Release Notes

• 1.1.57 September 29, 2023

  • Ensure group order is persisted when performing differential expression between two groups

  • Fixed drop-down arrow click for gene sets

  • Show delete dataset from open dataset dialog

• 1.1.56 August 25, 2023

  • Updated display for differential expression between two groups

• 1.1.55 August 16, 2023

  • Support saving specific fields in prepare_data command

• 1.1.54 April 26, 2023

  • Read Xenium output

• 1.1.53 April 25, 2023

  • Added keyboard shortcuts for selecting active chart

• 1.1.52.post2 April 21, 2023

  • Fixed swapping row and column spot coordinates for Space Ranger output prior to version 2.0

• 1.1.52.post1 April 21, 2023

  • Fixed error parsing command line argument in concat command

• 1.1.52 April 20, 2023

  • Added option to invert categorical filters

  • Added search to categorical legend

  • Compute and visualize cellular trajectories interactively

  • Added support for Space Ranger 2.0 output

  • Added concat command to concatenate spatial and non-spatial embeddings

• 1.1.51 March 22, 2023

  • Support saving default visualization state in database

• 1.1.50 March 20, 2023

  • Support saving/loading anndata layers in parquet format

• 1.1.49 March 16, 2023

  • Fix bug where heatmap custom color range had no effect

• 1.1.48 January 26, 2023

  • Fix error using gene filter when performing differential expression between two selected groups

• 1.1.47 January 23, 2023

  • Show last updated date in dataset browser

  • Improved memory consumption for spatial datasets

• 1.1.46 January 3, 2023

  • Fix error using lasso selection when performing differential expression between two selected groups

• 1.1.45 December 12, 2022

  • Added option to download job result without opening

  • Show renamed category names in composition plot

  • Show legend in saved composition plot image

  • Fix error performing differential expression between two selected groups

• 1.1.44 November 21, 2022

  • Fix bug when multiple gene features fail to update

• 1.1.43 November 8, 2022

  • Support multiple lasso/box selections for spatial images

• 1.1.42 October 21, 2022

  • Added range filters for features and continuous metadata fields

• 1.1.41 September 30, 2022

  • Distribution tab updates: Show selection on top. Toggle visibility of selected and non-selected distributions

  • Added taxonomy field to new dataset dialog

  • Added option to save categorical color scheme to file

• 1.1.40 September 23, 2022

  • Sort clusters by percentage of selected cells within a cluster only updates when button is clicked

  • Added option to sort clusters by number of selected cells within a cluster

• 1.1.39 September 13, 2022

  • Fixed sorting clusters by percentage bug

• 1.1.38 September 9, 2022

  • Fixed authenticating with Google on Safari and FireFox

• 1.1.37 September 8, 2022

  • Added option to sort clusters by percentage of selected cells within a cluster

• 1.1.36 July 18, 2022

  • Updated support for Google OAuth 2.0 and App Engine

  • Ensure anndata layers are stored in sparse csc format in cirro prepare_data

• 1.1.35 July 1, 2022

  • Fixed error when selecting more than one layer in anndata layers

• 1.1.34 June 22, 2022

  • Added support for anndata layers

• 1.1.33 June 10, 2022

  • Fixed error computing differential expression results using scanpy in cirro prepare_data with older h5ad files

  • Raise error in cirro prepare_data when specified group not found in dataset

• 1.1.32 May 20, 2022

  • Fix error saving spatial datasets in cirro prepare_data

  • Updated dot plot tooltips

  • Added Okta integration

• 1.1.31 May 5, 2022

  • Fix error when setting a color manually when more than 40 category values

  • Improved differential expression filter user interface

• 1.1.30 May 5, 2022

  • Show percent cells in dot plot

• 1.1.29 April 11, 2022

  • Skip groups with less than 3 cells when computing differential expression results in cirro prepare_data

• 1.1.28 April 4, 2022

  • Fixed incompatibility with some datasets prepared with an earlier version of cirrocumulus

• 1.1.27 March 30, 2022

  • Fixed incompatibility with Flask 2.1

• 1.1.26 March 17, 2022

  • Fixed incompatibility with anndata 0.8.0

  • Fixed error when normalizing differential expression results

• 1.1.25.post4 March 8, 2022

  • Minor user interface updates

• 1.1.25.post3 February 25, 2022

  • Fixed error displaying differential expression results

• 1.1.25.post2 February 23, 2022

  • Fixed bug in which lower values were sometimes rendered on top of higher values in embedding chart

