2020-11-03 - HackMD

--- tags: Tuesday --- # 2020-11-03 ## Attending: Will, Dominik, Frances, Petr, Jean-Marie, Josh, Sebastien, Simon, Wilma, Kevin, Jason, Melissa, Erin, Emil, Chris, Start: 2:00 pm UK ## Accepting minutes from [<u>last meeting</u>](https://github.com/ome/meeting-minutes) ## Project Status (2-3 minutes each) - IDR - Frances: busy with CSHL meeting (Wed-Fri) - prod90 release post conference - idr0088: compound screen. Issues with compounds to be reviewed - idr0095: e. coli study - NGFF - HCS status - Ongoing specification changes - well metadata and updating plate metadata - Next focus: multiple fields (and acquisitions) this week. - Demos, freeze, I2K - Make demo videos - meeting times tricky. - Aim to freeze spec end of next week - 'tabular' data - initial support for user-defined key-value pairs for labels. - J-m: have example notebook that would be useful. - Call Follow-ups - Monash: upcoming PR for [label classes](https://github.com/ome/ome-zarr-py/issues/60) - Marseille: issue for [meshes](https://forum.image.sc/t/mesh-data-in-ome-zarr/44653/3) - Janelia: neuroglancer/n5 scaled data - [UI][ng1], [website][ng2], and especially [metadata][ng3]: `"multiscales": [ { "datasets": [ { "path": "s0", "transform": { "axes": [ "z", "y", "x" ],` - Community Call feedback - Simon: not too many clear actions, but good to sync up with the community. - J-m: message to not lose the Java community - JRS: UK Volume EM meeting trying to decide how to build national center. EMPIAR has a new grant, and they intend to support N5. (FIB-SEM, 3D tomography) "cloud-competent streaming format" - Seb: interacting with actors more actively (compared to previous model iterations). - Will: we should mine the notes for actions and show being proactive. Chris: certainly aware of who to talk to in the future. - Will: updates to bioformats2raw? Josh: yes we should keep it in sync. - Simon: for i2K? Chris: not our deadline, but Glencoe needs it soon. - Melissa: starting this week (incl. raw2ometiff). Can schedule time to talk it through. - Seb: fairly sane version early next week. We'll ping when it starting to slow down. - Releases - N/A - SA - JD trying to combine support contracts between OME & NPSC. - Glencoe - bioformats2raw with HCS - filtering millions of rows with OMERO.tables to get IDs for showing in pathviewer - - Community - Josh: are we *signing up* for an I2K tutorials? (Twitter feedback) - limited spaces / competitive - All: have a look at I2K schedule - GBI - 4th week of Jan proposal for workshop - Request from Lausanne for workshop - Jason: UKRI funding call for data-sciences training ## AOB (5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled) ## Main Topic (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 [ng3]: https://open.quiltdata.com/b/janelia-cosem/tree/jrc_hela-2/jrc_hela-2.n5/em/fibsem-uint16/attributes.json