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IDR/celery-example 3

Example of using Celery as a lightweight distributed computing framework

joshmoore/agilo-hooks 3

Modification to the default post-commit hooks in agilo (http://agile42.com/cms/pages/agilo/) to support multi-repositories. Parts of this patch were submitted as https://dev.agile42.com/ticket/1086

cneves/openmicroscopy 2

OME (Open Microscopy Environment) develops open-source software and data format standards for the storage and manipulation of biological light microscopy data. A joint project between universities, research establishments and industry in Europe and the USA, OME has over 20 active researchers with strong links to the microscopy community. Funded by private and public research grants, OME has been a major force on the international microscopy stage since 2000.

ctrueden/bioformats 2

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment (particularly UW-Madison LOCI and Glencoe Software). Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

avalentino/PyTables 1

PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. This a git-svn clone of the Pro version recently released under a BSD-flavored license by Francesc Alted!

imagej/imagej-updater-tests 1

Docker-based test infrastructure for ImageJ Updater

joshmoore/aicsimageio 0

Delayed Parallel Image Reading for Microscopy Images in Python

joshmoore/ansible 0

Ansible is a radically simple IT automation platform that makes your applications and systems easier to deploy. Avoid writing scripts or custom code to deploy and update your applications— automate in a language that approaches plain English, using SSH, with no agents to install on remote systems.

Pull request review commentome/omero-insight

MDE: Feature parse ontology

+/*+ * Copyright (C) <2016-2019> University of Dundee & Open Microscopy Environment.+ * All rights reserved.+ *+ * This program is free software; you can redistribute it and/or modify+ * it under the terms of the GNU General Public License as published by+ * the Free Software Foundation; either version 2 of the License, or+ * (at your option) any later version.+ *+ * This program is distributed in the hope that it will be useful,+ * but WITHOUT ANY WARRANTY; without even the implied warranty of+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+ * GNU General Public License for more details.+ *+ * You should have received a copy of the GNU General Public License along+ * with this program; if not, write to the Free Software Foundation, Inc.,+ * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.+ */+package org.openmicroscopy.shoola.agents.fsimporter.mde.util.parser;++import com.fasterxml.jackson.databind.JsonNode;++import java.io.UnsupportedEncodingException;+import java.net.HttpURLConnection;+import java.net.URL;+import java.net.URLEncoder;+import java.util.ArrayList;++/**+ * 1/8/2021+ *+ * @author Susanne Kunis<susannekunis at gmail dot com>+ *+ *  doc: https://www.ebi.ac.uk/ols/docs/api+ **/+public class OLS_Parser extends OntologyParser {+    //static final String REST_URL = "https://www.ebi.ac.uk/ols";++    public OLS_Parser(String ontology_restapi_url) {+        super(ontology_restapi_url);+    }++    @Override+    protected String formatURL(String ontology_acronym, String termID_href) {+        String id_utf8 = null;+        // has to be double URL encoded (see https://www.ebi.ac.uk/ols/docs/api :Term)+        // or use : "?iri="+URLEncoder.encode(termID_href, "UTF-8");+        try{+            id_utf8= "/"+ URLEncoder.encode(URLEncoder.encode(termID_href,"UTF-8"),"UTF-8");+        }catch (UnsupportedEncodingException e) {+            e.printStackTrace();

capture in the log?

sukunis

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Pull request review commentome/omero-insight

MDE: Feature parse ontology

+/*+ * Copyright (C) <2016-2019> University of Dundee & Open Microscopy Environment.+ * All rights reserved.+ *+ * This program is free software; you can redistribute it and/or modify+ * it under the terms of the GNU General Public License as published by+ * the Free Software Foundation; either version 2 of the License, or+ * (at your option) any later version.+ *+ * This program is distributed in the hope that it will be useful,+ * but WITHOUT ANY WARRANTY; without even the implied warranty of+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+ * GNU General Public License for more details.+ *+ * You should have received a copy of the GNU General Public License along+ * with this program; if not, write to the Free Software Foundation, Inc.,+ * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.+ */+package org.openmicroscopy.shoola.agents.fsimporter.mde.util.parser;++import com.fasterxml.jackson.databind.JsonNode;++import java.io.UnsupportedEncodingException;+import java.net.HttpURLConnection;+import java.net.URL;+import java.net.URLEncoder;+import java.util.ArrayList;++/**+ * 1/8/2021+ *+ * @author Susanne Kunis<susannekunis at gmail dot com>+ *+ *  output inside a browser see for example: https://data.bioontology.org/ontologies/BRO/+ *  see also: https://github.com/molgenis/ontocat/blob/master/ontoCAT/src/uk/ac/ebi/ontocat/bioportal/BioportalOntologyService.java+ *  doc: https://www.bioontology.org/wiki/CTS2_BioPortal_Rest_mapping#Get_a_specific_ontology_based_on_a_version_id+ *  doc: https://data.bioontology.org/documentation+ **/+public class BioPortal_Parser extends OntologyParser {+    //static final String REST_URL = "http://data.bioontology.org";+    static final String API_KEY = "c6ae1b27-9f86-4e3c-9dcf-087e1156eabe";

shouldn't that be moved to the config file too?

