From bc05737cc0fb94b09a46296104e67157373b932a Mon Sep 17 00:00:00 2001 From: Petr Walczysko Date: Mon, 10 Oct 2022 15:35:08 +0100 Subject: [PATCH 1/3] Fix failing images, external and internal links --- 2018/2018-05-01.md | 1 - 2019/2019-03-05.md | 2 +- 2019/2019-03-12.md | 1 - 2019/2019-05-07.md | 1 - 2019/2019-06-04.md | 2 +- 2020/2020-01-14.md | 2 +- 2020/2020-06-23.md | 4 +--- 2020/2020-07-28.md | 17 +++++++---------- 2020/2020-09-01.md | 5 ----- 2020/2020-11-03.md | 2 +- 2020/2020-11-10.md | 2 +- 2021/2021-04-27.md | 2 +- 2022/2022-03-22.md | 2 +- 13 files changed, 15 insertions(+), 28 deletions(-) diff --git a/2018/2018-05-01.md b/2018/2018-05-01.md index 467a9b8..6d93c15 100644 --- a/2018/2018-05-01.md +++ b/2018/2018-05-01.md @@ -67,7 +67,6 @@ Start: 2:00 pm - Second round of notebooks testing on-going. Looking good. - One remaining Issue with - > [https://www.ebi.ac.uk/QuickGO-Old](https://www.ebi.ac.uk/QuickGO-Old) > (current idr-py). Not related to VAE. - Next: test with prod50 diff --git a/2019/2019-03-05.md b/2019/2019-03-05.md index 3101a61..a08e81c 100644 --- a/2019/2019-03-05.md +++ b/2019/2019-03-05.md @@ -64,7 +64,7 @@ and rescheduled) > information for ROIs - Chris: - > [https://openlayers.org/en/master/examples/icon-sprite-webgl.html](https://openlayers.org/en/master/examples/icon-sprite-webgl.html) + > [https://openlayers.org](https://openlayers.org) - Even tile-based loading is likely to be too slow with many > ROIs on multiple planes. Might be acceptable with vector diff --git a/2019/2019-03-12.md b/2019/2019-03-12.md index 0ce2313..1d0a8c5 100644 --- a/2019/2019-03-12.md +++ b/2019/2019-03-12.md @@ -70,7 +70,6 @@ Start: 2:00 pm > [https://trello.com/c/nSPx2UJX/235-light-microscopy-australia-09-03-2019](https://trello.com/c/nSPx2UJX/235-light-microscopy-australia-09-03-2019) - Fun in Singapore: - > - **L**earning Upgrade diff --git a/2019/2019-05-07.md b/2019/2019-05-07.md index 47466d0..e9f8e60 100644 --- a/2019/2019-05-07.md +++ b/2019/2019-05-07.md @@ -60,7 +60,6 @@ Start: 2:00 pm - To discuss: what DB to use. -[](https://merge-ci.openmicroscopy.org/jenkins/job/Trigger/) - Glencoe (Chris) diff --git a/2019/2019-06-04.md b/2019/2019-06-04.md index 9e85709..e8fd735 100644 --- a/2019/2019-06-04.md +++ b/2019/2019-06-04.md @@ -27,7 +27,7 @@ Start: 2:00 pm > idr0062 (nuclear segmentation). ETA: next week - Josh: working to get - > [idr-ci](https://idr-ci.openmicroscopy.org/jenkins/job/Trigger) + > Jenkins job > green. Testing Bio-Formats branch of IDR - Next: web apps diff --git a/2020/2020-01-14.md b/2020/2020-01-14.md index c4e77c2..35af864 100644 --- a/2020/2020-01-14.md +++ b/2020/2020-01-14.md @@ -53,7 +53,7 @@ Start: 2:00 pm - EBI facilities are booked a year in advance - Chris: cf. PathLake’s 5-day master class on ML, etc. - > [https://warwick.ac.uk/fac/cross\_fac/pathlake/events/pathlake\_masterclass\_data](https://warwick.ac.uk/fac/cross_fac/pathlake/events/pathlake_masterclass_data) + > [https://warwick.ac.uk](https://warwick.ac.uk) - JRS: “working with labelled data”? Yeah. diff --git a/2020/2020-06-23.md b/2020/2020-06-23.md index ed2f0a2..18f87c4 100644 --- a/2020/2020-06-23.md +++ b/2020/2020-06-23.md @@ -45,8 +45,6 @@ Start: 2:00 pm - Goal is to have masks in ome-zarr, i.e. bottom portion of: - - - - Simon working on spec - Dundee team working on ‘bottom’ path above @@ -89,7 +87,7 @@ Start: 2:00 pm > for Bio-Formats. - Also, successfully using - > [native-image](https://www.graalvm.org/docs/reference-manual/native-image/) + > [native-image](https://www.graalvm.org) > (from GraalVM) to compile Bio-Formats to native code. - Doesn’t support reflection - manual effort