diff --git a/README.md b/README.md
index 41136e0fd3..3ac31ba5ed 100644
--- a/README.md
+++ b/README.md
@@ -25,6 +25,7 @@ BIDS currently supports the following data modalities with more to come in the f
 - behavioral
 - physiological
 - PET
+- microscopy
 
 # Formatting your data with BIDS
 
diff --git a/mkdocs.yml b/mkdocs.yml
index 08f809aa0e..0f37932c70 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -39,6 +39,7 @@ nav:
         - Behavioral experiments (with no neural recordings): 04-modality-specific-files/07-behavioral-experiments.md
         - Genetic Descriptor: 04-modality-specific-files/08-genetic-descriptor.md
         - Positron Emission Tomography: 04-modality-specific-files/09-positron-emission-tomography.md
+        - Microscopy: 04-modality-specific-files/10-microscopy.md
       - Derivatives:
         - BIDS Derivatives: 05-derivatives/01-introduction.md
         - Common data types and metadata: 05-derivatives/02-common-data-types.md
diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index 337705235c..0736457e1c 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -56,6 +56,7 @@ misunderstanding we clarify them here.
     1.  `ieeg` (intracranial electroencephalography)
     1.  `beh` (behavioral)
     1.  `pet` (positron emission tomography)
+    1.  `micr` (microscopy)
 
     Data files are contained in a directory named for the data type.
     In raw datasets, the data type directory is nested inside subject and
diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index a6c911a2c4..5422515ad8 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -17,7 +17,7 @@ by Ben Inglis.
       "Manufacturer": ("RECOMMENDED", "Corresponds to DICOM Tag 0008, 0070 `Manufacturer`."),
       "ManufacturersModelName": ("RECOMMENDED", "Corresponds to DICOM Tag 0008, 1090 `Manufacturers Model Name`."),
       "DeviceSerialNumber": ("RECOMMENDED", "Corresponds to DICOM Tag 0018, 1000 `DeviceSerialNumber`."),
-      "StationName": "RECOMMENDED",
+      "StationName": ("RECOMMENDED", "Corresponds to DICOM Tag 0008, 1010 `Station Name`."),
       "SoftwareVersions": ("RECOMMENDED", "Corresponds to DICOM Tag 0018, 1020 `Software Versions`."),
       "HardcopyDeviceSoftwareVersion": "DEPRECATED",
       "MagneticFieldStrength": "RECOMMENDED, but REQUIRED for Arterial Spin Labeling",
diff --git a/src/04-modality-specific-files/09-positron-emission-tomography.md b/src/04-modality-specific-files/09-positron-emission-tomography.md
index 134512b81d..70e6d77f18 100644
--- a/src/04-modality-specific-files/09-positron-emission-tomography.md
+++ b/src/04-modality-specific-files/09-positron-emission-tomography.md
@@ -143,7 +143,7 @@ which we divide into several categories:
       "InstitutionName": ("RECOMMENDED", "Corresponds to DICOM Tag 0008, 0080 `InstitutionName`."),
       "InstitutionAddress": ("RECOMMENDED", "Corresponds to DICOM Tag 0008, 0081 `InstitutionAddress`."),
       "InstitutionalDepartmentName": ("RECOMMENDED", "Corresponds to DICOM Tag 0008, 1040 `Institutional Department Name`."),
-      "BodyPart": "RECOMMENDED",
+      "BodyPart": ("RECOMMENDED", "Corresponds to DICOM Tag 0018, 0015 `Body Part Examined`."),
    }
 ) }}
 
diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
new file mode 100644
index 0000000000..efb1542c52
--- /dev/null
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -0,0 +1,439 @@
+# Microscopy
+
+Support for Microscopy was developed as a
+[BIDS Extension Proposal](../07-extensions.md#bids-extension-proposals).
+
+Please see [Citing BIDS](../01-introduction.md#citing-bids)
+on how to appropriately credit this extension when referring to it in the
+context of the academic literature.
+
+Microscopy datasets formatted using this specification are available on the
+[BIDS examples repository](https://github.com/bids-standard/bids-examples#microscopy-datasets)
+and can be used for practical guidance when curating a new dataset.
+
+Further Microscopy datasets are available:
+
+-   In PNG format:  [`data_axondeepseg_sem`](https://doi.org/10.5281/zenodo.5498378)
+-   In OME-TIFF format: [`Broca's Area Light-Sheet Microscopy`](https://doi.org/10.5281/zenodo.5517223)
+
+## Microscopy imaging data
+
+{{ MACROS___make_filename_template(datatypes=["micr"], suffixes=["TEM", "SEM", "uCT", "BF", "DF",
+"PC", "DIC", "FLUO", "CONF", "PLI", "CARS", "2PE", "MPE", "SR", "NLO", "OCT", "SPIM"], n_dupes_to_combine=4) }}
+
+Microscopy data MUST be stored in the `micr` directory.
