STRABOSPOT

StraboMicro2 v2.0.55

This release brings sync and collaboration to StraboMicro: keep a project on StraboSpot, work on it from several computers, and share it with collaborators who see each other's changes within a second or two. It also adds Grain Spot, which outlines a grain where you click; automatic placement, which finds where an associated micrograph sits on its parent; auto spot mode, for placing many spots quickly without a dialog for each one; and Custom User Data, for attaching your own spreadsheet columns to spots.

New: Sync with StraboSpot

• Turn on sync for a project with File > Upload to Strabo Server... (or the cloud chip in the header). The project is uploaded once; after that only your changes go up. The dialog shows the upload size and lists any micrographs that still need a scale, a location or instrument details (you can sync now and finish them later).
• Sync automatically or when you click: in automatic mode your changes go up about a second after you finish an edit, and changes from your other computers or collaborators arrive by themselves. In "Sync when I click" mode nothing leaves your computer until you click Sync Now.
• Header sync chip shows what sync is doing (uploading with a percentage, up to date, changes waiting, offline, needs login) and offers Sync Now, the mode, and more.
• Your other computers: File > Open Remote Project... lists your projects on StraboSpot (most recently changed first, with who is in each) and downloads a synced copy. A project you already have on this computer is connected to the StraboSpot copy instead, and if the two differ you choose which one to keep.
• New Project asks where to keep the project: on this computer only, or synced to StraboSpot (Preferences > "Sync new projects to StraboSpot when I'm logged in" sets the default).
• Working offline is fine: changes wait on your computer and go up when the connection is back.
• When two people change the same thing, "Sync needs your decision" shows both versions side by side (with pictures for spot shapes and micrograph placement) so you can keep yours or theirs. It names who made the other change and when ("Fred Smith's, changed 10:21 AM"), so in a large group you know who to talk to. The same dialog handles "they deleted something you changed" and changes the server turned down.

New: Collaboration

• File > Collaborate... invites people by email and sets their role:
  • Owner: everything, including inviting and removing people
  • Editor: can change anything in the project
  • Contributor: can add anything anywhere, but change or delete only what they added
  • Viewer: can look (and chat) but not change anything
• Invitations show in the header until you answer them, and at the top of Open Remote Project.
• Classes and workshops: Open on StraboSpot... (in Collaborators) goes to the website's Collaborators page: paste a list of email addresses, or make a QR code with a printable page that people scan to ask to join. You approve each person.
• Live updates and presence: see who else has the project open, which micrograph they are viewing and what they are editing ("Ana is editing this spot right now").
• Project chat: a chat window for each shared project (the chat chip in the header). You can link a message to the selected micrograph or spot (clicking a spot link takes you to that spot, on its micrograph, zoomed in), pin the window on top, and get a notification when someone writes while StraboMicro is in the background (switch off in Preferences > Chat). The unread count shows on the Dock (macOS), the taskbar (Windows) or the launcher (Linux).
• Activity panel (View > Activity): who changed what, newest first, with Restore for deleted items and a link to the full project history on the StraboSpot website, where you can also download the project as it was on an earlier date.
• Leaving or being removed: Leave Project... (in Collaborators) lets you keep your copy as a separate project on your computer or remove it. If the owner removes you, your copy becomes a separate project, and changes you had not synced yet are sent to the owner, who reviews them in the Activity panel and accepts or discards each one.
• Delete from StraboSpot (owner, in Collaborators) removes the shared project from StraboSpot for everyone; each person keeps or removes their own copy.

New: Grain Spot

• Click a grain, get its outline: pick Grain Spot on the drawing toolbar (the magic wand, or press W) and click a grain. Its outline is saved as a polygon spot, so you no longer trace grains corner by corner. With auto spot mode on, click one grain after another; each is named and saved at once.
• See it before you click: the outline of the grain under the mouse is shown as you move.
• Correct an outline: Shift+click a part the outline missed to add it, or Cmd+click (Mac) / Ctrl+click (Windows, Linux) a part that does not belong to cut it. The same spot is updated, one Undo step each.
• You choose the scale: Grain Spot looks at what is on the screen, so zoom in for fine grains and out for coarse ones. A grain that runs off the screen is not saved (the status line says so); zoom out or pan and click it again.
• Runs on your computer: the first time, Grain Spot downloads its model once (about 143 MB; SAM 2.1, open source). After that it works offline and no image leaves your computer. It uses the graphics card where it can (a fraction of a second after each pan or zoom), otherwise the processor (a second or a few); the status line shows GPU or CPU and the time.
• Grain Spot spots are ordinary polygon spots: they work with Grain Size Analysis, presets, sync and everything else.

