breast cancer: different hot spot definitions versus true global score. **Breast Cancer Research and Treatment**. https://doi.org/10.1007/s10549-020-05752-w 📗
 
+1. Rodriguez-Hernandez, I. et al. (2020). WNT11-FZD7-DAAM1 signalling supports tumour initiating abilities and melanoma amoeboid invasion. **Nature Communications**. https://doi.org/10.1038/s41467-020-18951-2 📗
+
 1. Roelofs, A. J. (2020). Identification of the skeletal progenitor cells forming osteophytes in osteoarthritis. **Osteoarthritis**. https://doi.org/10.1136/annrheumdis-2020-218350 📗
 
 1. Roider, T. et al. (2020). Dissecting intratumour heterogeneity of nodal B-cell lymphomas at the transcriptional, genetic and drug-response levels. **Nature Cell Biology**. https://doi.org/10.1038/s41556-020-0532-x 📗
@@ -367,6 +393,8 @@ The following key indicates what, if anything, was cited in the main references
 
 1. Saleh, R. et al. (2020). Differential gene expression of tumor-infiltrating CD8+ T cells in advanced versus early-stage colorectal cancer and identification of a gene signature of poor prognosis. **Journal for ImmunoTherapy of Cancer**. http://dx.doi.org/10.1136/jitc-2020-001294 📗
 
+1. Saliakoura, M. et al. (2020). PLCγ1 suppression promotes the adaptation of KRAS-mutant lung adenocarcinomas to hypoxia. **Nature Cell Biology**. https://doi.org/10.1038/s41556-020-00592-8 😞
+
 1. Samueli, B. et al. (2020). Remote pathology education during the COVID-19 era: Crisis converted to opportunity. **Annals of Diagnostic Pathology**. https://doi.org/10.1016/j.anndiagpath.2020.151612 😞
 
 1. Schottlaender, L. V. et al. (2020). Bi-allelic JAM2 Variants Lead to Early-Onset Recessive Primary Familial Brain Calcification. **AJHG**. https://doi.org/10.1016/j.ajhg.2020.02.007 😞
@@ -375,6 +403,8 @@ The following key indicates what, if anything, was cited in the main references
 
 1. Ščupáková, K. et al. (2020). Morphometric Cell Classification for Single‐Cell MALDI‐Mass Spectrometry Imaging. **Angewandte Chemie**. https://doi.org/10.1002/ange.202007315 📗
 
+1. Sebastiano, M. R. et al. (2020). ACSL3–PAI-1 signaling axis mediates tumor-stroma cross-talk promoting pancreatic cancer progression. **Science Advances**. https://doi.org/10.1126/sciadv.abb9200 😞
+
 1. Sharps, M. C. et al. (2020). Increased Placental Macrophages and a Pro‐inflammatory Profile in Placentas and Maternal Serum in Infants with a Decreased Growth Rate in the Third Trimester of Pregnancy. **American Journal of Reproductive Immunology**. https://doi.org/10.1111/aji.13267 😞
 
 1. Shawer, H. et al. (2020). A missense mutation of ErbB2 produces a novel mouse model of stillbirth associated with a cardiac abnormality but lacking abnormalities of placental structure. **PLOS ONE**. https://doi.org/10.1371/journal.pone.0233007 📗

docs/reference/building.rst

@@ -26,9 +26,8 @@ Step 1: Installing prerequisites
 Install a Java Development Kit (JDK)
 ====================================
 
-QuPath requires OpenJDK 14 (or later).
-Typically, the latest stable JDK is used.
-There are a few places where you can find pre-built OpenJDK binaries - a popular source is AdoptOpenJDK_.
+QuPath v0.2 requires OpenJDK 14.
+There are a few places where you can find pre-built OpenJDK binaries -- a popular source is AdoptOpenJDK_.
 
 
 .. _AdoptOpenJDK: https://adoptopenjdk.net/
@@ -39,6 +38,11 @@ There are a few places where you can find pre-built OpenJDK binaries - a popular
   It usually makes things easier if you do.
 
   If you can't (e.g. because of some other Java software needing the PATH set to something else) I'm afraid I'll leave resolving that up to you.
+
+.. warning::
+
+  At the time of writing, OpenJDK 15 is the latest version -- this is not yet suitable for building QuPath (see `issue #615 <https://github.com/qupath/qupath/issues/615>`_).
+
 
 .. warning::