+
+### File formats
+The Microscopy community uses a variety of formats for storing raw data, and there is no single
+standard that all researchers agree on. However, a standardized file structure has been developed
+by the [Open Microscopy Environment](https://www.openmicroscopy.org/) for whole-slide imaging with
+the [OME-TIFF file specifications](https://docs.openmicroscopy.org/ome-model/6.1.2/ome-tiff/file-structure.html).
+The OME-TIFF file allows for multi-page TIFF files to store multiple image planes and supports
+multi-resolution pyramidal tiled images. An OME-XML data block is also embedded inside the
+file’s header.
+
+The BIDS standard accepts microscopy data in a number of file formats to accommodate datasets
+stored in 2D image formats and whole-slide imaging formats, to accommodate lossless and lossy
+compression, and to avoid unnecessary conversions of the original data from a non-tiled to a
+tiled format, or vice-versa.
+
+Microscopy raw data MUST be stored in one of the following formats:
+
+-   [Portable Network Graphics](http://www.libpng.org/pub/png/) (`.png`)
+
+-   [Tag Image File Format](https://www.adobe.io/open/standards/TIFF.html) (`.tif`)
+
+-   [OME-TIFF](https://docs.openmicroscopy.org/ome-model/6.1.2/ome-tiff/specification.html#)
+    (`.ome.tif` for standard TIFF files or `.ome.btf` for
+    [BigTIFF](https://www.awaresystems.be/imaging/tiff/bigtiff.html) files)
+
+If different from PNG, TIFF or OME-TIFF, the original unprocessed data in the native format MAY be
+stored in the [`/sourcedata` directory](../02-common-principles.md#source-vs-raw-vs-derived-data).
+
+Future versions may extend this list of supported file formats, for example with the
+Next-Generation File Formats currently developed by OME ([OME-NGFF](https://ngff.openmicroscopy.org/latest/))
+as a successor to OME-TIFF for better remote sharing of large datasets.
+
+### Modality suffixes
+Microscopy data currently support the following imaging modalities:
+
+{{ MACROS___make_suffix_table(
+      [
+         "TEM",
+         "SEM",
+         "uCT",
+         "BF",
+         "DF",
+         "PC",
+         "DIC",
+         "FLUO",
+         "CONF",
+         "PLI",
+         "CARS",
+         "2PE",
+         "MPE",
+         "SR",
+         "NLO",
+         "OCT",
+         "SPIM",
+      ]
+   )
+}}
+
+### Filename entities
+
+In the context of Microscopy, a session ([`ses-<label>`](../99-appendices/09-entities.md#ses))
+can refer to all the acquisitions between the start and the end of an imaging experiment
+for ex vivo imaging, or a subject lab visit for biopsy procedure and/or in vivo imaging.
+Consistent with other data types in BIDS, the session entity is optional.
+
+The [`sample-<label>`](../99-appendices/09-entities.md#sample) entity is REQUIRED for
+Microscopy data and is used to distinguish between different samples from the same subject.
+The label MUST be unique per subject and is RECOMMENDED to be unique throughout the dataset.
+
+For example: Three brain slices (`sample-01` to `sample-03`) extracted from subject `sub-01`,
+imaged by scanning electron microscopy (SEM) in PNG format
+
+{{ MACROS___make_filetree_example(
+   {
+   "sub-01": {
+      "micr": {
+         "sub-01_sample-01_SEM.png": "",
+         "sub-01_sample-02_SEM.png": "",
+         "sub-01_sample-03_SEM.png": "",
+         "sub-01_SEM.json": "",
+         },
+      }
+   }
+) }}
+
+In this example, the JSON metadata is common for all samples of `sub-01`.
+JSON metadata may be defined per subject or per sample as appropriate, as per the
+[inheritance principle](../02-common-principles.md#the-inheritance-principle).
+
+The [`acq-<label>`](../99-appendices/09-entities.md#acq) entity corresponds to a custom label that
+MAY be used to distinguish a different set of parameters used for acquiring the same modality.
+For example, two images of the same sample acquired by bright-field microscopy (BF) in PNG format at
+different magnification of 40x and 60x.
+In such case two files could have the following names: `sub-01_sample-01_acq-40x_BF.png` and
+`sub-01_sample-01_acq-60x_BF.png`, however the user is free to choose any other label as long as
+they are consistent across subjects and sessions.
+
+The [`stain-<label>`](../99-appendices/09-entities.md#stain) entity MAY be used to distinguish
+image files from the same sample using different stains or antibodies for contrast enhancement.