sukunis

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issue commentimageio/imageio

imread does not detect .tga format

I can reproduce this, and traced it down to here: https://github.com/imageio/imageio/blob/2ce79b91c5415dd3069be1050d979a5bfd4245e1/imageio/plugins/pillow.py#L100-L107

The Image.OPEN[self.plugin_id] returns a factory, but not an accept function (a function that can be given the first bytes to validate that it in fact a file that can be read). This is the case for 6 formats (on my current install of Pillow).

At the moment, the can_read() method must return either True or False. But in this case it's more of a "maybe" or "likely". If we'd return True here, there is a chance that the Pillow plugin will fail reading it afterall, and we have not given other plugins a chance. The downside is that for these formats, users need to specify the plugin explicitly.

That said, I think it may be reasonable to change this behavior, especially for the Pillow plugin which is the best option we have in many cases. The safest way to do this would be an allowlist for (at least) tga. What do you think?

djhoese

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issue commentNEUBIAS/training-resources

Example data for advanced workflow

image

tischi

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issue commentNEUBIAS/training-resources

Example data for advanced workflow

@tischi, and @seadaisy, I uploaded PLK1 example images (xy_8bit__nuclei_PLK1_control, + inhibition). I think they are noisy enough that a simple threshold gives a rough boundary so either one needs raw image filtering or binary operations to clean up.

If @seadaisy wants to acquire some additional data it could be nice. For instance the KiF11 one could also look at the tubulin phenotype (intensity values). In principle one would need a 2D image (quite small 500-600 pixels) with not too many nuclei so that we can easily separate them. One can acquire images at different quality (one rather low but still visible and a good image in both channels). For an LSM for instance by reducing the line-averaging, laser-power, or detector gain. Thanks

Antonio

tischi

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push eventNEUBIAS/training-resources

manerotoni

commit sha ca12d7e8f112d1f2197122d7d37e4f618a4cc4b6

add images for workflow

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manerotoni

commit sha 436c1624beef3401f1604eaa11b70781fa63149b

Merge branch 'master' into workflow_2d_noisyimages

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Antonio Politi

commit sha 42681c0b19577d1ff72f082ed3a71d96ba098d53

Merge pull request #98 from manerotoni/workflow_2d_noisyimages Workflow 2d noisyimages

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startedindy-lab/predikon-lib

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pull request commentome/design

OME005: navigation, state-of-art and resolution cleanup

All the relevant internal and external parties have been pointed to these changes. So far no objection has been raised either publicly or privately. I will leave a few more days for comments and then merge this PR in order to resolve the claims made on the image.sc.

sbesson

comment created time in 22 minutes

pull request commentome/omero-cli-render

Add batchset for rendering a hierarchy of containers (single file)

Adding support for other containers (screen, plate well) and images definitely makes sense. Ideally we'd have a simple graph-query method to obtain things like

  • Project[name=p1]/Dataset[name=d1]
  • Project[name=p2]/Dataset[name=d2]/Image[name=i2]
  • Plate[name=p3]/Image[name=i3]

but we don't, so it'll require some repetitive HQL- maybe that HQL could go into the BlitzGateway though?

manics

comment created time in 27 minutes

Pull request review commentome/omero-cli-render

Add batchset for rendering a hierarchy of containers (single file)

     # be updated individually. """ +BATCHSET_HELP = """Set rendering settings from a hierachy of rendering+    definitions corresponding to an OMERO container hierarchy.++    'projects' and 'datasets' are supported as top level containers, 'name'+    must be provided.+    If multiple containers have the same name they will all be processed.+    Top level keys beginning with '_' are ignored, so they could for example+    be used as YAML anchors.++    Definitions can be applied to projects, datasets, or datasets in projects.++    'renderdef' is a rendering definition as passed to 'set', except that

I think keepin the renderdef self-contained will make this spec easier to update, otherwise when adding a key to either the container definition or the renderdef spec you'll need to consider future conflicts or potential confusion.

In addition keeping the renderdef under it's own key means this could potentially be extended to handle other metadata e.g. for setting tags or other annotations.

manics

comment created time in 30 minutes

Pull request review commentome/omero-cli-render

Add batchset for rendering a hierarchy of containers (single file)

     # be updated individually. """ +BATCHSET_HELP = """Set rendering settings from a hierachy of rendering+    definitions corresponding to an OMERO container hierarchy.++    'projects' and 'datasets' are supported as top level containers, 'name'+    must be provided.+    If multiple containers have the same name they will all be processed.+    Top level keys beginning with '_' are ignored, so they could for example+    be used as YAML anchors.++    Definitions can be applied to projects, datasets, or datasets in projects.++    'renderdef' is a rendering definition as passed to 'set', except that+    'version' is omitted.

