Recent Releases of pinpoint
pinpoint - v2.0.1b0
Re-introduced uMp-3 support
Sensapex uMp-4 and uMp-3 manipulators are now accessed through the same manipulator type of "Sensapex uMp". We currently only support using one of the two platforms at a time, meaning all manipulators in the rig must be uMp-4 only or uMp-3 only.
What's Changed
- 775 re add ump 3 by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/776
Full Changelog: https://github.com/VirtualBrainLab/Pinpoint/compare/v2.0.0...v2.0.1b0
- C#
Published by kjy5 10 months ago
pinpoint - v2.0.0
This is the first 2.0 release of Pinpoint! We have a lot more features and changes coming, including a revamped UI and back-end changes. If you need to revert to v1 of Pinpoint, use the v1.1 branch on Steam or visit our GitHub to download v1.1.7.
Thank you for using Pinpoint! We will continue to roll out features and updates in the coming weeks.
What's Changed
- 676 increase delay and connection handling for ephys link by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/700
- 702 ephys link 20 support by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/703
- Increase exit margin distance, increase exit speeds by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/706
- 705 reduce ephys link log and log copilot actions by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/708
- Move log to EndMovement function (is also called on error) by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/710
- feat: MPM and automation support by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/711
- Unity 6 upgrade by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/757
- Updated to new 2.0 API by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/763
- 766 unable to continue using manual control if reached limit by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/770
- chore: update csharpier version and convert automation to um by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/771
Full Changelog: https://github.com/VirtualBrainLab/Pinpoint/compare/v1.1.7...v2.0.0
- C#
Published by kjy5 11 months ago
pinpoint - v2.0alpha
This is an alpha release of the 2.0 branch. It does not include many of the features we plan to roll out in 2.0 including a new UI.
It does include a bunch of new atlases. Enjoy!
The previous version of Pinpoint is still available at https://data.virtualbrainlab.org/Pinpoint11_7/
- C#
Published by dbirman about 1 year ago
pinpoint - v1.1.6
Ephys Link Bundling
Ephys Link is now bundled directly inside Pinpoint, meaning you no longer have to install it separately and run. Follow the instructions here to learn more about how to connect your manipulators to Pinpoint.
What's Changed
- 647 handle manipulator not making it to destination by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/651
- Drive on exit by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/653
- 646 null pointer when copilot window opens without any probes by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/654
- 658 bundle and launch ephys link from pinpoint by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/661
- Ephys link UI updates by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/662
- chore: Handle ephys link disconnect by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/663
- Fix menu UI ordering by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/665
- chore: Convert copilot to pydanic models by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/671
- Fix: unable to select 0 drive past distance by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/678
- chore: Bump Ephys Link to v1.3.0b2 by @kjy5 in https://github.com/VirtualBrainLab/Pinpoint/pull/679
Full Changelog: https://github.com/VirtualBrainLab/Pinpoint/compare/v1.1.2...v1.1.6
- C#
Published by kjy5 almost 2 years ago
pinpoint - v1.1.2
To access this release please go to https://data.virtualbrainlab.org/Pinpoint/ or through the main branch on Steam. You can also download the attached zip files.
Please note: there are known issues with transforms in this release, if you see a small discrepancy between your insertion in 3D space and the 2D slice panels, please use the "null" transform for planning. v1.1.3 will be released soon and will fix these issues.
If you are using Ephys Link, please make sure to upgrade to v1.2.3 as well, using the new self-contained executable (.exe) attached below or updating your current Python install with pip install -U ephys-link.
There are many more updates in the pipeline coming in the next few weeks. Thanks for your patience!
Major changes
- Accounts back-end has been updated and should be functional again
- Improvements to ephys-link
- Fixed a bug that caused the reference coordinate to default to (0,0,0) on startup
- Added a button to clear settings, useful when the program crashes on startup
Full Changelog: https://github.com/VirtualBrainLab/Pinpoint/compare/v1.1.1...v1.1.2
- C#
Published by dbirman about 2 years ago
pinpoint - v1.1.1
To access this release please go to https://data.virtualbrainlab.org/Pinpoint/ or through the main branch on Steam. You can also download the attached zip files.