+
+For example: One brain slice (`sample-01`) extracted from subject `sub-01` with three
+stains (`stain-01`, `stain-02` and `stain-03`) in three separate files, imaged by selective plane
+illumination microscopy (SPIM) in OME-TIFF format
+
+{{ MACROS___make_filetree_example(
+   {
+   "sub-01": {
+      "micr": {
+         "sub-01_sample-01_stain-01_SPIM.ome.tif": "",
+         "sub-01_sample-01_stain-01_SPIM.json": "",
+         "sub-01_sample-01_stain-02_SPIM.ome.tif": "",
+         "sub-01_sample-01_stain-02_SPIM.json": "",
+         "sub-01_sample-01_stain-03_SPIM.ome.tif": "",
+         "sub-01_sample-01_stain-03_SPIM.json": "",
+         },
+      }
+   }
+) }}
+
+In this example, the entity stain is used to distinguish images with different
+stains in separate files from the same sample.
+In the case where a single file contains different staining in each channel, the
+`stain-<label>` is omitted.
+
+Stains SHOULD be indicated in the `"SampleStaining"` key in the sidecar JSON file,
+although the label may be different.
+Description of antibodies SHOULD also be indicated in `"SamplePrimaryAntibodies"`
+and/or `"SampleSecondaryAntobodies"` as appropriate.
+
+If more than one run of the same sample, acquisition and stain are acquired during the same
+session, the [`run-<index>`](../99-appendices/09-entities.md#run) entity MUST be used:
+`_run-1`, `_run-2`, `_run-3`, and so on.
+If only one run was acquired the `run-<index>` can be omitted.
+
+The [`chunk-<index>`](../99-appendices/09-entities.md#chunk) entity is used when multiples
+regions (2D images or 3D volumes files) of the same physical sample are imaged with different
+fields of view, regardless if they overlap or not.
+
+In some cases, the chunks can be "ordered" and, for example, correspond to the displacement of the
+microscope stage.
+In other cases, the chunks can be different images of the same sample with no explicit
+spatial relation between them.
+
+Examples of different chunks configurations can be seen in Figure 1.
+![Figure 1](images/microscopy_chunks1.png "Examples of Microscopy chunks")
+
+Figure 1: Examples of chunks configurations.
+
+-   a) ordered 2D chunks without overlap,
+-   b) ordered 2D chunks with overlap,
+-   c) unordered 2D chunks with and without overlap,
+-   d) and e) ordered 2D chunks on different 3D planes,
+-   f) ordered 3D chunks.
+
+For example: Four chunks (`chunk-01` to `chunk-04`) from the same brain sample (`sample-01`)
+of subject `sub-01`, imaged by confocal microscopy (CONF) in OME-TIFF format
+
+{{ MACROS___make_filetree_example(
+   {
+   "sub-01": {
+      "micr": {
+         "sub-01_sample-01_chunk-01_CONF.ome.tif": "",
+         "sub-01_sample-01_chunk-01_CONF.json": "",
+         "sub-01_sample-01_chunk-02_CONF.ome.tif": "",
+         "sub-01_sample-01_chunk-02_CONF.json": "",
+         "sub-01_sample-01_chunk-03_CONF.ome.tif": "",
+         "sub-01_sample-01_chunk-03_CONF.json": "",
+         "sub-01_sample-01_chunk-04_CONF.ome.tif": "",
+         "sub-01_sample-01_chunk-04_CONF.json": "",
+         },
+      }
+   }
+) }}
+
+The index number can be assigned arbitrarily and, in the case of "ordered" chunks, the chunks'
+relative positions (in terms of scaling and translation) SHOULD be defined by an affine
+transformation matrix in the JSON sidecar file of each chunk, as described in
+[Chunk Transformations](10-microscopy.md#chunk-transformations).
+
+In this example, the JSON metadata is different for each chunk of `sub-01_sample-01`.
+JSON metadata may be defined per sample or per chunk as appropriate, as per the
+[inheritance principle](../02-common-principles.md#the-inheritance-principle).
+
+In microscopy, many pyramidal file formats store multiple resolutions for the same acquisition.
+In the case where a multiple resolutions file format is converted to single resolution file format,
+only the higher resolution file is present in the raw data.
+Lower resolutions files MUST be placed under the `derivatives` folder and use the
+[`res-<label>`](../99-appendices/09-entities.md#res) entity.
+
+For example:
+
+{{ MACROS___make_filetree_example(
+   {
+   "my_dataset": {
+      "derivatives": {
+         "downsampled": {
+            "sub-01": {
+               "micr": {
+                  "sub-01_sample-01_res-4x_TEM.png": "",
+                  "sub-01_sample-01_res-4x_TEM.json": "",
+                  },
+               }
+            }
+         },
+      "sub-01": {
+         "micr": {
+            "sub-01_sample-01_TEM.png": "",
+            "sub-01_sample-01_TEM.json": "",
+            },
+         }
+      }
+   }
+) }}
+
+See [Preprocessed, coregistered and/or resampled volumes](../05-derivatives/03-imaging.md#preprocessed-coregistered-andor-resampled-volumes)
+for details.
+
+### Microscopy metadata (Sidecar JSON)
+
+Microscopy data MUST be described by metadata fields, stored in sidecar JSON files.
