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BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230616T090000
DTEND;TZID=Europe/Stockholm:20230616T100000
DTSTAMP:20260526T040033
CREATED:20230607T155128Z
LAST-MODIFIED:20230607T155437Z
UID:10000905-1686906000-1686909600@www.scilifelab.se
SUMMARY:steinbock: a toolkit for processing multiplexed tissue images
DESCRIPTION:Multiplexed imaging enables the simultaneous spatial profiling of dozens of biological molecules in tissues at single-cell resolution. Extracting biologically relevant information from multi-channel images involves computational tasks such as image segmentation and feature extraction\, which can pose technology-specific challenges to experimental biologists lacking adequate bioinformatics training. \n\n\n\nIn this hands-on webinar\, we will showcase steinbock\, a computational toolkit for batch-processing multiplexed tissue images using established tools and approaches\, without the need for additional programming. The steinbock toolkit can be used to rapidly extract spatially resolved single-cell data for downstream statistical analysis\, interfacing with popular analysis environments such as Python or R/Bioconductor. It is an essential part of the Analysis workflow for IMC data (Bodenmiller Lab\, ETH Zurich/University of Zurich) and further information can be found in the steinbock online documentation. \n\n\n\nThe webinar will be given by Jonas Windhager\, the creator and former maintainer of steinbock\, who recently joined the SciLifeLab BioImage Informatics Facility. It is aimed at experimental biologists with an interest in image analysis and is scheduled to last one hour or longer\, depending on interest. \n\n\n\nregistration
URL:https://www.scilifelab.se/event/steinbock-a-toolkit-for-processing-multiplexed-tissue-images/
LOCATION:Online event via Zoom
CATEGORIES:Event
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/06/steinbock-logo.png
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230404T080000
DTEND;TZID=Europe/Stockholm:20230509T170000
DTSTAMP:20260526T040033
CREATED:20230307T080222Z
LAST-MODIFIED:20230307T091417Z
UID:10000828-1680595200-1683651600@www.scilifelab.se
SUMMARY:Digital image analysis for scientific applications
DESCRIPTION:Language of instruction: EnglishCourse period: 2023-04-11– 2023-05-09Course structure: The course will be hybrid on site and via zoom to facilitate remote participation. For computer exercises we encourage on-site participation for best possible support\, but will do our best to also support those participating remotely. \n\n\n\nRECOMMENDED PREREQUISITES\n\n\n\nThe target group is PhD students from all subjects where digital image analysis (IA)  is used as a research tool. No previous experience in IA is required from the course participants\, but an interest in its potential as a tool in their own research is important. The course can be followed with a basic knowledge of mathematics (corresponding to upper‐ secondary level entry requirements) and basic computer skills. \n\n\n\nLEARNING OUTCOMES\n\n\n\n\nexplain fundamental notions of IA\, such as digitization\, image enhancement\, segmentation\, and feature extraction and classification;\n\n\n\ncritically evaluate several different methods for image segmentation\, compression\, distance computation\, frequency analysis\, etc.\n\n\n\nuse software to apply and evaluate algorithms for solving image analysis problems;\n\n\n\nanalyze and plan the steps necessary to solve a realistic image analysis problem;\n\n\n\ngive examples of applications in research and industry where image analysis is used.\n\n\n\n\nLEARNING OUTCOMES FOR DOCTORAL DEGREE \n\n\n\nThe course participants will practice their ability to perform scientific analyses\, find and test appropriate IA methods\, and present and discuss their scientific results. \n\n\n\nCOURSE CONTENTS\n\n\n\nThe focus of the course is on reaching a broad understanding of IA and a basic understanding of the theory and algorithms behind the IA methods. The course starts with basic IA methods and computer exercises\, including IA research methodology and IA research ethics. Modern techniques based on Artificial Intelligence will also be discussed in relation to the classical approaches.  \n\n\n\nINSTRUCTION\n\n\n\nThe pedagogical approach will combine traditional lectures\, examples of real life applications and hands-on exercises. We also use a flipped classroom approach based on our pre-recorded course material which enables participants to prepare for discussions and exercises. \n\n\n\nASSESSMENT\n\n\n\nThe examination will be divided into two parts: \n\n\n\n\ncompleted four computer exercises\, which enable the course participants to both get familiar with the interfaces of common software and to solve realistic image processing problems\,\n\n\n\na written exam\n\n\n\n\nCompleted exercises and passing written exam gives 5hp.  \n\n\n\nCOURSE EXAMINER\n\n\n\nCarolina Wählby\, carolina.wahlby@it.uu.se together with other seniors involved in the BioImage Informatics Unit of SciLifeLab (https://www.scilifelab.se/units/bioimage-informatics/)\, the Image analysis node of the National Microscopy Infrastructure (http://www.nmisweden.se/)\, and the Centre for Image Analysis (https://www.cb.uu.se/) hosted at the Dept. of Information Technology. \n\n\n\nDEPARTMENT WITH MAIN RESPONSIBILITY\n\n\n\nDept. of Information Technology \n\n\n\nCONTACT PERSON/S \n\n\n\nCarolina Wählby\, carolina.wahlby@it.uu.se \n\n\n\nAPPLICATION\n\n\n\nSubmit the application for admission to: carolina.wahlby@it.uu.seSubmit the application not later than: March 25\, 2023