If you are using Ephys Link, please make sure to upgrade to v1.2.1 as well, using the new self-contained executable (.exe) attached below or updating your current Python install with pip install -U ephys-link.
There are many more updates in the pipeline coming in the next few weeks. Thanks for your patience!
Major changes - Critical bug fixes to the in-plane slice, probe panels, and roll angle - Critical bug fixes to how transforms update the 3D scene - Updates to the New Scale Pathfinder/Pinpoint integration
- C#
Published by dbirman about 2 years ago
pinpoint - v1.1.0
To access this release please go to https://data.virtualbrainlab.org/Pinpoint/ or through the main branch on Steam. You can also download the attached zip files.
If you are using ephys-link, please make sure to upgrade to v1.1.0 as well, using pip install ephys-link -U
There are many more updates in the pipeline coming in the next few weeks. Thanks for your patience!
Major changes
- Improved surface entry coordinate calculations and bug fixes
- Pathfinder / Pinpoint is updated for 4-shank probes
- ephys-link issues with manipulator axis directions should now be fixed
- Backend data improvements
Full Changelog: https://github.com/VirtualBrainLab/Pinpoint/compare/v1.0.0b...v1.1.0
- C#
Published by kjy5 about 2 years ago
pinpoint - v1.0.0b
This is the beta release of v1.0.0 of Pinpoint. Thank you for helping us debug Pinpoint so far, our goal is to no longer introduce breaking changes in future releases.
There are still several major features and many bug fixes that we hope to roll out before considering Pinpoint stable. These include improved area search, a revamped UI, better import/export tools, better Accounts, additional integrations with Open Ephys and SpikeGLX, experiment automation, and a lot more. We're working hard to make Pinpoint your go-to planning tool!
To access this release please go to https://data.virtualbrainlab.org/Pinpoint/ or through the main branch on Steam. You can also download the attached zip files
Major changes in this release - Many bug fixes, many internal refactors to improve future release speed - Re-integrated ephys-link - Reduced rotation increments - Added fuzzy position checks to reduce updates in SpikeGLX API
- C#
Published by dbirman about 2 years ago
pinpoint - v1.0.0a
This is the alpha release of v1.0.0 of Pinpoint. Thank you for helping us debug Pinpoint so far, our goal will to no longer introduce breaking changes in future releases.
There are still several major features and many bug fixes that we hope to roll out before considering Pinpoint stable. These include improved area search, a revamped UI, better import/export tools, better Accounts, additional integrations with Open Ephys and SpikeGLX, experiment automation, and a lot more. We're working hard to make Pinpoint your go-to planning tool!
To access this release please go to https://data.virtualbrainlab.org/Pinpoint-develop/ or through the Steam beta branch (right click on Pinpoint in Steam, select Properties, go to Betas, enable the beta branch). You can also download the attached zip files
See you at SfN!
Major changes in this release - Pinpoint is now integrated with Urchin. After launching Urchin in Python, copy the ID to the Pinpoint API tab. - The under-the-hood reference atlases are now pulled directly from the BrainGlobe Atlas API. We are releasing immediately the Waxholm rat atlas. - Many graphical and stability improvements across all the internal systems
- C#
Published by dbirman over 2 years ago
pinpoint - v0.9.7
Desktop releases of Pinpoint are now available through Steam. You can also download the latest release files from this page. There is no Linux release for this version.
The web app continues to be available online. We are including experimental Linux releases now on Steam, please let us know if you run into issues with them (you probably will).
Bug fixes - Issue in Accounts that was causing probe data to be wiped out when multiple probes were loaded at once - Issue in relative coordinate controls that caused DV value to be ignored - Issue on load that caused Accounts to incorrectly load before the user has a chance to restore the previous session - Many minor bug fixes to UI/UX
Full Changelog: https://github.com/VirtualBrainLab/Pinpoint/compare/v0.9.6...v0.9.7
- C#
Published by dbirman over 2 years ago
pinpoint - v0.9.6
Desktop releases of Pinpoint are now available through Steam. You can also download the latest release files from this page.