+
+#### Device Hardware
+
+{{ MACROS___make_metadata_table(
+   {
+      "Manufacturer": "RECOMMENDED",
+      "ManufacturersModelName": "RECOMMENDED",
+      "DeviceSerialNumber": "RECOMMENDED",
+      "StationName": "RECOMMENDED",
+      "SoftwareVersions": "RECOMMENDED",
+      "InstitutionName": "RECOMMENDED",
+      "InstitutionAddress": "RECOMMENDED",
+      "InstitutionalDepartmentName": "RECOMMENDED",
+   }
+) }}
+
+#### Image Acquisition
+
+{{ MACROS___make_metadata_table(
+   {
+      "PixelSize": "REQUIRED",
+      "PixelSizeUnits": "REQUIRED",
+      "Immersion": "OPTIONAL",
+      "NumericalAperture": "OPTIONAL",
+      "Magnification": "OPTIONAL",
+      "ImageAcquisitionProtocol": "OPTIONAL",
+      "OtherAcquisitionParameters": "OPTIONAL",
+   }
+) }}
+
+#### Sample
+
+{{ MACROS___make_metadata_table(
+   {
+      "BodyPart": ("RECOMMENDED", "From [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L) (for example `\"BRAIN\"`)."),
+      "BodyPartDetails": "RECOMMENDED",
+      "BodyPartDetailsOntology": "OPTIONAL",
+      "SampleEnvironment": "RECOMMENDED",
+      "SampleEmbedding": "OPTIONAL",
+      "SampleFixation": "OPTIONAL",
+      "SampleStaining": "RECOMMENDED",
+      "SamplePrimaryAntibody": "RECOMMENDED",
+      "SampleSecondaryAntibody": "RECOMMENDED",
+      "SliceThickness": "OPTIONAL",
+      "TissueDeformationScaling": "OPTIONAL",
+      "SampleExtractionProtocol": "OPTIONAL",
+      "SampleExtractionInstitution": "OPTIONAL",
+   }
+) }}
+
+#### Chunk Transformations
+
+Chunk transformations metadata describes the spatial relation between chunks
+of the same sample in an implicit coordinate system.
+
+-   The source frame of reference is the frame of reference of the associated image.
+
+-   The target frame of reference is the implicit coordinate system of the transform.
+
+-   The target frame of reference has the same units as the `PixelSizeUnits` metadata.
+
+-   The chunk transformation is described by 2 metadata fields: an affine transformation matrix
+    and a description of the axis of the matrix.
+
+-   Other transformations should be described in derivatives.
+
+{{ MACROS___make_metadata_table(
+   {
+      "ChunkTransformationMatrix": "RECOMMENDED if `<chunk-index>` is used in filenames",
+      "ChunkTransformationMatrixAxis": "REQUIRED if `ChunkTransformationMatrix` is present",
+   }
+) }}
+
+An example of chunk transformations JSON metadata for `chunk-01` and `chunk-05` of Figure 2
+is shown below:
+
+![Figure 2](images/microscopy_chunks2.png "Example figure for chunks transformations")
+
+Figure 2: Example figure for chunks transformations.
+
+In this example, there is no scaling and `chunk-01` is at the origin.
+`chunk-05` is translated by 5 um along `X+` and by 3 um along `Y+`.
+
+**`*_chunk-01_<suffix>.json`**:
+```JSON
+{
+        "PixelSize": [1, 1],
+        "PixelSizeUnits": "um",
+        "ChunkTransformationMatrix": [[1, 0, 0],
+                                      [0, 1, 0],
+                                      [0, 0, 1]],
+        "ChunkTransformationMatrixAxis": ["X", "Y"]
+}
+```
+
+**`*_chunk-05_<suffix>.json`**:
+```JSON
+{
+        "PixelSize": [1, 1],
+        "PixelSizeUnits": "um",
+        "ChunkTransformationMatrix": [[1, 0, 5],
+                                      [0, 1, 3],
+                                      [0, 0, 1]],
+        "ChunkTransformationMatrixAxis": ["X", "Y"]
+}
+```
+
+#### Example of sidecar JSON file (`*_<suffix>.json`)
+```JSON
+{
+        "Manufacturer": "Hamamatsu",
+        "ManufacturersModelName": "C9600-12",
+        "PixelSize": [0.23, 0.23],
+        "PixelSizeUnits": "um",
+        "Magnification": 40,
+        "BodyPart": "BRAIN",
+        "BodyPartDetails": "corpus callosum",
+        "SampleEnvironment": "ex vivo",
+        "SampleFixation": "4% paraformaldehyde, 2% glutaraldehyde",
+        "SampleStaining": "LFB",
+        "SliceThickness": 5,
+        "TissueDeformationScaling": 97
+}
+```
+
+## Required Samples file
+
+For Microscopy data, the [Samples file](../03-modality-agnostic-files.md#samples-file)
+`samples.tsv` is REQUIRED and its associated sidecar `samples.json` file is RECOMMENDED.
+
+Additional optional columns MAY be used to describe other samples' attributes.