I thought it would simplify things if we avoided mixed versioning though that's probably not a major problem to support. You're right that it should be specified somewhere though, so the question is should we require the version

  • as part of every renderdef
  • as part of the top-level version for this file i.e. version indicates the version of the renderdef spec + the version of this hierarchical definition
  • in a dedicated top-level renderdef_version key And if renderdef has it's own version indicator how do we version this hierarchy spec?
manics

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MemberEvent

issue commentopenjournals/joss-reviews

[REVIEW]: Visualization of Multi-Dimensional Data - The data-slicer Package

@sabinomaggi, @Chilipp I've just re-invited you to this review to make sure you have full access.

whedon

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issue commentopenjournals/joss-reviews

[REVIEW]: Visualization of Multi-Dimensional Data - The data-slicer Package

OK, the reviewer has been re-invited.

@chilipp please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

whedon

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issue commentopenjournals/joss-reviews

[REVIEW]: Visualization of Multi-Dimensional Data - The data-slicer Package

@whedon re-invite @Chilipp as reviewer

whedon

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issue commentopenjournals/joss-reviews

[REVIEW]: Visualization of Multi-Dimensional Data - The data-slicer Package

OK, the reviewer has been re-invited.

@sabinomaggi please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

whedon

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issue commentopenjournals/joss-reviews

[REVIEW]: Visualization of Multi-Dimensional Data - The data-slicer Package

@whedon re-invite @sabinomaggi as reviewer

whedon

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issue commentopenjournals/joss-reviews

[PRE REVIEW]: NLSIG-COVID19Lab

It looks like a very interesting package @somefunAgba . However, I only have access to Matlab 2014b with a limited set of packages? What Matlab version and what packages does your package need?

whedon

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manerotoni

commit sha 3b7ba6e60404ac7bd2cd0f00e7cf3d314375cded

Additional images for connectivity

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Antonio Politi

commit sha 908c23f901f6886906c413a4e8ea18235cc7fcdd

Merge pull request #97 from manerotoni/cca_extraimages Additional images for connectivity

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issue closedNEUBIAS/training-resources

Connected components

Add explanation (with image) about the different connectivities.

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tischi

issue commentNEUBIAS/training-resources

Connected components

Done

tischi

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issue commentmobie/mobie

Grid view of many sources

Thanks a lot! I will only have time in two weeks from now to work on it. In fact, I got a little heart attack getting an e-mail reminder right now that I should give a presentation about MoBIE next week during a NEuBIAS webinar next week Wednesday afternoon! Would you be motivated to contribute a little bit?!!! I will send a mail.

tischi

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Snoopy Crime Cop

commit sha 6d7553520a9a9440daa8d8f7e77c3c3d9058f695

merge develop -Dnone -Ihotfix -Ssuccess-only Repository: openmicroscopy/ome-documentation Excluded PRs: - PR 2167 kkoz 'Add slice examples to Tables docs' (user: kkoz) - PR 2136 dgault 'Temporarily add imagej.net to ignore list' (user: dgault) Already up-to-date. Generated by OMERO-docs#578 (https://latest-ci.openmicroscopy.org/jenkins/job/OMERO-docs/578/)

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issue commentNEUBIAS/training-resources

Example data for advanced workflow

Hi both, If needed, we have a plate with fixed cells with PLK1 and KIF11 phenotypes (cells have a nuclear marker and labeled tubulin). I could take images in the condition you need for your teaching. All the best Sabine

tischi

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merge master -Dnone -Ihotfix -Ssuccess-only Repository: ome/scripts Excluded PRs: - PR 180 will-moore 'bom fix populate metadata' (user: will-moore) - PR 176 will-moore 'readthedocs build with autodoc' (user: will-moore) - PR 173 will-moore 'ROI export with Well ID' (user: will-moore) - PR 103 joshmoore 'Script for calculating min/max' (user: joshmoore) Already up-to-date. Generated by OMERO-plugins-push#544 (https://latest-ci.openmicroscopy.org/jenkins/job/OMERO-plugins-push/544/)

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Josh Moore

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Merge pull request #49 from jburel/actions Actions

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merge master -Dorg -Snone: PR 17 (Override omero.db.name (fix #16))

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Snoopy Crime Cop

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merge master -Dorg -Snone Repository: ome/omero-server-docker Already up-to-date. Merged PRs: - PR 2 dpwrussell 'Enable public user' - PR 17 joshmoore 'Override omero.db.name (fix #16)' - PR 39 manics 'Add infrastructure for a server extras image' Conflicting PRs (not included): - PR 19 joshmoore 'SQL backup/restore (WIP)' - PR 21 joshmoore 'Auto import, figure, wheel, etc.' Generated by DOCKER-merge#1354 (https://ci.openmicroscopy.org/job/DOCKER-merge/1354/)

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