URL:https://www.scilifelab.se/event/digital-image-analysis-for-scientific-applications/
LOCATION:Uppsala University\, Uppsala\, Sweden
CATEGORIES:Course
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2023/03/Course.jpg
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230214T100000
DTEND;TZID=Europe/Stockholm:20230214T120000
DTSTAMP:20260526T040033
CREATED:20230118T154441Z
LAST-MODIFIED:20230213T082420Z
UID:10000787-1676368800-1676376000@www.scilifelab.se
SUMMARY:TissUUmaps 3: Interactive visualization and quality assessment of large-scale spatial omics
DESCRIPTION:We present TissUUmaps\, browser-based tool for GPU-accelerated visualization and interactive exploration of tens of millions of datapoints overlaying tissue samples. Users can visualize markers and regions\, explore spatial statistics and quantitative analyses of tissue morphology\, and assess the quality of decoding in situ transcriptomics data. TissUUmaps provides instant multi-resolution image viewing\, can be customized\, shared\, and also integrated in Jupyter Notebooks. It is also possible to directly connect spatial markers with markers in feature space\, such as UMAP plots\, to interactively relate feature space with physical space. TissUUmaps was created in collaboration between BIIF and the Wählby lab. You can read more about it and test the software on its web page: https://tissuumaps.github.io/ \n\n\n\nDuring the seminar\, we will specifically showcase new features of TissUUmaps 3.1\, such as: \n\n\n\n\nHDF5 / AnnData files loading\n\n\n\nNetwork diagram visualization\n\n\n\nMultiple datasets displayed on a grid\n\n\n\nPlugin engine\n\n\n\n\nThe webinar will be given by Christophe Avenel and Fredrik Nysjö. \n\n\n\n 
URL:https://www.scilifelab.se/event/tissuumaps-3-interactive-visualization-and-quality-assessment-of-large-scale-spatial-omics-2/
LOCATION:Online event via Zoom
CATEGORIES:Event
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2023/01/tissuumaps_webinar.jpg
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20221011T090000
DTEND;TZID=Europe/Stockholm:20221011T120000
DTSTAMP:20260526T040033
CREATED:20220920T161925Z
LAST-MODIFIED:20220927T123606Z
UID:10000686-1665478800-1665489600@www.scilifelab.se
SUMMARY:BioImage Analysis support – Call4Help
DESCRIPTION:Every month (mainly on Tuesdays\, but there might be exceptions) the BioImage Informatics Facility together with microscopy expert Sylvie Le Guyader (LCI\, Karolinska Institutet) organizes a Call4Help session. The aim is to offer combined expertise towards microscopy and bioimage analysis. All researchers from Swedish institutes can participate. \nThe ideal timepoint to join the Call4Help session is when a researcher has performed pilot experiments and has tried out first analysis approaches – but before having recorded hundreds of images. Combining BIIF’s expertise in BioImage Analysis with microscopy expertise we can discuss ways to record the images that allow analysis afterwards. We will discuss different analysis approaches using mainly open-source software (Fiji\, CellProfiler\, QuPath\, Ilastik\, KNIME)\, but also commercial systems\, if needed (Imaris). \nThe Call4Help session format has been introduced to the BioImage Analysis community by NEUBIAS and ScopeM. \n  \nHow to participate? \nStep1: \nPrepare a short presentation (5-7 min)  – use the following template for your presentation: \nhttp://bit.ly/BIIF_C4H_slideTemplate \nSlide template by NEUBIAS/ScopeM \nStep2: \n\na) Upload your presentation \n\n  \nUpload your presentation to a drive of your choice. You can also use our Call4Help google drive. Note that files shared on our Call4Help drive will be available to everyone until the session is over. \nhttp://bit.ly/BIIF_C4H_Drive \n\nb) Upload example images for testing. \n\nUpload example images for testing either to the drive of your choice or our Call4Help google drive above. \nhttp://bit.ly/BIIF_C4H_Drive \n\nc) Register by filling out the registration form: \n\nhttp://bit.ly/BIIF_C4H_Registration \nStep 3: \nJoin the zoom-session. \nIf your problem is selected for presentation\, you will get a time-slot of 30 – 60 minutes within the session. \n  \nWhat are the Deadlines \nSubmission of a problem and upload of example data: Friday the week before the session. \nNotification about participation: The day before the session. \nNext Call4Help session: Tuesday\, October 11\, 2022\, 9.00-12.00 \nDeadline for application: Friday\, October 7\, 2022
URL:https://www.scilifelab.se/event/bioimage-analysis-support-call4help-7/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220823T090000