New: Place automatically on parent

• No more placing by hand: "Place automatically on parent" is a new Location Method in New Associated Micrograph and Edit Micrograph Location. StraboMicro finds where the image sits on its parent by matching features in both images (grain edges, inclusions, opaque minerals), works out its scale, and shows it in place for you to check and adjust. It handles images that are turned, several times finer than the parent, or taken with different lighting.
• Clear results: "Found it", or "Low confidence, please check" when fewer features matched. An image that needs a slight skew to fit is saved like a 3-Point Registration, with Adjust points to fine-tune it. If nothing fits, or the image fits more than one place, nothing is placed and you can place it by hand.
• Place a whole batch at once: after Batch Import Associated Micrographs, StraboMicro offers to place them all ("Place them automatically now?"). It also asks when you click a micrograph without a location whose parent has others without one, and the micrograph menu has Place children automatically... A list shows each result with its outline on the parent; found ones are checked, the others stay for you to place later. One Undo takes the whole batch back.
• Runs on your computer: the matching takes a few seconds per image and no image leaves your computer. It works best with the same kind of view (PPL on PPL, XPL on XPL) and images up to about 8 times finer than their parent.

New: Auto spot mode

• Place spots without a dialog: turn on the Auto spot mode button on the drawing toolbar (next to the spot tools). With Point Spot, each click saves a spot; with Line Spot or Polygon Spot, the spot is saved when you double-click to finish it. The tool stays active for the next spot until you press Esc or pick another tool.
• Automatic names: spots are numbered for you (Spot 1, Spot 2, ...). Set the project's pattern in File > Edit Project > Default Spot Name, using {n} for the number (for example "Grain {n}"). Numbering continues across all micrographs of the sample, from the highest number already used.
• Presets with names: give a Quick Spot Preset a Spot Name such as "Ol-{n}", then pick it in the bar at the top of the image (or press the number key 1-9 bound to it). Each spot gets that name, plus the preset's color and data: Ol-1, Ol-2, ...
• The bar at the top of the image shows the next name ("Next: Ol-7"). Hold Option (Mac) or Alt (Windows, Linux) while clicking to open the New Spot dialog for one spot, already filled in.
• Each auto spot is its own Undo step, and auto spots are ordinary spots: rename them or add data any time. Auto spot mode is a setting on your computer; your collaborators share the project's name patterns but turn the mode on or off for themselves.

New: Custom User Data

• Your own data on spots: Tools > Custom User Data... downloads a template with one row per spot (for the whole project or the selected micrograph). Add your own columns, such as "Mg#", "Age (Ma)" or an analysis number, fill them in, and import the file. Each row is matched to its spot by its Spot ID.
• Excel or CSV: the template comes as .xlsx or .csv. In the Excel file the columns that identify each spot (Sample Name, Micrograph Name, Spot Name, Spot ID) are locked, and an Instructions sheet explains how to fill it in.
• Kept as typed: values are stored as text, so 0.820, <0.01 and n.d. stay exactly as you entered them.
• Check before import: StraboMicro shows what will change before anything is applied: matched rows, new columns, rows it could not match, and names that differ from the project. A file with a problem (a missing Spot ID column, the same header twice) is refused with a clear message. The import is one Undo step.
• Import again any time: only the columns in the file are updated, and an empty cell removes that value. The downloaded file includes the current values, so you can edit it and import it again.
• Where it shows: a Custom User Data section in a spot's Properties panel; for a micrograph, Show Custom User Data... opens a table of its spots (click a row to select the spot) with Download, Remove column and Remove All. The Project tab has the same table for the whole project, with Sample and Micrograph columns; clicking a row takes you to that spot. It is also in the PDF report, in .smz files, and in the StraboSpot web viewer.
• Shared projects: Custom User Data syncs like any other spot data. A Contributor's import changes only the spots they added; only the owner and Editors can remove columns.