+
+## Recommended Participants data
+
+For Microscopy data, we RECOMMEND to make use of the columns `species`, `strain` and
+`strain_rrid` in the [Participants file](../03-modality-agnostic-files.md#participants-file)
+when applicable.
+
+Additional optional columns MAY be used to describe other subjects' attributes.
+
+`participants.tsv` example:
+```Text
+participant_id species strain strain_rrid
+sub-01 mus musculus C57BL/6J RRID:IMSR_JAX:000664
+sub-02 mus musculus C57BL/6J RRID:IMSR_JAX:000664
+```
+
+`participants.json` example:
+```JSON
+{
+    "species": {
+        "Description": "binomial species name from the NCBI Taxonomy (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi)"
+    },
+    "strain": {
+        "Description": "name of the strain of the species"
+    },
+    "strain_rrid": {
+        "Description": "research resource identifier (RRID) of the strain (https://scicrunch.org/resources/Organisms/search)"
+    }
+}
+```
+
+## Photos of the samples (`*_photo.<extension>`)
+Photos of the tissue sample, overview microscopy scans or blockface images from cutting
+MAY be included for visualization of large samples or to indicate the location of chunks
+in a sample.
+
+{{ MACROS___make_filename_template(datatypes=["micr"], suffixes=["photo"], n_dupes_to_combine=3) }}
+
+The file `<extension>` for photos MUST be either `.jpg`, `.png` or `.tif`.
+
+The [`acq-<label>`](../99-appendices/09-entities.md#acq) entity MAY be used to indicate
+acquisition of different photos of the same sample.
+
+For example:
+
+{{ MACROS___make_filetree_example(
+   {
+   "sub-01": {
+      "micr": {
+         "sub-01_sample-01_acq-1_photo.jpg": "",
+         "sub-01_sample-01_acq-2_photo.jpg": "",
+         },
+      }
+   }
+) }}
+
+Below is an example of a spinal cord SEM overview, modified from Zaimi et al., 2018.
+[doi:10.1038/s41598-018-22181-4](https://doi.org/10.1038/s41598-018-22181-4).
+```Text
+    sub-01_sample-01_photo.jpg
+```
+![SEM overview](images/microscopy_sem_overview.jpg "SEM overview")
+
+<!-- Link Definitions -->
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diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index 1afd0771a9..91bf0381a6 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -37,3 +37,7 @@ while entity definitions are in [Appendix IX](09-entities.md).
 ## Behavioral Data
 
 {{ MACROS___make_entity_table(datatypes=["beh"], auxdatatypes=[]) }}
+
+## Microscopy
+
+{{ MACROS___make_entity_table(datatypes=["micr"], auxdatatypes=[]) }}
diff --git a/src/schema/objects/datatypes.yaml b/src/schema/objects/datatypes.yaml
index 1366f66da9..06c059eedc 100644
--- a/src/schema/objects/datatypes.yaml
+++ b/src/schema/objects/datatypes.yaml
@@ -31,6 +31,9 @@ ieeg:
 meg:
   name: Magnetoencephalography
   description: Magnetoencephalography
+micr:
+  name: Microscopy
+  description: Microscopy
 perf:
   name: Perfusion imaging
   description: |
diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
index e6a3db6ca3..de278d3dc3 100644
--- a/src/schema/objects/entities.yaml
+++ b/src/schema/objects/entities.yaml
@@ -36,6 +36,15 @@ ceagent:
     with the same label.
   type: string
   format: label
+chunk:
+  name: Chunk
+  entity: chunk
+  description: |
+    The `chunk-<index>` key/value pair is used to distinguish between different
+    regions, 2D images or 3D volumes files, of the same physical sample with
+    different fields of view acquired in the same imaging experiment.
+  type: string
+  format: index
 density:
   name: Density
   entity: den
@@ -306,6 +315,18 @@ split:
     [Scans file](../03-modality-agnostic-files.md#scans-file).
   type: string
   format: index
+stain:
+  name: Stain
+  entity: stain
+  description: |
+    The `stain-<label>` key/pair values can be used to distinguish image files
+    from the same sample using different stains or antibodies for contrast enhancement.
+    Stains SHOULD be indicated in the `"SampleStaining"` key in the sidecar JSON file,
+    although the label may be different.
+    Description of antibodies SHOULD also be indicated in `"SamplePrimaryAntibodies"`
+    and/or `"SampleSecondaryAntobodies"` as appropriate.
+  type: string
+  format: label
 subject:
   name: Subject
   entity: sub
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index f8118c6351..d391384fbd 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -251,8 +251,19 @@ BodyPart:
   name: BodyPart
   description: |
     Body part of the organ / body region scanned.
-    Corresponds to DICOM Tag 0018, 0015 `Body Part Examined`.
   type: string
+BodyPartDetails:
+  name: BodyPartDetails
+  description: |
+    Additional details about body part or location (for example: `"corpus callosum"`).