The web app continues to be available online. We are including experimental Linux releases now on Steam, please let us know if you run into issues with them (you probably will).
Features - Added a file picker to HelloSGLX input field - Fixed bugs with SpikeGLX error codes - Completed controller controls and improved documentation - Improved tutorials for API
Bug fixes
- Fixed issues with input fields
- Many UI/UX issues fixed in Copilot
Full Changelog: https://github.com/VirtualBrainLab/Pinpoint/compare/v0.9.4...v0.9.6
- C#
Published by dbirman over 2 years ago
pinpoint - v0.9.3
Desktop releases of Pinpoint are now available through Steam. You can also download the latest release files from this page.
The web app continues to be available online. We are including experimental Linux releases now on Steam, please let us know if you run into issues with them (you probably will).
Important
We've changed the internal definition of Pitch to be more intuitive starting in this version. A Pitch of 0 indicates a probe that is pointing down (ventral), and pitch increase as the probe becomes more horizontal. We've also changed the default setting to show this pitch and yaw value, instead of the "IBL angle" conventions.
Hotfixes
- UI bug fixes related to b-l distance setting
- Added additional tip/entry coordinates to the probe export
- Added camera zoom/rotation to settings
- Raised double-click time on orientation widget
- Moved speed controls to a UI element, and changed to tap
- Enabled 4-shank probes in SpikeGLX API
- Updated ephys-link API to fix bugs and update paths when probes are moved
- Fixed bug causing UI inputs to trigger movements
- C#
Published by dbirman over 2 years ago
pinpoint - v0.9.2
Desktop releases of Pinpoint are now available through Steam. You can also download the latest release files from this page.
The web app continues to be available online. We are including experimental Linux releases now on Steam, please let us know if you run into issues with them (you probably will).
Hotfix - This release fixes several feature regressions in the SpikeGLX API, basic probe functionality, and Accounts API
Full Changelog: https://github.com/VirtualBrainLab/Pinpoint/compare/v0.9.0...v0.9.2
- C#
Published by dbirman over 2 years ago
pinpoint - v0.9.1
Desktop releases of Pinpoint are now available through Steam. You can also download the latest release files from this page.
The web app continues to be available online. We are including experimental Linux releases now on Steam, please let us know if you run into issues with them (you probably will).
What's changed
- SpikeGLX API
- Keyboard control of linked manipulators
- Copilot automation features
- New probes
- Bregma-lambda distance ratio
- Many many bug fixes, UI, and UX improvements
Hotfix 7/29 (0.9.1)
- SpikeGLX API fixes
- Added controller support
- New Scale API fixes
- Accounts issue with insertions being reset fixed
- Many minor bug fixes
Hotfix 7/19
- SpikeGLX API fixes
Full Changelog: https://github.com/VirtualBrainLab/Pinpoint/compare/v0.8.5...v0.9.0
- C#
Published by dbirman over 2 years ago
pinpoint - v0.8.5-develop
This a development release, the full 0.8.5 will be rolled out soon. You can access 0.8.5 online
Features
- OpenEphys API
- Channel API
- Channel maps
- Share button
- Probe ap/ml coordinates to forward/side conversion is now re-enabled
- Better links to tutorials
- Many many bug fixes
Full Changelog: https://github.com/VirtualBrainLab/Pinpoint/compare/v0.8.4...v0.8.5
- C#
Published by dbirman almost 3 years ago
pinpoint - v0.8.4
Hotfix there is a bug in the Accounts system that is fixed in the development build of v0.8.5 at this link. If you aren't using Accounts, you should continue to use 0.8.4 below.
Access the latest release of Pinpoint v0.8.4 at this link, or using the attached binary for Windows desktop. This is a pre-release build, except bugs! You can report them on the issues page.