  • Performance improvements

• 1.1.25.post1 January 13, 2022

  • Preserve colors in h5ad file in cirro prepare_data

  • Set environment variable CIRRO_AUTH_CLIENT_ID to enable OAuth 2.0 with Google

  • User interface updates

• 1.1.25 December 20, 2021

  • Added option to compute differential expression results for all groups vs. rest

  • Updated tooltip display

• 1.1.24.post4 December 2, 2021

  • Removed –email flag from cirro serve

  • Fixed error storing large precomputed results

• 1.1.24.post3 November 23, 2021

  • Enable double-click to select on spatial images

  • Use spawn for running background jobs

  • Fixed bug in which dataset dialog remained open on save

  • Fixed error getting precomputed results

• 1.1.24.post2 November 19, 2021

  • Fixed error editing dataset

• 1.1.24.post1 November 15, 2021

  • Fixed error selecting all features in differential expression results

  • Added additional fields for new datasets

• 1.1.24 November 10, 2021

  • Changed default output format to zarr in cirro prepare_data

  • Fixed error retrieving job results stored in GridFS

• 1.1.23.post1 November 9, 2021

  • Fixed gzip encoding when writing to remote storage (e.g S3)

• 1.1.23 November 3, 2021

  • Style updates

  • Fixed error loading differential expression results

• 1.1.22.post10 November 2, 2021

  • Made left-side drawer collapsible

  • Fixed error saving cluster markers

  • Improved point size when saving embedding images

• 1.1.22.post9 October 29, 2021

  • Fixed error showing gallery labels

• 1.1.22.post8 October 28, 2021

  • Show zero cells instead of all cells when no cells pass filters

• 1.1.22.post7 October 28, 2021

  • Fixed default color scale for displaying features in sets

  • Changed single-click to double-click for selecting categorical values on primary embedding

• 1.1.22.post6 October 25, 2021

  • Preserve embeddings when multiple datasets passed to cirro prepare_data

  • Fixed error saving dataset views

• 1.1.22.post5 October 22, 2021

  • Separate color schemes for continuous observations, features, and modules

  • Explore gene modules stored in adata.uns[‘module’]

• 1.1.22.post4 October 19, 2021

  • Added ability to select all members of a set

  • Fixed bug displaying renamed category labels on embedding

  • Added option to integrate Mixpanel. Set environment variable CIRRO_MIXPANEL to your project token to track open dataset events

• 1.1.22.post3 October 13, 2021

  • Fixed bug that required two clicks to load differential expression results

  • Remove jobs from database when deleting datasets

• 1.1.22.post2 October 12, 2021

  • Fixed error when computing differential expression between two lasso’ed selections using cirro serve

  • Fixed display of “Sign In” button using cirro serve

  • Added ability to control the visibility of table columns in dataset chooser

• 1.1.22.post1 October 8, 2021

  • Save categorical legend scroll bar position when switching features

• 1.1.22 October 7, 2021

  • Added –ontology option to cirro serve and cirro launch

  • Fixed error saving colors from h5ad files in cirro prepare

  • Added option to search specific fields in dataset chooser

  • Save results in GridFS when using MongoDB without –results option

• 1.1.21 October 5, 2021

  • Removed –backed option in cirro launch

  • Added zarr format support in cirro prepare_data

  • Added –results option to cirro serve and cirro launch

  • Added ability to compute differential expression between all pairs of clusters

  • Select category by clicking cell on an embedding

• 1.1.20.post4 September 17, 2021

  • Style updates

• 1.1.20.post3 September 10, 2021

  • Fixed error computing differential expression in cirro prepare_data using Pegasus/Cumulus when categories contain the : character

• 1.1.20.post2 September 9, 2021

  • cirro prepare_data can output directly to S3 or GCP bucket

• 1.1.20.post1 September 8, 2021

  • Save categorical colors to database

  • Save cluster positive and negative markers to database

• 1.1.20 September 2, 2021

  • Added static website hosting capabilities

  • Performance improvements

• 1.1.19.post1 August 25, 2021

  • Fixed error getting precomputed results

• 1.1.19 August 25, 2021

  • Show distributions for numerical cell metadata

  • Improve interactive differential expression performance

• 1.1.18 August 16, 2021

  • cirro prepare_data accepts multiple input datasets to better support multimodal data

• 1.1.17.post4 August 13, 2021

  • Fixed error in cirro launch that prevented h5ad files from loading

• 1.1.17.post3 August 13, 2021

  • Compute complete differential expression results in cirro prepare_data using Scanpy or Pegasus/Cumulus