Improvements

• Drawing spots: you can now drag the image to move around while Point Spot, Line Spot or Polygon Spot is selected (before, you had to switch the tool off first).
• Properties panel: the Grain Size Analysis, Point Count, StraboTools and Custom User Data sections stay open or closed the way you left them (before, they closed again when you selected a spot and went back to the micrograph).
• Filter Spots: View > Filter Spots... (Cmd+Shift+F / Ctrl+Shift+F) dims or hides spots by the data they have or do not have (Mineralogy/Lithology, Links, Notes, Custom User Data and every other data section), for example to find the spots that still need a link. A notice on the image shows how many spots match, with Clear. The filter is not saved in the project.
• Links section always shown: the Links section is always in the Properties panel for a spot or micrograph, like Notes and Associated Files, so you can add a link with its pencil (before, it appeared only once something had a link).
• Clickable links: web links in the Links section of the Properties panel now open in your default browser.
• Edit Selected Spots: the Edit n Spots dialog (Spot > Edit Selected Spots..., or right-click the selected spots) can now add links to all the selected spots at once. The links are added to each spot's existing links; a spot that already has a link's URL is not given it twice.
• Mineralogy/Lithology: pressing Save while a mineral or lithology is chosen but not yet added (with Add) now asks whether to add it, save without it, or go back. Before, it was left out without a word. The Mineral field also starts empty each time the dialog opens (in Quick Spot Presets it kept the last mineral).
• Undo: a slider drag (such as opacity) is one undo step, and undo history starts fresh when you open another project (before, Undo right after switching projects could bring back changes from the previous one).
• The header shows your name (email in a tooltip); logging out with unsynced changes offers to sync first.
• Staying logged in: your StraboSpot login now lasts 30 days from the last time you used it (before, it ran out 7 days after you logged in, even if you used StraboMicro every day). If it does run out while a synced project is open, the sync chip says "Log in to sync" and a notice offers Log in; your changes wait on your computer until then (before, the chip could still say "Synced" while nothing arrived).
• Opening a project file (.smz) never replaces your synced copy of the same project; you can open your copy or import the file as a separate copy.
• Open Shared Project makes its own copy for each share code, so two shared copies of the same project no longer replace each other.
• Changing the server in Preferences logs you out of the old server.
• Deep links to a project that is not available on strabospot.org say so clearly.
• StraboSpot web viewer: a micrograph that has not been placed on its parent is no longer drawn in the parent's corner, and the project tree marks it "Location not set". A project deleted by its owner shows "This project was deleted".
• Names that are not in the mineral list: every mineral field (Mineralogy, Fabric phases, point counting shortcuts, mineral colors and others) now takes a name that is not a mineral in the list, such as lithic fragments or glass. Type it and choose Use "..." at the end of the list; it is marked "not in mineral list", and names already used in the project are offered again when you type. Scrolling shows the 150 common minerals; typing searches all of the more than 5,500 minerals in the list.
• Tags in Create New Spot: choose tags for a spot while you create it. The next new spot in the project starts with the tags you chose last, so tagging a run of spots takes no extra steps.
• Reuse Quick Spot Presets in new projects: copy presets between the Global and Project tabs (Copy from Global, Copy All to Project, Copy All to Global), or export them to a file and import them on another computer. Only Project presets are shared with collaborators, and the dialog now says so. Number keys 1-9 are now remembered per project on each computer.
• Tags in Quick Spot Presets: a Project preset can now add tags to the spots it is applied to (Quick Edit, auto spot mode, or chosen in Create New Spot). Global presets cannot, because tags belong to a project.
• Overlapping spots: a smaller spot inside a larger one is now always drawn on top, so you can click it (before, a large polygon drawn later covered it). Where spots overlap, right-click and choose the one you want under Select Spot Here.
• Same area as parent: an associated micrograph can now cover its parent exactly, for example element maps collected with the BSE image they belong to. Choose Same area as parent as the location method (New Associated Micrograph or Edit Micrograph Location), or place all unplaced children at once from the parent's menu: Place unplaced children on its full area... The images must have the parent's proportions.
• Finish Importing: one place to complete batch imported micrographs, opened by clicking one with a warning dot and at the end of Batch Import. It lists the unfinished micrographs on the same parent and what each needs, then asks for rotation, for instrument information once for all (each can have its own image type, for example PPL and XPL, or the elements of a set of maps), and how to place them: automatically, cover the parent's full area, copy the placement of one already placed, or by hand one at a time. Cancel changes nothing. Batch Import now has Instrument and Image Info checked by default; uncheck it to enter this later.
• Place like a placed micrograph: give a whole set of unplaced micrographs (for example element maps of one area) the location, scale and rotation of one already placed: Place unplaced children like... in the parent's menu, or Copy the placement in Finish Importing.
• Copy scale from an existing micrograph: a new scale method when placing an associated micrograph. It takes the scale of any micrograph in the project taken at the same magnification; you only drag the image into place.
• Micrograph Visibility: View > Micrograph Visibility... (Cmd+Shift+V / Ctrl+Shift+V) lists the micrographs placed on the one you are viewing. Show or hide each, filter by name, set opacity, or use Show only this one and the Up and Down arrow keys to step through them one at a time (for example a stack of element maps).
• Show Parent Spots: View > Show Parent Spots shows, on the micrograph you are viewing, the spots of every micrograph it is placed on (for example the reference's spots on an element map), faded and dashed and labelled with their micrograph. Right-click one and choose Go to Spot to open it where it was made.