required diff --git a/2020/2020-07-28.md b/2020/2020-07-28.md index 0e040ac..bc3e5b5 100644 --- a/2020/2020-07-28.md +++ b/2020/2020-07-28.md @@ -62,7 +62,7 @@ Start: 2:00 pm > meeting](https://docs.google.com/document/d/1kd5F97ogdiPNhLTnkei-RVR8TC8Ohpc5QSPX3KsfDrk/edit?pli=1#) - Interested in having datasets marked up with - > [Gene](https://bioschemas.org/profiles/Gene/0.7-RELEASE/) + > [Gene](https://bioschemas.org/) - Simon: ok for mapr, but the ?show= … pages won’t work great > (images, datasets) @@ -136,15 +136,15 @@ and rescheduled) - Examples (below) - - [Flight markup from gmail](#kix.xkqlh7e5b7dr) + - Flight markup from gmail - - [Fake example](#2yedp8u2kth) + - Fake example - - [Current difficulty of size](#7oslterkgyhf) + - Current difficulty of size - - [omero-marshal example](#weqiqbdudk3f) + - omero-marshal example - - [Provenance example](#b8xikqg8x6li) + - Provenance example - Open questions @@ -155,7 +155,7 @@ and rescheduled) - Cf. relationship to (bio)schemas.org ([community > meeting](https://docs.google.com/document/d/1kd5F97ogdiPNhLTnkei-RVR8TC8Ohpc5QSPX3KsfDrk/edit?pli=1#)) - - [http://metadataplus.biothings.io/about](http://metadataplus.biothings.io/about) + - [http://metadataplus.biothings.io](http://metadataplus.biothings.io - [http://crawler.biothings.io](http://crawler.biothings.io) @@ -267,9 +267,6 @@ Fake example > > “../../../.zattrs” > -> "[https://openmicroscopy.org/json-ld/v1/image.jsonld](https://openmicroscopy.org/json-ld/image.jsonld)", -> -> "[https://openmicroscopy.org/json-ld/v1/masks.jsonld](https://openmicroscopy.org/json-ld/image.jsonld)" > > \], > diff --git a/2020/2020-09-01.md b/2020/2020-09-01.md index b7ad185..eee64a5 100644 --- a/2020/2020-09-01.md +++ b/2020/2020-09-01.md @@ -154,20 +154,15 @@ Expect more discussions in public when released. Bio-Formats Total - Bio-Formats Unique - OMERO Clients Total - OMERO Clients Unique - OMERO server Unique - diff --git a/2020/2020-11-03.md b/2020/2020-11-03.md index fbc222e..7395348 100644 --- a/2020/2020-11-03.md +++ b/2020/2020-11-03.md @@ -74,5 +74,5 @@ Start: 2:00 pm UK (20-25 minutes plus 15 minutes questions max) [ng1]: http://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22position%22:%5B23650.5%2C3200.5%2C13784.5%5D%2C%22crossSectionScale%22:50%2C%22projectionScale%22:65536%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22n5://https://janelia-cosem-datasets.s3.amazonaws.com/jrc_hela-2/jrc_hela-2.n5/predictions/er_seg%22%2C%22opacity%22:0.75%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20vec3%20color%20color%28default=%5C%22blue%5C%22%29%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20void%20main%28%29%20%7BemitRGB%28color%20%2A%20ceil%28float%28getDataValue%28%29.value%5B0%5D%29%20/%204294967295.0%29%29%3B%7D%22%2C%22name%22:%22ER%22%7D%2C%7B%22type%22:%22image%22%2C%22source%22:%22n5://https://janelia-cosem-datasets.s3.amazonaws.com/jrc_hela-2/jrc_hela-2.n5/predictions/golgi_seg%22%2C%22opacity%22:0.75%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20vec3%20color%20color%28default=%5C%22cyan%5C%22%29%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20void%20main%28%29%20%7BemitRGB%28color%20%2A%20ceil%28float%28getDataValue%28%29.value%5B0%5D%29%20/%204294967295.0%29%29%3B%7D%22%2C%22name%22:%22Golgi%22%7D%2C%7B%22type%22:%22image%22%2C%22source%22:%22n5://https://janelia-cosem-datasets.s3.amazonaws.com/jrc_hela-2/jrc_hela-2.n5/predictions/mito_seg%22%2C%22opacity%22:0.75%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20vec3%20color%20color%28default=%5C%22green%5C%22%29%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20void%20main%28%29%20%7BemitRGB%28color%20%2A%20ceil%28float%28getDataValue%28%29.value%5B0%5D%29%20/%204294967295.0%29%29%3B%7D%22%2C%22name%22:%22Mitochondria%22%7D%2C%7B%22type%22:%22image%22%2C%22source%22:%22n5://https://janelia-cosem-datasets.s3.amazonaws.com/jrc_hela-2/jrc_hela-2.n5/predictions/mvb_seg%22%2C%22opacity%22:0.75%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20vec3%20color%20color%28default=%5C%22magenta%5C%22%29%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20void%20main%28%29%20%7BemitRGB%28color%20%2A%20ceil%28float%28getDataValue%28%29.value%5B0%5D%29%20/%204294967295.0%29%29%3B%7D%22%2C%22name%22:%22Endosomal%20network%22%7D%2C%7B%22type%22:%22image%22%2C%22source%22:%22n5://https://janelia-cosem-datasets.s3.amazonaws.com/jrc_hela-2/jrc_hela-2.n5/predictions/plasma_membrane_seg%22%2C%22opacity%22:0.75%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20vec3%20color%20color%28default=%5C%22orange%5C%22%29%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20void%20main%28%29%20%7BemitRGB%28color%20%2A%20ceil%28float%28getDataValue%28%29.value%5B0%5D%29%20/%204294967295.0%29%29%3B%7D%22%2C%22name%22:%22Plasma%20membrane%22%7D%2C%7B%22type%22:%22image%22%2C%22source%22:%22n5://https://janelia-cosem-datasets.s3.amazonaws.com/jrc_hela-2/jrc_hela-2.n5/predictions/vesicle_seg%22%2C%22opacity%22:0.75%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20vec3%20color%20color%28default=%5C%22red%5C%22%29%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20void%20main%28%29%20%7BemitRGB%28color%20%2A%20ceil%28float%28getDataValue%28%29.value%5B0%5D%29%20/%204294967295.0%29%29%3B%7D%22%2C%22name%22:%22Vesicles%22%7D%2C%7B%22type%22:%22image%22%2C%22source%22:%22precomputed://https://janelia-cosem-datasets.s3.amazonaws.com/jrc_hela-2/neuroglancer/fibsem/aligned_uint8_v0.precomputed%22%2C%22opacity%22:0.75%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20float%20min%20slider%28min=0%2C%20max=1%2C%20step=0.001%2C%20default=0.415%29%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20#uicontrol%20float%20max%20slider%28min=0%2C%20max=1%2C%20step=0.001%2C%20default=0.716%29%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20#uicontrol%20float%20gamma%20slider%28min=0%2C%20max=3%2C%20step=0.001%2C%20default=1%29%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20#uicontrol%20int%20invertColormap%20slider%28min=0%2C%20max=1%2C%20step=1%2C%20default=0%29%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20#uicontrol%20vec3%20color%20color%28default=%5C%22white%5C%22%29%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20float%20inverter%28float%20val%2C%20int%20invert%29%20%7Breturn%200.5%20+%20%28%282.0%20%2A%20%28-float%28invert%29%20+%200.5%29%29%20%2A%20%28val%20-%200.5%29%29%3B%7D%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20float%20normer%28float%20val%29%20%7Breturn%20%28clamp%28val%2C%20min%2C%20max%29%20-%20min%29%20/%20%28max-min%29%3B%7D%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20void%20main%28%29%20%7BemitRGB%28color%20%2A%20pow%28inverter%28normer%28toNormalized%28getDataValue%28%29%29%29%2C%20invertColormap%29%2C%20gamma%29%29%3B%7D%22%2C%22name%22:%22FIB-SEM%20Data%20%28compressed%29%22%7D%5D%2C%22selectedLayer%22:%7B%22layer%22:%22ER%22%2C%22visible%22:true%7D%2C%22crossSectionBackgroundColor%22:%22#000000%22%2C%22layout%22:%224panel%22%2C%22partialViewport%22:%5B0%2C0%2C1%2C1%5D%7D -[ng2]: https://openorganelle.janelia.org/datasets/jrc_hela-2 +[ng2]: https://openorganelle.janelia.org [ng3]: https://open.quiltdata.com/b/janelia-cosem/tree/jrc_hela-2/jrc_hela-2.n5/em/fibsem-uint16/attributes.json \ No newline at end of file diff --git