DTEND;TZID=Europe/Stockholm:20220823T120000
DTSTAMP:20260526T040033
CREATED:20220622T145418Z
LAST-MODIFIED:20220622T145419Z
UID:10000637-1661245200-1661256000@www.scilifelab.se
SUMMARY:BioImage Analysis support – Call4Help
DESCRIPTION:Every month (mainly on Tuesdays\, but there might be exceptions) the BioImage Informatics Facility together with microscopy expert Sylvie Le Guyader (LCI\, Karolinska Institutet) organizes a Call4Help session. The aim is to offer combined expertise towards microscopy and bioimage analysis. All researchers from Swedish institutes can participate. \nThe ideal timepoint to join the Call4Help session is when a researcher has performed pilot experiments and has tried out first analysis approaches – but before having recorded hundreds of images. Combining BIIF’s expertise in BioImage Analysis with microscopy expertise we can discuss ways to record the images that allow analysis afterwards. We will discuss different analysis approaches using mainly open-source software (Fiji\, CellProfiler\, QuPath\, Ilastik\, KNIME)\, but also commercial systems\, if needed (Imaris). \nThe Call4Help session format has been introduced to the BioImage Analysis community by NEUBIAS and ScopeM. \n  \nHow to participate? \nStep1: \nPrepare a short presentation (5-7 min)  – use the following template for your presentation: \nhttp://bit.ly/BIIF_C4H_slideTemplate \nSlide template by NEUBIAS/ScopeM \nStep2: \n\na) Upload your presentation \n\n  \nUpload your presentation to a drive of your choice. You can also use our Call4Help google drive. Note that files shared on our Call4Help drive will be available to everyone until the session is over. \nhttp://bit.ly/BIIF_C4H_Drive \n\nb) Upload example images for testing. \n\nUpload example images for testing either to the drive of your choice or our Call4Help google drive above. \nhttp://bit.ly/BIIF_C4H_Drive \n\nc) Register by filling out the registration form: \n\nhttp://bit.ly/BIIF_C4H_Registration \nStep 3: \nJoin the zoom-session. \nIf your problem is selected for presentation\, you will get a time-slot of 30 – 60 minutes within the session. \n  \nWhat are the Deadlines \nSubmission of a problem and upload of example data: Friday the week before the session. \nNotification about participation: The day before the session. \nNext Call4Help session: Tuesday\, August 23\, 2022\, 9.00-12.00 \nDeadline for application: Friday\, August 19\, 2022
URL:https://www.scilifelab.se/event/bioimage-analysis-support-call4help-6/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220607T090000
DTEND;TZID=Europe/Stockholm:20220607T120000
DTSTAMP:20260526T040033
CREATED:20220121T160255Z
LAST-MODIFIED:20220121T160256Z
UID:10000515-1654592400-1654603200@www.scilifelab.se
SUMMARY:BioImage Analysis support - Call4Help
DESCRIPTION:Every 1st week of the month (mainly on Tuesdays\, but there might be exceptions) the BioImage Informatics Facility together with microscopy expert Sylvie Le Guyader (LCI\, Karolinska Institutet) organizes a Call4Help session. The aim is to offer combined expertise towards microscopy and bioimage analysis. All researchers from Swedish institutes can participate. \n\n\n\nThe ideal timepoint to join the Call4Help session is when a researcher has performed pilot experiments and has tried out first analysis approaches – but before having recorded hundreds of images. Combining BIIF’s expertise in BioImage Analysis with microscopy expertise we can discuss ways to record the images that allow analysis afterwards. We will discuss different analysis approaches using mainly open-source software (Fiji\, CellProfiler\, QuPath\, Ilastik\, KNIME)\, but also commercial systems\, if needed (Imaris). \n\n\n\nThe Call4Help session format has been introduced to the BioImage Analysis community by NEUBIAS and ScopeM. \n\n\n\nHow to participate? \n\n\n\nStep1: \n\n\n\nPrepare a short presentation (5-7 min)  – use the following template for your presentation: \n\n\n\nhttp://bit.ly/BIIF_C4H_slideTemplate \n\n\n\nSlide template by NEUBIAS/ScopeM \n\n\n\nStep2: \n\n\n\na) Upload your presentation \n\n\n\nUpload your presentation to a drive of your choice. You can also use our Call4Help google drive. Note that files shared on our Call4Help drive will be available to everyone until the session is over. \n\n\n\nhttp://bit.ly/BIIF_C4H_Drive \n\n\n\nb) Upload example images for testing. \n\n\n\nUpload example images for testing either to the drive of your choice or our Call4Help google drive above. \n\n\n\nhttp://bit.ly/BIIF_C4H_Drive \n\n\n\nc) Register by filling out the registration form: \n\n\n\nhttp://bit.ly/BIIF_C4H_Registration \n\n\n\nStep 3: \n\n\n\nJoin the zoom-session. \n\n\n\nIf your problem is selected for presentation\, you will get a time-slot of 30 – 60 minutes within the session. \n\n\n\nWhat are the Deadlines \n\n\n\nSubmission of a problem and upload of example data: Friday the week before the session. \n\n\n\nNotification about participation: The day before the session. \n\n\n\nNext Call4Help session \n\n\n\nTuesday\, June 7\, 2022\, 9.00-12.00. Deadline for application: Friday\, June 3\, 2022.