+  type: string
+BodyPartDetailsOntology:
+  name: BodyPartDetailsOntology
+  description: |
+    [URI](/02-common-principles.html#uniform-resource-indicator) of ontology used for
+    BodyPartDetails (for example: `"https://www.ebi.ac.uk/ols/ontologies/uberon"`).
+  type: string
+  format: uri
 BolusCutOffDelayTime:
   name: BolusCutOffDelayTime
   description: |
@@ -324,6 +335,45 @@ CellType:
     Values SHOULD come from the
     [cell ontology](http://obofoundry.org/ontology/cl.html).
   type: string
+ChunkTransformationMatrix:
+  name: ChunkTransformationMatrix
+  description: |
+    3x3 or 4x4 affine transformation matrix describing spatial chunk transformation,
+    for 2D and 3D respectively (for examples: `[[2, 0, 0], [0, 3, 0], [0, 0, 1]]`
+    in 2D for 2x and 3x scaling along the first and second axis respectively; or
+    `[[1, 0, 0, 0], [0, 2, 0, 0], [0, 0, 3, 0], [0, 0, 0, 1]]` in 3D for 2x and 3x
+    scaling along the second and third axis respectively).
+    Note that non-spatial dimensions like time and channel are not included in the
+    transformation matrix.
+  anyOf:
+  - type: array
+    minItems: 3
+    maxItems: 3
+    items:
+      type: array
+      minItems: 3
+      maxItems: 3
+      items:
+        type: number
+  - type: array
+    minItems: 4
+    maxItems: 4
+    items:
+      type: array
+      minItems: 4
+      maxItems: 4
+      items:
+        type: number
+ChunkTransformationMatrixAxis:
+  name: ChunkTransformationMatrixAxis
+  description: |
+    Describe the axis of the ChunkTransformationMatrix
+    (for examples: `["X", "Y"]` or `["Z", "Y", "X"]`).
+  type: array
+  items:
+    type: string
+    minItems: 2
+    maxItems: 3
 Code:
   name: Code
   description: |
@@ -1083,6 +1133,13 @@ HowToAcknowledge:
     This field can also be used to define a publication that should be cited in
     publications that use the dataset.
   type: string
+ImageAcquisitionProtocol:
+  name: ImageAcquisitionProtocol
+  description: |
+    Description of the image acquisition protocol or
+    [URI](/02-common-principles.html#uniform-resource-indicator)
+    (for example from [protocols.io](https://www.protocols.io/)).
+  type: string
 ImageDecayCorrected:
   name: ImageDecayCorrected
   description: |
@@ -1095,6 +1152,12 @@ ImageDecayCorrectionTime:
     TimeZero in the default unit seconds.
   type: number
   unit: s
+Immersion:
+  name: Immersion
+  description: |
+    Lens immersion medium. If the file format is OME-TIFF, the value MUST be consistent
+    with the `Immersion` OME metadata field.
+  type: string
 InfusionRadioactivity:
   name: InfusionRadioactivity
   description: |
@@ -1526,6 +1589,13 @@ MagneticFieldStrength:
     Nominal field strength of MR magnet in Tesla.
     Corresponds to DICOM Tag 0018, 0087 `Magnetic Field Strength`.
   type: number
+Magnification:
+  name: Magnification
+  description: |
+    Lens magnification (for example: `40`). If the file format is OME-TIFF,
+    the value MUST be consistent with the `NominalMagnification` OME metadata field.
+  type: number
+  exclusiveMinimum: 0
 Manual:
   name: Manual
   description: |
@@ -1710,12 +1780,24 @@ NumberShots:
   - type: array
     items:
       type: number
+NumericalAperture:
+  name: NumericalAperture
+  description: |
+    Lens numerical aperture (for example: `1.4`). If the file format is OME-TIFF,
+    the value MUST be consistent with the `LensNA` OME metadata field.
+  type: number
+  exclusiveMinimum: 0
 OperatingSystem:
   name: OperatingSystem
   description: |
     Operating system used to run the stimuli presentation software
     (for formatting recommendations, see examples below this table).
   type: string
+OtherAcquisitionParameters:
+  name: OtherAcquisitionParameters
+  description: |
+    Description of other relevant image acquisition parameters.
+  type: string
 PASLType:
   name: PASLType
   description: |
@@ -1823,6 +1905,32 @@ PhaseEncodingDirection:
   - i-
   - j-
   - k-
+PixelSize:
+  name: PixelSize
+  description: |
+    A 2- or 3-number array of the physical size of a pixel, either `[PixelSizeX, PixelSizeY]`
+    or `[PixelSizeX, PixelSizeY, PixelSizeZ]`, where X is the width, Y the height and Z the
+    depth.
+    If the file format is OME-TIFF, these values need to be consistent with `PhysicalSizeX`,
+    `PhysicalSizeY` and `PhysicalSizeZ` OME metadata fields, after converting in
+    `PixelSizeUnits` according to `PhysicalSizeXunit`, `PhysicalSizeYunit` and
+    `PhysicalSizeZunit` OME fields.