a/2020/2020-11-10.md b/2020/2020-11-10.md index 71af77c..37b9ab7 100644 --- a/2020/2020-11-10.md +++ b/2020/2020-11-10.md @@ -38,7 +38,7 @@ Start: 2:00 pm UK - BioHackathon Europe 2020 (cf. https://dev.idpcentral.org/registry) - BioSchemas & Google Search-indexing - production: Organism, Gene, Compound - - draft: [Phenotypes](https://bioschemas.org/profiles/Phenotype/0.2-DRAFT/) + - draft: [Phenotypes](https://bioschemas.org/profiles) - Not yet: Cell Line - J-m: re: derived labels. Try to engage with RIKEN regarding BDML format within OME-Zarr. JRS: in the process of setting up a call to discuss with them. diff --git a/2021/2021-04-27.md b/2021/2021-04-27.md index 0fd2d2b..9b1f6cf 100644 --- a/2021/2021-04-27.md +++ b/2021/2021-04-27.md @@ -55,7 +55,7 @@ Start: 2:00 pm UK - Annotations - OME2021 - - Key note and 14 speakers confirmed ([list](www.openmicroscopy.org/events/ome-community-meeting-2021/speakers/)) + - Key note and 14 speakers confirmed ([list](www.openmicroscopy.org/events/ome-community-meeting-2021)) - Flash talks in the pipeline already - Registration to open next week - In process of sending video instructions, 1 month for content diff --git a/2022/2022-03-22.md b/2022/2022-03-22.md index 89853cc..193ec6f 100644 --- a/2022/2022-03-22.md +++ b/2022/2022-03-22.md @@ -20,7 +20,7 @@ Start: 2:00 pm UK - Ongoing search - NGFF: - - See [notes](/0aD4FfzCS5C5TWbLmk-cxA) from the extended discussion on rich metadata in OME-Zarr + - See [notes] from the extended discussion on rich metadata in OME-Zarr - Governance discussion - Django From 4ee60f009e0f7aa1f22c0b1a9d55ef2b1613c8b5 Mon Sep 17 00:00:00 2001 From: pwalczysko Date: Mon, 10 Oct 2022 15:40:20 +0100 Subject: [PATCH 2/3] Update 2022/2022-03-22.md Co-authored-by: Josh Moore --- 2022/2022-03-22.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/2022/2022-03-22.md b/2022/2022-03-22.md index 193ec6f..ca9f901 100644 --- a/2022/2022-03-22.md +++ b/2022/2022-03-22.md @@ -20,7 +20,7 @@ Start: 2:00 pm UK - Ongoing search - NGFF: - - See [notes] from the extended discussion on rich metadata in OME-Zarr + - See [notes](https://hackmd.io/0aD4FfzCS5C5TWbLmk-cxA) from the extended discussion on rich metadata in OME-Zarr - Governance discussion - Django From e08d85af479a7b8d7aab7c03831add0d3ff0bc85 Mon Sep 17 00:00:00 2001 From: Petr Walczysko Date: Mon, 10 Oct 2022 16:26:52 +0100 Subject: [PATCH 3/3] Add alt --- 2019/2019-03-12.md | 1 + 2020/2020-06-23.md | 5 +++++ 2020/2020-09-01.md | 5 +++++ 3 files changed, 11 insertions(+) diff --git a/2019/2019-03-12.md b/2019/2019-03-12.md index 1d0a8c5..85157b7 100644 --- a/2019/2019-03-12.md +++ b/2019/2019-03-12.md @@ -70,6 +70,7 @@ Start: 2:00 pm > [https://trello.com/c/nSPx2UJX/235-light-microscopy-australia-09-03-2019](https://trello.com/c/nSPx2UJX/235-light-microscopy-australia-09-03-2019) - Fun in Singapore: + > workshop in Singapore - **L**earning Upgrade diff --git a/2020/2020-06-23.md b/2020/2020-06-23.md index 18f87c4..4c08d07 100644 --- a/2020/2020-06-23.md +++ b/2020/2020-06-23.md @@ -45,6 +45,11 @@ Start: 2:00 pm - Goal is to have masks in ome-zarr, i.e. bottom portion of: +<<<<<<< HEAD +======= + - zarr schema + +>>>>>>> 0a37477... Add alt - Simon working on spec - Dundee team working on ‘bottom’ path above diff --git a/2020/2020-09-01.md b/2020/2020-09-01.md index eee64a5..4d6d142 100644 --- a/2020/2020-09-01.md +++ b/2020/2020-09-01.md @@ -154,15 +154,20 @@ Expect more discussions in public when released. Bio-Formats Total +BF Total stats Bio-Formats Unique +BF Unique stats OMERO Clients Total +Clients Total stats OMERO Clients Unique +Clients Unique stats OMERO server Unique +Server unique stats