URL:https://www.scilifelab.se/event/bioimage-analysis-support-call4help-5/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220503T090000
DTEND;TZID=Europe/Stockholm:20220503T120000
DTSTAMP:20260526T040033
CREATED:20220121T160156Z
LAST-MODIFIED:20220121T160157Z
UID:10000514-1651568400-1651579200@www.scilifelab.se
SUMMARY:BioImage Analysis support - Call4Help
DESCRIPTION:Every 1st week of the month (mainly on Tuesdays\, but there might be exceptions) the BioImage Informatics Facility together with microscopy expert Sylvie Le Guyader (LCI\, Karolinska Institutet) organizes a Call4Help session. The aim is to offer combined expertise towards microscopy and bioimage analysis. All researchers from Swedish institutes can participate. \n\n\n\nThe ideal timepoint to join the Call4Help session is when a researcher has performed pilot experiments and has tried out first analysis approaches – but before having recorded hundreds of images. Combining BIIF’s expertise in BioImage Analysis with microscopy expertise we can discuss ways to record the images that allow analysis afterwards. We will discuss different analysis approaches using mainly open-source software (Fiji\, CellProfiler\, QuPath\, Ilastik\, KNIME)\, but also commercial systems\, if needed (Imaris). \n\n\n\nThe Call4Help session format has been introduced to the BioImage Analysis community by NEUBIAS and ScopeM. \n\n\n\nHow to participate? \n\n\n\nStep1: \n\n\n\nPrepare a short presentation (5-7 min)  – use the following template for your presentation: \n\n\n\nhttp://bit.ly/BIIF_C4H_slideTemplate \n\n\n\nSlide template by NEUBIAS/ScopeM \n\n\n\nStep2: \n\n\n\na) Upload your presentation \n\n\n\nUpload your presentation to a drive of your choice. You can also use our Call4Help google drive. Note that files shared on our Call4Help drive will be available to everyone until the session is over. \n\n\n\nhttp://bit.ly/BIIF_C4H_Drive \n\n\n\nb) Upload example images for testing. \n\n\n\nUpload example images for testing either to the drive of your choice or our Call4Help google drive above. \n\n\n\nhttp://bit.ly/BIIF_C4H_Drive \n\n\n\nc) Register by filling out the registration form: \n\n\n\nhttp://bit.ly/BIIF_C4H_Registration \n\n\n\nStep 3: \n\n\n\nJoin the zoom-session. \n\n\n\nIf your problem is selected for presentation\, you will get a time-slot of 30 – 60 minutes within the session. \n\n\n\nWhat are the Deadlines \n\n\n\nSubmission of a problem and upload of example data: Friday the week before the session. \n\n\n\nNotification about participation: The day before the session. \n\n\n\nNext Call4Help session \n\n\n\nTuesday\, May 3\, 2022\, 9.00-12.00. Deadline for application: Friday\, April 29\, 2022.