+  type: array
+  minItems: 2
+  maxItems: 3
+  items:
+    type: number
+    minimum: 0
+PixelSizeUnits:
+  name: PixelSizeUnits
+  description: |
+    Unit format of the specified `PixelSize`. MUST be one of: `"mm"` (millimeter), `"um"`
+    (micrometer) or `"nm"` (nanometer).
+  type: string
+  enum:
+  - mm
+  - um
+  - nm
 PlasmaAvail:
   name: PlasmaAvail
   description: |
@@ -2098,6 +2206,40 @@ SEEGChannelCount:
     Number of SEEG channels.
   type: integer
   minimum: 0
+SampleEmbedding:
+  name: SampleEmbedding
+  description: |
+    Description of the tissue sample embedding (for example: `"Epoxy resin"`).
+  type: string
+SampleEnvironment:
+  name: SampleEnvironment
+  description: |
+    Environment in which the sample was imaged. MUST be one of: `"in vivo"`, `"ex vivo"`
+    or `"in vitro"`.
+  type: string
+  enum:
+  - in vivo
+  - ex vivo
+  - in vitro
+SampleExtractionInstitution:
+  name: SampleExtractionInstitution
+  description: |
+    The name of the institution in charge of the extraction of the sample,
+    if different from the institution in charge of the equipment that produced the image.
+  type: string
+SampleExtractionProtocol:
+  name: SampleExtractionProtocol
+  description: |
+    Description of the sample extraction protocol or
+    [URI](/02-common-principles.html#uniform-resource-indicator)
+    (for example from [protocols.io](https://www.protocols.io/)).
+  type: string
+SampleFixation:
+  name: SampleFixation
+  description: |
+    Description of the tissue sample fixation
+    (for example: `"4% paraformaldehyde, 2% glutaraldehyde"`).
+  type: string
 SampleOrigin:
   name: SampleOrigin
   description: |
@@ -2114,6 +2256,47 @@ SampleOrigin:
   - bile
   - amniotic fluid
   - other biospecimen
+SamplePrimaryAntibody:
+  name: SamplePrimaryAntibody
+  description: |
+    Description(s) of the primary antibody used for immunostaining.
+    Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalogue
+    number of a commercial antibody.
+    For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the
+    host-animal and immunogen used (for examples: `"RRID:AB_2122563"` or
+    `"Rabbit anti-Human HTR5A Polyclonal Antibody, Invitrogen, Catalog # PA1-2453"`).
+    MAY be an array of strings if different antibodies are used in each channel of the file.
+  anyOf:
+  - type: string
+  - type: array
+    items:
+      type: string
+SampleSecondaryAntibody:
+  name: SampleSecondaryAntibody
+  description: |
+    Description(s) of the secondary antibody used for immunostaining.
+    Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalogue
+    number of a commercial antibody.
+    For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the
+    host-animal and immunogen used (for examples: `"RRID:AB_228322"` or
+    `"Goat anti-Mouse IgM Secondary Antibody, Invitrogen, Catalog # 31172"`).
+    MAY be an array of strings if different antibodies are used in each channel of the file.
+  anyOf:
+  - type: string
+  - type: array
+    items:
+      type: string
+SampleStaining:
+  name: SampleStaining
+  description: |
+    Description(s) of the tissue sample staining (for example: `"Osmium"`).
+    MAY be an array of strings if different stains are used in each channel of the file
+    (for example: `["LFB", "PLP"]`).
+  anyOf:
+  - type: string
+  - type: array
+    items:
+      type: string
 SamplingFrequency:
   name: SamplingFrequency
   description: |
@@ -2222,6 +2405,13 @@ SliceEncodingDirection:
   - i-
   - j-
   - k-
+SliceThickness:
+  name: SliceThickness
+  description: |
+    Slice thickness of the tissue sample in the unit micrometers (`"um"`) (for example: `5`).
+  type: number
+  unit: um
+  exclusiveMinimum: 0
 SliceTiming:
   name: SliceTiming
   description: |
@@ -2425,7 +2615,6 @@ StationName:
   name: StationName
   description: |
     Institution defined name of the machine that produced the measurements.
-    Corresponds to DICOM Tag 0008, 1010 `Station Name`.
   type: string
 StimulusPresentation:
   name: StimulusPresentation
@@ -2484,6 +2673,14 @@ TimeZero:
     This should be equal to `InjectionStart` or `ScanStart`.
   type: string
   pattern: ^(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9]$
+TissueDeformationScaling:
+  name: TissueDeformationScaling
+  description: |
+    Estimated deformation of the tissue, given as a percentage of the original
+    tissue size (for examples: for a shrinkage of 3%, the value is `97`;
+    and for an expansion of 100%, the value is `200`).