Bug Fixes

• Grain Size Analysis after deleting or editing spots: the Grain Size section in the right pane (and the full analysis) now updates right away. Before, it kept counting deleted grains, or showed old sizes after a spot was reshaped, until the project was opened again.
• Model downloads that fail now say why: when the FastSAM model (Detect Grains) or the Grain Spot model cannot be downloaded, the message says whether huggingface.co could not be reached (some networks and countries block it), the connection dropped partway, or the server answered with an error. Before, it showed a raw technical message.
• Scale of micrographs placed with 3-Point Registration: they now store their real scale, worked out from their parent. Before, they kept a stand-in value, so spot lengths and areas, Grain Size Analysis, the PDF report and the web viewer could be off by a large factor (the image viewer itself was right). Projects saved with an earlier version are corrected when you open them; micrographs placed on such a micrograph keep their size and place.
• Affine registration control points are now saved with the project, so Edit Location shows them again after the project is reopened (before, they were lost when the project closed).
• Lines and polygons drawn quickly no longer lose their last point: a fast click at a new point was taken as the double-click that finishes the shape.
• Export as .smz no longer hangs on "Exporting..." when the file cannot be written; it says Export Failed.
• Spot and micrograph delete confirmations no longer say the delete cannot be undone.
• Point count sessions of deleted micrographs are cleaned up when the project opens.
• A damaged or incomplete image file (for example, one cut off while it was being copied or exported) now shows a clear message when you add it as a micrograph, a sibling image or in Batch Import, instead of a technical error.
• The spot and tag color pickers no longer show a transparency slider that could not be moved. Opacity is set with each dialog's own Opacity or Transparency control, as before.
• Custom User Data: a .csv template of a project made with the original StraboMicro (v1) can be opened and saved in Excel without breaking the import. Excel used to round the long Spot IDs (1.76712E+13) so rows looked alike and the file was refused; the template now keeps them as text, and a file already rounded is matched by sample, micrograph and spot name.
• TIFF images with a color table (indexed color, as some EDS/microanalysis software saves element maps) now import in color; before, they came in black and white. 16-bit TIFFs (for example BSE and other electron images) now keep their real brightness differences; before, only part of each value was kept, so contrast such as core vs rim was lost. Images imported with an earlier version stay as they are: delete and import them again.
• Micrographs that have not been placed yet can now be deleted from their three-dot menu, and a micrograph's three-dot menu has Delete unplaced children... to remove all of them at once (for example after a Batch Import of the wrong files). Before, a micrograph had to be placed before it could be deleted.
• Mineral lists (Mineralogy, Fabric, point counting shortcuts, mineral colors, Edit Selected Spots and others) show all 150 common minerals again; before, they stopped at Dolomite. In Fabric > Grain Shape > Phases you can type a mineral name again; before, the typed text was cleared at each key.
• macOS: Cmd+M minimizes the window again, and the standard Window menu is back. Merge Selected Spots is now Option+Cmd+M (Alt+Ctrl+M on Windows and Linux).
• Hiding or showing a micrograph (the eye in the project tree) is now your own view: it is saved on your computer but no longer changes what your collaborators see. The web viewer and PDFs made on the server show every micrograph.
• Edit Micrograph Location with Locate by an approximate point now saves the scale you enter (scale bar, pixel conversion factor, or image width or height). Before, it kept the parent micrograph's scale whatever you entered.
• Zooming out with a Mac trackpad or Magic Mouse works again: a swipe to zoom out could stop partway or zoom back in, because sideways movement in the swipe counted as zooming in. This applied to the image viewer and every other zoomable view (placement, image comparison, grain detection and others).

Good to know

• Sync and collaboration need version 2.0.55 or later on every computer that uses the project. Projects that are only on your computer work exactly as before.
• Custom User Data is new in 2.0.55. Older versions of StraboMicro (and the original StraboMicro) still open the project, but saving it there removes the Custom User Data.
• File > Upload to Strabo Server... now turns on sync. The old one-time upload of the whole project is gone; projects uploaded with earlier versions can still be opened from Open Remote Project.