URL:https://www.scilifelab.se/event/bioimage-analysis-support-call4help-4/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220405T090000
DTEND;TZID=Europe/Stockholm:20220405T120000
DTSTAMP:20260526T040033
CREATED:20220121T160038Z
LAST-MODIFIED:20220121T160039Z
UID:10000513-1649149200-1649160000@www.scilifelab.se
SUMMARY:BioImage Analysis support - Call4Help
DESCRIPTION:Every 1st week of the month (mainly on Tuesdays\, but there might be exceptions) the BioImage Informatics Facility together with microscopy expert Sylvie Le Guyader (LCI\, Karolinska Institutet) organizes a Call4Help session. The aim is to offer combined expertise towards microscopy and bioimage analysis. All researchers from Swedish institutes can participate. \n\n\n\nThe ideal timepoint to join the Call4Help session is when a researcher has performed pilot experiments and has tried out first analysis approaches – but before having recorded hundreds of images. Combining BIIF’s expertise in BioImage Analysis with microscopy expertise we can discuss ways to record the images that allow analysis afterwards. We will discuss different analysis approaches using mainly open-source software (Fiji\, CellProfiler\, QuPath\, Ilastik\, KNIME)\, but also commercial systems\, if needed (Imaris). \n\n\n\nThe Call4Help session format has been introduced to the BioImage Analysis community by NEUBIAS and ScopeM. \n\n\n\nHow to participate? \n\n\n\nStep1: \n\n\n\nPrepare a short presentation (5-7 min)  – use the following template for your presentation: \n\n\n\nhttp://bit.ly/BIIF_C4H_slideTemplate \n\n\n\nSlide template by NEUBIAS/ScopeM \n\n\n\nStep2: \n\n\n\na) Upload your presentation \n\n\n\nUpload your presentation to a drive of your choice. You can also use our Call4Help google drive. Note that files shared on our Call4Help drive will be available to everyone until the session is over. \n\n\n\nhttp://bit.ly/BIIF_C4H_Drive \n\n\n\nb) Upload example images for testing. \n\n\n\nUpload example images for testing either to the drive of your choice or our Call4Help google drive above. \n\n\n\nhttp://bit.ly/BIIF_C4H_Drive \n\n\n\nc) Register by filling out the registration form: \n\n\n\nhttp://bit.ly/BIIF_C4H_Registration \n\n\n\nStep 3: \n\n\n\nJoin the zoom-session. \n\n\n\nIf your problem is selected for presentation\, you will get a time-slot of 30 – 60 minutes within the session. \n\n\n\nWhat are the Deadlines \n\n\n\nSubmission of a problem and upload of example data: Friday the week before the session. \n\n\n\nNotification about participation: The day before the session. \n\n\n\nNext Call4Help session \n\n\n\nTuesday\, April 5\, 2022\, 9.00-12.00. Deadline for application: Friday\, April 1\, 2022.
URL:https://www.scilifelab.se/event/bioimage-analysis-support-call4help-3/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220301T090000
DTEND;TZID=Europe/Stockholm:20220301T120000
DTSTAMP:20260526T040033
CREATED:20220121T155935Z
LAST-MODIFIED:20220121T155936Z
UID:10000512-1646125200-1646136000@www.scilifelab.se
SUMMARY:BioImage Analysis support - Call4Help
DESCRIPTION:Every 1st week of the month (mainly on Tuesdays\, but there might be exceptions) the BioImage Informatics Facility together with microscopy expert Sylvie Le Guyader (LCI\, Karolinska Institutet) organizes a Call4Help session. The aim is to offer combined expertise towards microscopy and bioimage analysis. All researchers from Swedish institutes can participate. \n\n\n\nThe ideal timepoint to join the Call4Help session is when a researcher has performed pilot experiments and has tried out first analysis approaches – but before having recorded hundreds of images. Combining BIIF’s expertise in BioImage Analysis with microscopy expertise we can discuss ways to record the images that allow analysis afterwards. We will discuss different analysis approaches using mainly open-source software (Fiji\, CellProfiler\, QuPath\, Ilastik\, KNIME)\, but also commercial systems\, if needed (Imaris). \n\n\n\nThe Call4Help session format has been introduced to the BioImage Analysis community by NEUBIAS and ScopeM. \n\n\n\nHow to participate? \n\n\n\nStep1: \n\n\n\nPrepare a short presentation (5-7 min)  – use the following template for your presentation: \n\n\n\nhttp://bit.ly/BIIF_C4H_slideTemplate \n\n\n\nSlide template by NEUBIAS/ScopeM \n\n\n\nStep2: \n\n\n\na) Upload your presentation \n\n\n\nUpload your presentation to a drive of your choice. You can also use our Call4Help google drive. Note that files shared on our Call4Help drive will be available to everyone until the session is over. \n\n\n\nhttp://bit.ly/BIIF_C4H_Drive \n\n\n\nb) Upload example images for testing. \n\n\n\nUpload example images for testing either to the drive of your choice or our Call4Help google drive above. \n\n\n\nhttp://bit.ly/BIIF_C4H_Drive \n\n\n\nc) Register by filling out the registration form: \n\n\n\nhttp://bit.ly/BIIF_C4H_Registration \n\n\n\nStep 3: \n\n\n\nJoin the zoom-session. \n\n\n\nIf your problem is selected for presentation\, you will get a time-slot of 30 – 60 minutes within the session. \n\n\n\nWhat are the Deadlines \n\n\n\nSubmission of a problem and upload of example data: Friday the week before the session. \n\n\n\nNotification about participation: The day before the session. \n\n\n\nNext Call4Help session \n\n\n\nTuesday\, March 1\, 2022\, 9.00-12.00. Deadline for application: Friday\, February 25\, 2022.