New features
Accounts: you can now create an account in Pinpoint in the "Saved Exps" tab of the settings. Accounts hold experiments, which are buckets for probe insertions. You can share your account with collaborators or keep it private. Please note that all features in Pinpoint are experimental at this time: we will do our best to ensure stability and to prevent data loss, but your planned insertions could be lost at any time.
Coming soon to the accounts features: - Data import/export (via a JSON file) - Option to mark insertions as "recorded" and visually show coverage
Previous versions of Pinpoint are still available but will be deprecated on the release of v1.0.0. We can't provide support for older versions at this time. - v0.8.3
What's Changed
- Ephys link now supports "infinite" probes in an improved UI system
- All probes have a UUID to ensure continuity in Accounts
- Added support for multiple craniotomies
- Added support for clipboard copying of probe data in the browser
- Added many behind-the-scenes quality of life improvements, e.g. static instances and UnityEvents
- Added a lock feature on the quick settings panel to freeze probes in the scene
- Added a copy button on the quick settings panel
- Added automatic probe naming using the area with the largest coverage on the probe recording region (can be overridden in Accounts)
- Refactored collisions to improve performance and reduce complexity
- Refactored settings to reduce complexity
- Improved the probe color system and added support for retaining color when the program is closed
- Many many bugfixes
Full Changelog: https://github.com/VirtualBrainLab/Pinpoint/compare/v0.8.3...v0.8.4
- C#
Published by dbirman about 3 years ago
pinpoint - v0.8.3
Access the latest release of Pinpoint v0.8.3 at this link, or using the attached binary for Windows desktop. This is a pre-release build, except bugs! You can report them on the issues page.
The latest develop build v0.8.4 will be available at this link
Previous versions of Pinpoint are still available but will be deprecated on the release of v1.0.0. We can't provide support for older versions at this time.
What's Changed
- Ephys link protocol changed to strings
- Fixed a bug in the slice renderer causing brain chunks to vanish
- Changed logo
- Added a new rig by request
- Added a UI-rescale setting
- Added a graphics option to make un-targeted areas invisible
- Fixed a bug related to loading timing
- Fixed a bug causing the Beryl setting to not get passed properly
- Fixed a bug causing probe panels to overlap when >8 panels were visible
- Updated the probe add panel so it is more easily extendable in the future
- Fixed various bugs related to ghost probe transparency
- Fixed bugs with the "drop-to-surface" button
- Updated atlas options to reflect the actual atlases
- C#
Published by dbirman over 3 years ago
pinpoint - v0.8.2
Access the latest release of Pinpoint v0.8.2 at this link, or using the attached binary for Windows desktop. This is a pre-release build, except bugs! You can report them on the issues page.
The latest develop build v0.8.3 is available at this link
Previous versions of Pinpoint are still available but will be deprecated on the release of v1.0.0. We can't provide support for older versions at this time.
What's Changed
- Adding IBL Needles, making MRI toronto default coordinate transform
- Allowing larger camera rotations
- Fixing an in-plane slice bug where the forward axis was being miscalculated
- Fixed a rounding bug in in-plane slice
- Fixed a bug preventing warp at startup
- Fixed a bug preventing drop to surface on DV axis
- Fixed various bugs in ephys link causing rotations to work incorrectly
- Added a graphics option for transparent probes
- Fixed redundant calls to draw in-plane slice
- C#
Published by dbirman over 3 years ago
pinpoint - v0.8.1
Known Issues in 0.8.1 - There is a bug causing the in-plane slice coordinates to be calculated incorrectly when probes are rotated, please don't use the in-plane slice for planning if phi or theta are not = 0
Access the latest release of Pinpoint v0.8.1 at this link, or using the attached binary for Windows desktop. This is a pre-release build, except bugs! You can report them on the issues page.
Previous versions of Pinpoint are still available but will be deprecated on the release of v1.0.0. We can't provide support for older versions at this time.
What's changed
- Defined CoordinateSpaces and CoordinateTransforms to go back and forth between CCFSpace, CCFSpace25 and the three transform spaces (CCF, Needles, and MRI)
- Re-factored ProbeInsertion to handle new functionality
- Added brain warping to the current transform space
- Many many many bug fixes to enable the ^ functionality
- C#
Published by dbirman over 3 years ago
pinpoint - v0.8.0
The latest release of Pinpoint is v0.8.0a available here. This is a pre-release build, please except bugs! You can report them on the issues page. There are no standalone desktop builds available at this time.
