Merge pull request #5 from ome/fix-failures

Fix failing images, external and internal links
ome · Oct 10, 2022 · 2a9044d · 2a9044d
2 parents 0d6b494 + e08d85a
commit 2a9044d
Show file tree

Hide file tree

Showing 13 changed files with 25 additions and 27 deletions.
diff --git 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
-            > [<u>https://www.ebi.ac.uk/QuickGO-Old</u>](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
@@ -64,7 +64,7 @@ and rescheduled)
         > information for ROIs
 
     -   Chris:
-        > [<u>https://openlayers.org/en/master/examples/icon-sprite-webgl.html</u>](https://openlayers.org/en/master/examples/icon-sprite-webgl.html)
+        > [<u>https://openlayers.org</u>](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
@@ -70,7 +70,7 @@ Start: 2:00 pm
         > [<u>https://trello.com/c/nSPx2UJX/235-light-microscopy-australia-09-03-2019</u>](https://trello.com/c/nSPx2UJX/235-light-microscopy-australia-09-03-2019)
 
     -   Fun in Singapore:
-        > <img src="../images/2019-03-12-image1.png" style="width:2.95313in;height:1.65849in" />
+        > <img src="../images/2019-03-12-image1.png" alt="workshop in Singapore" style="width:2.95313in;height:1.65849in" />
 
     -   **<u>L</u>**earning Upgrade
 

diff --git 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.
 
-[<img src="../images/2019-05-07-image1.png" style="width:3.81579in;height:2.72396in" />](https://merge-ci.openmicroscopy.org/jenkins/job/Trigger/)
 
 -   Glencoe (Chris)
 

diff --git 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
-            > [<u>idr-ci</u>](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
@@ -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.  
-            > [<u>https://warwick.ac.uk/fac/cross\_fac/pathlake/events/pathlake\_masterclass\_data</u>](https://warwick.ac.uk/fac/cross_fac/pathlake/events/pathlake_masterclass_data)
+            > [<u>https://warwick.ac.uk</u>](https://warwick.ac.uk)
 
             -   JRS: “working with labelled data”? Yeah.
 

diff --git a/2020/2020-06-23.md b/2020/2020-06-23.md
@@ -45,8 +45,11 @@ Start: 2:00 pm
 
         -   Goal is to have masks in ome-zarr, i.e. bottom portion of:
 
-        -   <img src="../images/2020-06-23-image1.png" style="width:3.34896in;height:1.55926in" />
+<<<<<<< HEAD
+=======
+        -   <img src="../images/2020-06-23-image1.png" alt="zarr schema" style="width:3.34896in;height:1.55926in" />
 
+>>>>>>> 0a37477... Add alt
         -   Simon working on spec
 
         -   Dundee team working on ‘bottom’ path above
@@ -89,7 +92,7 @@ Start: 2:00 pm
             > for Bio-Formats.
 
         -   Also, successfully using
-            > [<u>native-image</u>](https://www.graalvm.org/docs/reference-manual/native-image/)
+            > [<u>native-image</u>](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
@@ -62,7 +62,7 @@ Start: 2:00 pm
         > meeting</u>](https://docs.google.com/document/d/1kd5F97ogdiPNhLTnkei-RVR8TC8Ohpc5QSPX3KsfDrk/edit?pli=1#)
 
         -   Interested in having datasets marked up with
-            > [<u>Gene</u>](https://bioschemas.org/profiles/Gene/0.7-RELEASE/)
+            > [<u>Gene</u>](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)
 
-        -   [<u>Flight markup from gmail</u>](#kix.xkqlh7e5b7dr)
+        -   Flight markup from gmail
 
-        -   [<u>Fake example</u>](#2yedp8u2kth)
+        -   Fake example
 
-        -   [<u>Current difficulty of size</u>](#7oslterkgyhf)
+        -   Current difficulty of size
 
-        -   [<u>omero-marshal example</u>](#weqiqbdudk3f)
+        -   omero-marshal example
 
-        -   [<u>Provenance example</u>](#b8xikqg8x6li)
+        -   Provenance example
 
     -   Open questions
 
@@ -155,7 +155,7 @@ and rescheduled)
     -   Cf. relationship to (bio)schemas.org ([<u>community
         > meeting</u>](https://docs.google.com/document/d/1kd5F97ogdiPNhLTnkei-RVR8TC8Ohpc5QSPX3KsfDrk/edit?pli=1#))
 
-        -   [<u>http://metadataplus.biothings.io/about</u>](http://metadataplus.biothings.io/about)
+        -   [<u>http://metadataplus.biothings.io</u>](http://metadataplus.biothings.io
 
         -   [<u>http://crawler.biothings.io</u>](http://crawler.biothings.io)
 
@@ -267,9 +267,6 @@ Fake example
 >
 > “../../../.zattrs”
 >
-> "[<u>https://openmicroscopy.org/json-ld/v1/image.jsonld</u>](https://openmicroscopy.org/json-ld/image.jsonld)",
->
-> "[<u>https://openmicroscopy.org/json-ld/v1/masks.jsonld</u>](https://openmicroscopy.org/json-ld/image.jsonld)"
 >
 > \],
 >

diff --git a/2020/2020-09-01.md b/2020/2020-09-01.md
@@ -154,20 +154,20 @@ Expect more discussions in public when released.
 
 Bio-Formats Total
 
-<img src="../images/2020-09-01/image3.png" style="width:7.26772in;height:8.70833in" />
+<img src="../images/2020-09-01/image3.png" alt="BF Total stats" style="width:7.26772in;height:8.70833in" />
 
 Bio-Formats Unique
 
-<img src="../images/2020-09-01/image4.png" style="width:7.26772in;height:9.5in" />
+<img src="../images/2020-09-01/image4.png" alt="BF Unique stats" style="width:7.26772in;height:9.5in" />
 
 OMERO Clients Total
 
-<img src="../images/2020-09-01/image2.png" style="width:7.26772in;height:8.63889in" />
+<img src="../images/2020-09-01/image2.png" alt="Clients Total stats" style="width:7.26772in;height:8.63889in" />
 
 OMERO Clients Unique
 
-<img src="../images/2020-09-01/image5.png" style="width:7.26772in;height:9.26389in" />
+<img src="../images/2020-09-01/image5.png" alt="Clients Unique stats" style="width:7.26772in;height:9.26389in" />
 
 OMERO server Unique
 
-<img src="../images/2020-09-01/image1.png" style="width:7.26772in;height:9.47222in" />
+<img src="../images/2020-09-01/image1.png" alt="Server unique stats" style="width:7.26772in;height:9.47222in" />
diff --git 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
diff --git 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
@@ -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
@@ -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](https://hackmd.io/0aD4FfzCS5C5TWbLmk-cxA) from the extended discussion on rich metadata in OME-Zarr
   - Governance discussion
 
 - Django
Original file line number	Diff line number	Diff line change
Expand Up		@@ -60,7 +60,6 @@ Start: 2:00 pm

		- To discuss: what DB to use.

		[<img src="../images/2019-05-07-image1.png" style="width:3.81579in;height:2.72396in" />](https://merge-ci.openmicroscopy.org/jenkins/job/Trigger/)

		- Glencoe (Chris)

Expand Down