URL:https://www.scilifelab.se/event/bioimage-analysis-support-call4help-2/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220211T140000
DTEND;TZID=Europe/Stockholm:20220211T160000
DTSTAMP:20260526T040033
CREATED:20220121T155806Z
LAST-MODIFIED:20220121T155807Z
UID:10000511-1644588000-1644595200@www.scilifelab.se
SUMMARY:BioImage Analysis support - Call4Help
DESCRIPTION:Every 1st week of the month (mainly on Tuesdays\, but there might be exceptions) the BioImage Informatics Facility together with microscopy expert Sylvie Le Guyader (LCI\, Karolinska Institutet) organizes a Call4Help session. The aim is to offer combined expertise towards microscopy and bioimage analysis. All researchers from Swedish institutes can participate. \n\n\n\nThe ideal timepoint to join the Call4Help session is when a researcher has performed pilot experiments and has tried out first analysis approaches – but before having recorded hundreds of images. Combining BIIF’s expertise in BioImage Analysis with microscopy expertise we can discuss ways to record the images that allow analysis afterwards. We will discuss different analysis approaches using mainly open-source software (Fiji\, CellProfiler\, QuPath\, Ilastik\, KNIME)\, but also commercial systems\, if needed (Imaris). \n\n\n\nThe Call4Help session format has been introduced to the BioImage Analysis community by NEUBIAS and ScopeM. \n\n\n\nHow to participate? \n\n\n\nWe prefer if you prepare a short presentation and upload it together with some example images according to the steps 1 and 2 below. This makes it easier for us when we have to prioritize between projects and allows us to prepare for the meeting. But if time permits\, we can also accept participants without this info. \n\n\n\nStep1: \n\n\n\nPrepare a short presentation (5-7 min)  – use the following template for your presentation: \n\n\n\nhttp://bit.ly/BIIF_C4H_slideTemplate \n\n\n\nSlide template by NEUBIAS/ScopeM \n\n\n\nStep2: \n\n\n\na) Upload your presentation \n\n\n\nUpload your presentation to a drive of your choice. You can also use our Call4Help google drive. Note that files shared on our Call4Help drive will be available to everyone until the session is over. \n\n\n\nhttp://bit.ly/BIIF_C4H_Drive \n\n\n\nb) Upload example images for testing. \n\n\n\nUpload example images for testing either to the drive of your choice or our Call4Help google drive above. \n\n\n\nhttp://bit.ly/BIIF_C4H_Drive \n\n\n\nc) Register by filling out the registration form: \n\n\n\nhttp://bit.ly/BIIF_C4H_Registration \n\n\n\nStep 3: \n\n\n\nJoin the zoom-session. \n\n\n\nIf your problem is selected for presentation\, you will get a time-slot of 30 – 60 minutes within the session. \n\n\n\nWhat are the Deadlines \n\n\n\nSubmission of a problem and upload of example data: Friday the week before the session. \n\n\n\nNotification about participation: The day before the session. \n\n\n\nNext Call4Help session \n\n\n\nFriday\, February 11\, 2022\, 14:00-16:00. Deadline for application: Tuesday\, February 8\, 2022.
URL:https://www.scilifelab.se/event/bioimage-analysis-support-call4help/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20211207T090000
DTEND;TZID=Europe/Stockholm:20211207T110000
DTSTAMP:20260526T040033
CREATED:20210902T061020Z
LAST-MODIFIED:20211005T085331Z
UID:10000426-1638867600-1638874800@www.scilifelab.se
SUMMARY:BioImage Informatics Call4Help
DESCRIPTION:Every 1st week of the month (mainly on Tuesdays\, but there might be exceptions) the BioImage Informatics Facility together with microscopy expert Sylvie Le Guyader (LCI\, Karolinska Institutet) organizes a Call4Help session. The aim is to offer combined expertise towards microscopy and bioimage analysis. All researchers from Swedish institutes can participate. \n\n\n\nThe ideal timepoint to join the Call4Help session is when a researcher has performed pilot experiments and has tried out first analysis approaches – but before having recorded hundreds of images. Combining BIIF’s expertise in BioImage Analysis with microscopy expertise we can discuss ways to record the images that allow analysis afterwards. We will discuss different analysis approaches using mainly open-source software (Fiji\, CellProfiler\, QuPath\, Ilastik\, KNIME)\, but also commercial systems\, if needed (Imaris). \n\n\n\nThe Call4Help session format has been introduced to the BioImage Analysis community by NEUBIAS and ScopeM. \n\n\n\nHow to participate? \n\n\n\nWe prefer if you prepare a short presentation and upload it together with some example images according to the steps 1 and 2 below. This makes it easier for us when we have to prioritize between projects and allows us to prepare for the meeting. But if time permits\, we can also accept participants without this info. \n\n\n\nStep1: \n\n\n\nPrepare a short presentation (5-7 min)  – use the following template for your presentation: \n\n\n\nhttp://bit.ly/BIIF_C4H_slideTemplate \n\n\n\nSlide template by NEUBIAS/ScopeM \n\n\n\nStep2: \n\n\n\na) Upload your presentation \n\n\n\nUpload your presentation to a drive of your choice. You can also use our Call4Help google drive. Note that files shared on our Call4Help drive will be available to everyone until the session is over. \n\n\n\nhttp://bit.ly/BIIF_C4H_Drive \n\n\n\nb) Upload example images for testing. \n\n\n\nUpload example images for testing either to the drive of your choice or our Call4Help google drive above. \n\n\n\nhttp://bit.ly/BIIF_C4H_Drive \n\n\n\n \n\n\n\nc) Register by filling out the registration form: \n\n\n\nhttp://bit.ly/BIIF_C4H_Registration \n\n\n\nStep 3: \n\n\n\nJoin the zoom-session. \n\n\n\nIf your problem is selected for presentation\, you will get a time-slot of 30 – 60 minutes within the session. \n\n\n\nWhat are the Deadlines \n\n\n\nSubmission of a problem and upload of example data: Friday the week before the session. \n\n\n\nNotification about participation: The day before the session. \n\n\n\nNext Call4Help session \n\n\n\nTuesday\, December 7\, 2021\, 9.00-12.00. Deadline for application: Friday\, December 3\, 2021.