Please see the help menu for important changes from v0.7. Most important is that we've gone back to using [W/A/S/D] for AP/ML movement and [Z/X] for depth. Movement on the DV axis is now done using the [Q/E] keys.
Previous versions of Pinpoint are still available but will be deprecated in the coming weeks. - v0.7.0
What's Changed
- Ephys link is now available with Sensapex uMP-4 manipulators
- New quick settings panel replaces the manual coordinate entry feature
- Home button returns to bregma and snap-to-surface button does that
- Registering and logging into accounts is now possible (but they don't do anything else... coming soon)
- Rig models are now aligned properly to bregma
- Added many new settings options
- Refactored how surface entry points are discovered
Bug fixes
- Fixed floating point errors
- Fixed a bug causing probe tips to be offset incorrectly
- Fixed a bug where clicking through UI menus caused probes to jump unexpectedly
- Removed loading screen
- Fixed bugs related to colliders
- Input fields don't incorrectly grab focus when using keyboard controls
- Reduced clutter on UI panel text fields
- C#
Published by dbirman over 3 years ago
pinpoint - v0.7.0
Hotfix (v0.8.0alpha)
The browser build of Pinpoint v0.7.0 is still available but is having some issues due to an upgrade we made on the server. If you are running into problems please download the alpha release of v0.8 below (Windows only).
Important information
In v0.7.x and onwards you will find that the control system for probes has changed. You are no longer in direct control of the probe depth, instead you now control the target brain coordinate and the probe angles. The depth and surface coordinate required to reach your target are calculated for you. The advantage of this is that we can now do fancy things like snap to brain regions (coming in v0.7.1) and proper setting of positions using the manual coordinate entry. The disadvantage of this is that you learned a different system in previous versions. Sorry about that! Email Dan if you have any questions or run into any bugs.
v0.7.0 of Pinpoint is now available at this link v0.6.0 is now deprecated
There are some missing features in this build that will arrive soon, including: manual entry based on brain surface coordinates, snapping to brain areas, reducing text clutter in the probe interpolation views
Changelog
Features - UI refactor - Rig refactor(also added IBL headbars - Fixed craniotomy coordinates - Coordinate transformation refactor - Added phi/theta control with dragging - Refactored insertions to use ProbeInsertion class, easier to pass around and convert - Modified how coordinates work so that probe positions are defined by their target coordinate (ap,ml,dv) and angles (phi,theta,spin) in CCF space. - Fixed manual coordinate entry system to work in all scenarios - Changed defaults so that Bregma is stored inside the CoordinateTransform - Changed defaults so probe depth is always calculated from the brain surface (and never reported as the DV value, which is confusing)
Bugfixes - Fixed a bug where the craniotomy was visible before the setting was enabled - Fixed a bug where collisions didn't cause other objects to show up as colliders - Fixed a bug preventing users from switching back and forth between CCF and IBL Needles space
- C#
Published by dbirman over 3 years ago
pinpoint - v0.6.2
The latest WebGL build is v0.6.2.
The windows desktop client is no longer functional for v0.6.2, please use the web client.
This is a partial version release, not all features I intended to include in 0.6 are currently available. There are two really important things to be aware of: coordinate systems: right now you must keep the (0,0,0) at IBL bregma setting turned ON (it is on by default) exporting probes: because of the ^ issue, you still can't export and import probes, sorry! in vivo offset angle: the CCF atlas is known to be angled off from in vivo brains by about 5 degrees, you may miss small targets that are in deep structures if you don't account for this offset
Features
- Changed movement functionality to increment in discrete steps when clicking buttons. Holding buttons down continues to move at a rate / second. Pressing [ctrl] and [shift] makes smaller and larger increments, respectively.