• 1.1.17.post2 August 11, 2021

  • Preserve category order only when < 1000 categories

  • Synchronize 3-d gallery chart rotation with primary view

  • Added separate marker size for filtered points

• 1.1.17.post1 June 29, 2021

  • Fixed error computing differential expression results when using cirro launch

• 1.1.17 June 28, 2021

  • Added TileDB support

• 1.1.16.post3 June 3, 2021

  • Embedding chart performance improvements

  • Replace saved filters with links in order to save complete state

• 1.1.16.post2 May 26, 2021

  • Drag and drop chips to reorder

  • Handle thousands of categories in violin plot

• 1.1.16.post1 April 28, 2021

  • Plot selected cells on top of unselected cells in embedding chart

• 1.1.16 April 28, 2021

  • Enable selecting top markers by a field in ascending or descending order

  • Updated auto-display logic

• 1.1.15.post4 April 22, 2021

  • Changed –header flag in cirro serve to accept Markdown file

• 1.1.15.post3 April 20, 2021

  • Fixed opening files with drive names on Windows

• 1.1.15.post2 April 13, 2021

  • Fixed error adding new dataset on Google App Engine

  • Show cirrocumulus version

• 1.1.15.post1 April 12, 2021

  • Moved composition plot to separate tab

  • Added –header flag to cirro serve to customize application header

  • Auto-display cluster annotation by default

• 1.1.15 April 6, 2021

  • Added composition plot

  • Pass –upload flag to cirro serve to enable file uploads

  • Show plot tooltips in bottom bar

  • Export data from dot plot

• 1.1.14.post5 March 30, 2021

  • Fixed issue that distribution charts did not update when color scheme changed

• 1.1.14.post4 March 26, 2021

  • Fixed issue that primary embedding chart did not update when color scheme changed

• 1.1.14.post3 March 9, 2021

  • Added ability to customize footer in cirro serve

• 1.1.14.post2 March 2, 2021

  • Click and drag to resize primary embedding chart

  • Added landing page

• 1.1.14.post1 February 24, 2021

  • Fixed error performing interactive differential expression analysis using cirro launch

  • Sort gallery charts by first by feature and then by embedding

• 1.1.14 February 23, 2021

  • Added interactive differential expression analysis

  • To add to current selection, hold down the Ctrl or Command keys when using lasso or box select tools

• 1.1.13.post2 February 10, 2021

  • Added standardize option that scales each feature or categorical group from zero to one for distributions and results visualization

  • Added species to dataset import when using cirro serve

  • Added option to show/hide labels in embedding gallery

  • cirro launch now accepts Seurat objects

• 1.1.13.post1 February 2, 2021

  • Added sort functionality to full differential expression results visualization

• 1.1.13 February 1, 2021

  • Explore complete differential expression results generated by Scanpy or Pegasus/Cumulus

  • Added reverse option to color schemes

• 1.1.12 January 20, 2021

  • Added violin plots

• 1.1.11.post3 December 14, 2020

  • Include categorical labels and dot plot options in Copy Link URL

• 1.1.11.post2 December 8, 2020

  • Use anndata.uns[field_colors] if present for cell metadata default colors

  • Added ability to view features in saved sets

  • Use reticulate to convert Seurat objects to h5ad in cirro prepare_data

• 1.1.11.post1 December 6, 2020

  • Convert seurat_clusters cell metadata field in Seurat objects to categorical in cirro prepare_data

• 1.1.11 December 4, 2020

  • Automatically compute cluster markers when using cirro prepare_data without –group flag

  • Show categorical labels on gene/feature embedding plots

  • Updated code for reading Seurat objects in cirro prepare_data

• 1.1.10.post8 November 24, 2020

  • Fixed error in cirro prepare_data when saving cell metadata names containing spaces

• 1.1.10.post7 November 23, 2020

  • Plot higher values on top of lower values for continuous values in saved embedding image.

  • Improved performance computing markers using cirro prepare_data with –group flag

• 1.1.10.post6 November 20, 2020

  • Fixed bug that prevented genes in sets from being displayed in selection dot plot.