URL:https://www.scilifelab.se/event/bioimage-informatics-call4help-6/
CATEGORIES:Event
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20211102T090000
DTEND;TZID=Europe/Stockholm:20211102T100000
DTSTAMP:20260526T040033
CREATED:20210902T060701Z
LAST-MODIFIED:20211019T152930Z
UID:10000425-1635843600-1635847200@www.scilifelab.se
SUMMARY:BioImage Informatics Call4Help Webinar: CellPose
DESCRIPTION:For our next Call4Help session we are organizing a tool-presentation seminar about CellPose\, a generalist algorithm for cell and nuclei segmentation. CellPose is a deep learning-based segmentation method trained on a wide range of image types. It can be applied to both 2D and 3D images.  \n\n\n\nDuring this seminar we will explore different ways to run CellPose\, including demos powered by the ImJoy server which aim to make it easier for users to analyse large datasets in computing clusters. The webinar will be given by Gisele Miranda (BIIF) and Wei Ouyang (KTH\, developer of ImJoy) and will take place on November 2nd\, 09:00-10:00. There will be time for questions and discussion\, so we hope this event to be very interactive. Please register here. \n\n\n\nregistration\n\n\n\nImportant links\n\n\n\nhttps://github.com/MouseLand/cellposehttps://imjoy.io/
URL:https://www.scilifelab.se/event/bioimage-informatics-call4help-5/
CATEGORIES:Event
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20211001T090000
DTEND;TZID=Europe/Stockholm:20211001T110000
DTSTAMP:20260526T040033
CREATED:20210902T060431Z
LAST-MODIFIED:20210902T060444Z
UID:10000424-1633078800-1633086000@www.scilifelab.se
SUMMARY:BioImage Informatics Call4Help
DESCRIPTION:Every 1st week of the month (mainly on Tuesdays\, but there might be exceptions) the BioImage Informatics Facility together with microscopy expert Sylvie Le Guyader (LCI\, Karolinska Institutet) organizes a Call4Help session. The aim is to offer combined expertise towards microscopy and bioimage analysis. All researchers from Swedish institutes can participate. \n\n\n\nThe ideal timepoint to join the Call4Help session is when a researcher has performed pilot experiments and has tried out first analysis approaches – but before having recorded hundreds of images. Combining BIIF’s expertise in BioImage Analysis with microscopy expertise we can discuss ways to record the images that allow analysis afterwards. We will discuss different analysis approaches using mainly open-source software (Fiji\, CellProfiler\, QuPath\, Ilastik\, KNIME)\, but also commercial systems\, if needed (Imaris). \n\n\n\nThe Call4Help session format has been introduced to the BioImage Analysis community by NEUBIAS and ScopeM. \n\n\n\nHow to participate? \n\n\n\nStep1: \n\n\n\nPrepare a short presentation (5-7 min)  – use the following template for your presentation: \n\n\n\nhttp://bit.ly/BIIF_C4H_slideTemplate \n\n\n\nSlide template by NEUBIAS/ScopeM \n\n\n\nStep2: \n\n\n\na) Upload your presentation \n\n\n\nUpload your presentation to a drive of your choice. You can also use our Call4Help google drive. Note that files shared on our Call4Help drive will be available to everyone until the session is over. \n\n\n\nhttp://bit.ly/BIIF_C4H_Drive \n\n\n\nb) Upload example images for testing. \n\n\n\nUpload example images for testing either to the drive of your choice or our Call4Help google drive above. \n\n\n\nhttp://bit.ly/BIIF_C4H_Drive \n\n\n\nc) Register by filling out the registration form: \n\n\n\nhttp://bit.ly/BIIF_C4H_Registration \n\n\n\nStep 3: \n\n\n\nJoin the zoom-session. \n\n\n\nIf your problem is selected for presentation\, you will get a time-slot of 30 – 60 minutes within the session. \n\n\n\nWhat are the Deadlines \n\n\n\nSubmission of a problem and upload of example data: Deadline for application: Tuesday\, September 28\, 2021. \n\n\n\nNotification about participation: The day before the session. \n\n\n\nNext Call4Help session \n\n\n\nFriday\, October 1\, 2021\, 9.00-12.00. Deadline for application: Tuesday\, September 28\, 2021.