- Added an in-vivo stereotaxic transform setting, which outputs in vivo coordinates rather than ccf coordinates
- Added the ability to click on a probe and then press an axis key ([W/S] or [A/D] or [Z/X]), you can then drag the probe along that axis for faster position control
- Replaced the coronal and sagittal slice renderers with shaders to improve performance, this has a substantial cost at startup as textures are transferred to the GPU in exchange for a huge gain at runtime
- Replaced the probe panel slice renderer with a shader to improve performance
- Replaced the in-plane panel slice renderer with a shader to improve performance
- Changed how collision detection works so that it doesn't prevent probe movement, just warns you that probes are colliding
- Change recording region to white
- Added a mini axis-control gizmo thing, you can double click the arms to rotate the brain automatically
- Press [CTRL+Backspace] or [C+Backspace] to recover a probe you deleted
- Added an IBL coverage map showing the current state of the second pass map (as of 4/19/22)
- Added zoom functions to the in-plane slice
Backend
- Refactored 3D datasets into the generic VolumetricDataset class, all datasets now use row-order
Bugs
- Azimuth and Spin angles now wrap around
- Removed unintentional shadows from main directional light source
- Fixed a bug where the acronym flag didn't caused the search window to update
- Fixed a bug where area boundaries were being poorly defined in the in-plane slice when the probe was slicing off the coronal plane
- Fixed a bug where moving the camera past a clipping change when the sagittal/coronal slices were visible would cause the camera to "jump"
- Probe panels now re-order to prioritize keeping NP2.4 probe panels grouped on the same row
Hotfixes
v0.6.1 fixed mouse skull issues and added a craniotomy option v0.6.1 added ibl coverage data v0.6.2 fixed a bug where probe colors could be duplicated v0.6.2 fixed bugs with craniotomy feature
- C#
Published by dbirman almost 4 years ago
pinpoint - v0.5.2
Features
- Changed CCF assets to be downloaded and cached locally, reducing the size of builds substantially
- Added probe saving and loading
- Added alpha clipping when the sagittal and coronal slice views are enabled from the camera direction
Bugs
- Fixed a bug that caused key presses while searching to activate their regular functions
- Search window now shows acronyms when in acronym mode
Hotfix
0.5.1 - Fixed an unknown bug causing files not to load
0.5.2 - Fixed a variety of issues with materials and 3D models, and incorporated improved CCF model loading functions
- C#
Published by dbirman almost 4 years ago
pinpoint - v0.4.0
PLEASE NOTE I changed the azimuth and elevation angles to match those used by the IBL in this release. If you want alternate angles for your recordings please open an issue on github with a request that defines the angle orientations you prefer to use.
Features
- Added a search window, clicking an area in the window rotates the graphics between opaque and transparent shaders
- Added a mouse skull to the rig options
- Added preferences which save+load settings across sessions
Bugs
- Changed phi/theta angles to match the IBL defaults, see https://docs.google.com/document/d/1TTLBMpluXyEPbxzAhQkUWALGweJ-l8aF8HeHgwhDweM/edit#
- Changed units to um instead of mm
- Prevent [Backspace] from deleting probes when manual entry window open
- Fixed a bug where AP axis was flipped in the manual coordinate entry window
Graphics
Hotfix - Fixed a post-release issue where depth from brain was failing and in-plane slices were not rendering correctly
- C#
Published by dbirman about 4 years ago
pinpoint - v0.3.0
Bugfixes - Probes leaving the brain no longer fail to update their recording region - Depth from brain setting works again - Sagittal/coronal slices spawn at the tip position - Update area text/acronyms properly when adding probes that change the probe panel heights
Features - Probes can be deleted with [Backspace] - Black outlines around annotation regions in the in-plane slice
Graphics - Reduce size of recording regions on probes
- C#
Published by dbirman about 4 years ago
pinpoint - v0.2.0
Added features for in-plane slicing - In-plane slice is enabled by default - Hovering displays area names and clicking highlights the region by changing the visible shader
- Fixed minor bugs related to probe positioning and viewport
- Added a linux build
- C#
Published by dbirman about 4 years ago