• 1.1.10.post5 November 18, 2020

  • Fixed error when computing markers using cirro prepare_data with –group flag

  • Added ability to enter dataset description in Markdown when using cirro serve

• 1.1.10.post4 November 12, 2020

  • Toggle between dot plot and heatmap

• 1.1.10.post3 November 6, 2020

  • Added option to change dot plot color scheme

• 1.1.10.post2 October 30, 2020

  • Fixed display of set names

  • Fixed bug updating selected dot plot when selection changes

• 1.1.10.post1 October 28, 2020

  • Create dot plots by grouping by more than one category

  • Search dataset names and descriptions when using cirro serve

• 1.1.10 October 25, 2020

  • Fixed error selecting more than one cell metadata field

• 1.1.9.post3 October 21, 2020

  • Fixed error on startup using cirro launch

• 1.1.9.post2 October 20, 2020

  • Fixed serving spatial images using cirro serve

• 1.1.9.post1 October 13, 2020

  • Fixed error reading old datasets generated with cirro prepare_data

• 1.1.9 October 13, 2020

  • Added user interface to create gene/feature sets

• 1.1.8.post5 October 5, 2020

  • Updated dataset chooser

• 1.1.8.post4 October 2, 2020

  • Added dataset descriptions

• 1.1.8.post3 October 1, 2020

  • Show labels in gallery

  • Updated dark mode

• 1.1.8.post2 September 29, 2020

  • Removed active list. Select a feature/category to view details and filter

• 1.1.8.post1 September 25, 2020

  • Shuffle plot order in embedding plot for categorical values

  • Fixed scrolling bug in active list

• 1.1.8 September 24, 2020

  • Added support for generic spatial data in addition to 10x visium

  • Made primary embedding chart responsive

  • Added option to set min and max of color scale

  • Updated gallery chart size

  • Updated prepare_data command

  • Changed dot plot default min to zero

  • Added option to dot plot mean and percent expressed scales

• 1.1.7.post3 September 18, 2020

  • Plot higher values on top of lower values in embedding plot

• 1.1.7.post2 September 17, 2020

  • Save state when toggling between datasets

  • Fixed bug in dot plot tooltips

  • Changed dot plot color scheme

• 1.1.7.post1 September 2, 2020

  • Fixed bug passing markers to launch command

  • launch command takes multiple datasets

• 1.1.7 August 28, 2020

  • Use median instead of mean for categorical label position on data

  • Fixed Safari embedding label shadow bug

  • Save pan and zoom values in link URL

• 1.1.6 August 27, 2020

  • Added option to set embedding label font size

  • Show shadow around embedding label

• 1.1.5.post3 August 26, 2020

  • Fixed embedding label and tooltip color in dark mode

  • Fixed embedding label font size

• 1.1.5.post2 August 25, 2020

  • Save additional chart options when copying link

  • Support multiple differential expression results produced by Scanpy

• 1.1.5.post1 August 24, 2020

  • Fixed dot plot background color in dark mode

• 1.1.5 August 24, 2020

  • Allow dataset sharing within an email domain

  • Added additional 3-d chart options

  • Added dark theme

  • Added timeout to serve command

  • Support markers generated with Pegasus

• 1.1.4 August 17, 2020

  • Added spatial support

• 1.1.3 August 13, 2020

  • Improved support for Google authentication in serve command

• 1.1.2.post2 August 12, 2020

  • Fixed bug in prepare_data for saving markers

  • Added gunicorn and pymongo to requirements

• 1.1.2.post1 August 11, 2020

  • Added pyarrow to requirements

• 1.1.2 August 11, 2020

  • Show separate dot plots for all cells and selected cells

  • Added support for renaming clusters

  • Added prepare_data command for generating cirrocumulus formatted files for viewing on the cloud

  • Added ‘serve’ command to serve multiple users and datasets

• 1.1.1 July 24, 2020

  • Load marker genes from h5ad or JSON file

• 1.1.0.post3 July 17, 2020

  • Fixed embedding hover formatting issue

• 1.1.0.post2 July 16, 2020

  • Fixed Safari bug that caused gallery images to be flipped

  • Improved performance loading local h5ad files

• 1.1.0.post1 June 15, 2020

  • Fixed bug that sometimes prevented dot plot from showing

• 1.1.0 June 1, 2020

  • Added support for STARFusion output

  • Include labels in saved image

• 1.0.1 May 7, 2020

  • Draw labels on embedding

• 1.0.0 May 5, 2020

  • Lasso and box selection

• 0.0.6.post2 Mar 25, 2020

  • Added tabs for navigation

  • Use pandas for serialization

• 0.0.6.post1 Mar 20, 2020

  • Improved chart performance

• 0.0.6 Mar 19, 2020

  • Gallery view

• 0.0.5 Mar 19, 2020

  • Export filters

• 0.0.4 Jan 16, 2020

  • Autorotate 3d embeddings

• 0.0.3.post2 Jan 14, 2020

  • Save local filters to file

• 0.0.3.post1 Jan 9, 2020

  • Support 3d embeddings

• 0.0.3 Jan 9, 2020

  • Added filters

  • Added launch command

• 0.0.2 Nov 5, 2019

  • Initial release