URL:https://www.scilifelab.se/event/bioimage-informatics-call4help-4/
CATEGORIES:Event
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210907T090000
DTEND;TZID=Europe/Stockholm:20210907T110000
DTSTAMP:20260526T040033
CREATED:20210902T060222Z
LAST-MODIFIED:20210902T060229Z
UID:10000423-1631005200-1631012400@www.scilifelab.se
SUMMARY:BioImage Informatics Call4Help
DESCRIPTION:Every 1st week of the month (mainly on Tuesdays\, but there might be exceptions) the BioImage Informatics Facility together with microscopy expert Sylvie Le Guyader (LCI\, Karolinska Institutet) organizes a Call4Help session. The aim is to offer combined expertise towards microscopy and bioimage analysis. All researchers from Swedish institutes can participate. \n\n\n\nThe ideal timepoint to join the Call4Help session is when a researcher has performed pilot experiments and has tried out first analysis approaches – but before having recorded hundreds of images. Combining BIIF’s expertise in BioImage Analysis with microscopy expertise we can discuss ways to record the images that allow analysis afterwards. We will discuss different analysis approaches using mainly open-source software (Fiji\, CellProfiler\, QuPath\, Ilastik\, KNIME)\, but also commercial systems\, if needed (Imaris). \n\n\n\nThe Call4Help session format has been introduced to the BioImage Analysis community by NEUBIAS and ScopeM. \n\n\n\nHow to participate? \n\n\n\nStep1: \n\n\n\nPrepare a short presentation (5-7 min)  – use the following template for your presentation: \n\n\n\nhttp://bit.ly/BIIF_C4H_slideTemplate \n\n\n\nSlide template by NEUBIAS/ScopeM \n\n\n\nStep2: \n\n\n\na) Upload your presentation \n\n\n\nUpload your presentation to a drive of your choice. You can also use our Call4Help google drive. Note that files shared on our Call4Help drive will be available to everyone until the session is over. \n\n\n\nhttp://bit.ly/BIIF_C4H_Drive \n\n\n\nb) Upload example images for testing. \n\n\n\nUpload example images for testing either to the drive of your choice or our Call4Help google drive above. \n\n\n\nhttp://bit.ly/BIIF_C4H_Drive \n\n\n\nc) Register by filling out the registration form: \n\n\n\nhttp://bit.ly/BIIF_C4H_Registration \n\n\n\nStep 3: \n\n\n\nJoin the zoom-session. \n\n\n\nIf your problem is selected for presentation\, you will get a time-slot of 30 – 60 minutes within the session. \n\n\n\nWhat are the Deadlines \n\n\n\nSubmission of a problem and upload of example data: Friday the week before the session. \n\n\n\nNotification about participation: The day before the session. \n\n\n\nNext Call4Help session \n\n\n\nTuesday\, September 7\, 2021\, 9.00-11.00.  \n\n\n\nDeadline for application: Friday\, September 3\, 2021.
URL:https://www.scilifelab.se/event/bioimage-informatics-call4help-3/
CATEGORIES:Event
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210504T090000
DTEND;TZID=Europe/Stockholm:20210504T100000
DTSTAMP:20260526T040033
CREATED:20210428T091829Z
LAST-MODIFIED:20210428T091856Z
UID:10000365-1620118800-1620122400@www.scilifelab.se
SUMMARY:BioImage Informatics Call4Help
DESCRIPTION:The April version of the Call4Help session will be a “special edition”. We will present ZeroCostDL4Mic. ZeroCostDL4Mic is a toolbox for the training and implementation of common Deep Learning approaches to microscopy imaging. It exploits the ease-of-use and access to GPU provided by Google Colab. https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki \n\n\n\nPresenter:Petter Ranefall\, BIIF \n\n\n\nTime and location:4 May 2021 (Tuesday)\, 09:00 – 10:00 AMzoom (link will be sent to registered users)
URL:https://www.scilifelab.se/event/bioimage-informatics-call4help/
CATEGORIES:Event
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
LOCATION:
END:VEVENT
END:VCALENDAR