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Fix failing images, external and internal links #5

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Oct 10, 2022
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Fix failing images, external and internal links #5

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bc05737
Fix failing images, external and internal links
pwalczysko Oct 10, 2022
4ee60f0
Update 2022/2022-03-22.md
pwalczysko Oct 10, 2022
e08d85a
Add alt
pwalczysko Oct 10, 2022
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1 change: 0 additions & 1 deletion 2018/2018-05-01.md
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion 2019/2019-03-05.md
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion 2019/2019-03-12.md
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Expand Up @@ -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" />
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These images are present, but I'm not sure why they aren't being found:

commit 9806d5586726db3bf29d4496e83c4bb367cecf6c
Author: jmoore <[email protected]>
Date:   Tue Sep 29 21:40:55 2020 +0200

    More image fixes

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Based on https://github.com/ome/www.openmicroscopy.org/actions/runs/3219662885/jobs/5265329745, the issue with this image is the absence of an alt attribute rather than the fact the source is missing.

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Yes, @sbesson is right, @joshmoore I am removing them because I do not have an easy solution about adding an alt attribute. It seems that this needs javascript abilities, or somesuch ?

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That should be as easy as adding alt="some description" to the <img .../> block.

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thanks @joshmoore fixed in e08d85a

> <img src="../images/2019-03-12-image1.png" alt="workshop in Singapore" style="width:2.95313in;height:1.65849in" />

- **<u>L</u>**earning Upgrade

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1 change: 0 additions & 1 deletion 2019/2019-05-07.md
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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)

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2 changes: 1 addition & 1 deletion 2019/2019-06-04.md
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion 2020/2020-01-14.md
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Expand Up @@ -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.

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7 changes: 5 additions & 2 deletions 2020/2020-06-23.md
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Expand Up @@ -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
Expand Down Expand Up @@ -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
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17 changes: 7 additions & 10 deletions 2020/2020-07-28.md
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Expand Up @@ -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)
Expand Down Expand Up @@ -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

Expand All @@ -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)

Expand Down Expand Up @@ -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)"
>
> \],
>
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10 changes: 5 additions & 5 deletions 2020/2020-09-01.md
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Expand Up @@ -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" />
2 changes: 1 addition & 1 deletion 2020/2020-11-03.md
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Expand Up @@ -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
2 changes: 1 addition & 1 deletion 2020/2020-11-10.md
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Expand Up @@ -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.

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2 changes: 1 addition & 1 deletion 2021/2021-04-27.md
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion 2022/2022-03-22.md
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Expand Up @@ -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
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