+  type: number
+  exclusiveMinimum: 0
 TissueOrigin:
   name: TissueOrigin
   description: |
diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index 38911367ec..e809e375ea 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -1,6 +1,14 @@
 ---
 # This file defines valid BIDS file suffixes.
 # For rules regarding how suffixes relate to datatypes, see files in `rules/datatypes/`.
+2PE:
+  name: 2-photon excitation microscopy
+  description: |
+    2-photon excitation microscopy imaging data
+BF:
+  name: Bright-field microscopy
+  description: |
+    Bright-field microscopy imaging data
 Chimap:
   name: Quantitative susceptibility map (QSM)
   description: |
@@ -11,6 +19,22 @@ Chimap:
     Chi maps are REQUIRED to use this suffix regardless of the method used to
     generate them.
   unit: ppm
+CARS:
+  name: Coherent anti-Stokes Raman spectroscopy
+  description: |
+    Coherent anti-Stokes Raman spectroscopy imaging data
+CONF:
+  name: Confocal microscopy
+  description: |
+    Confocal microscopy imaging data
+DIC:
+  name: Differential interference contrast microscopy
+  description: |
+    Differential interference contrast microscopy imaging data
+DF:
+  name: Dark-field microscopy
+  description: |
+    Dark-field microscopy imaging data
 FLAIR:
   name: Fluid attenuated inversion recovery image
   description: |
@@ -31,6 +55,10 @@ FLASH:
     When used in a file collection, it may result in conflicts across filenames of
     different applications.
     **Change:** Removed from suffixes.
+FLUO:
+  name: Fluorescence microscopy
+  description: |
+    Fluorescence microscopy imaging data
 IRT1:
   name: Inversion recovery T1 mapping
   description: |
@@ -66,6 +94,10 @@ MP2RAGE:
     different flip angles and inversion times to create a parametric T1map by
     combining the magnitude and phase images
     ([Marques et al. 2010](https://doi.org/10.1016/j.neuroimage.2009.10.002)).
+MPE:
+  name: Multi-photon excitation microscopy
+  description: |
+    Multi-photon excitation microscopy imaging data
 MPM:
   name: Multi-parametric Mapping
   description: |
@@ -125,6 +157,18 @@ MWFmap:
   unit: arbitrary
   minValue: 0
   maxValue: 100
+NLO:
+  name: Nonlinear optical microscopy
+  description: |
+    Nonlinear optical microscopy imaging data
+OCT:
+  name: Optical coherence tomography
+  description: |
+    Optical coherence tomography imaging data
+PC:
+  name: Phase-contrast microscopy
+  description: |
+    Phase-contrast microscopy imaging data
 PD:
   name: Proton density image
   description: |
@@ -164,6 +208,10 @@ PDw:
     In a gradient-echo acquisition, PD weighting dominates the contrast at long
     repetition and short echo times, and at small flip angles.
   unit: arbitrary
+PLI:
+  name: Polarized-light microscopy
+  description: |
+    Polarized-light microscopy imaging data
 R1map:
   name: Longitudinal relaxation rate image
   description: |
@@ -213,6 +261,18 @@ S0map:
     [the tedana documentation](https://tedana.readthedocs.io/en/latest/\
     approach.html#monoexponential-decay-model-fit).
     S0 maps are RECOMMENDED to use this suffix if derived from an ME-FMRI dataset.
+SEM:
+  name: Scanning electron microscopy
+  description: |
+    Scanning electron microscopy imaging data
+SPIM:
+  name: Selective plane illumination microscopy
+  description: |
+    Selective plane illumination microscopy imaging data
+SR:
+  name: Super-resolution microscopy
+  description: |
+    Super-resolution microscopy imaging data
 T1map:
   name: Longitudinal relaxation time image
   description: |
@@ -347,6 +407,10 @@ TB1map:
     multiplicative factors such that FlipAngle<sub>effective</sub> =
     B1+<sub>intensity</sub>\*FlipAngle<sub>nominal</sub> .
   unit: arbitrary
+TEM:
+  name: Transmission electron microscopy
+  description: |
+    Transmission electron microscopy imaging data
 UNIT1:
   name: Homogeneous (flat) T1-weighted MP2RAGE image
   description: |
@@ -544,8 +608,7 @@ phasediff:
 photo:
   name: Photo File
   description: |
-    Photos of the anatomical landmarks and/or head localization coils
-    (`*_photo.jpg`).
+    Photos of the anatomical landmarks, head localization coils or tissue sample.
 physio:
   name: Physiological recording
   description: |
@@ -558,3 +621,7 @@ stim:
   name: Continuous recording
   description: |
     Continuous measures, such as parameters of a film or audio stimulus.
+uCT:
+  name: Micro-CT
+  description: |
+    Micro-CT imaging data
diff --git a/src/schema/objects/top_level_files.yaml b/src/schema/objects/top_level_files.yaml
index 12e1823472..79eab838c0 100644
--- a/src/schema/objects/top_level_files.yaml
+++ b/src/schema/objects/top_level_files.yaml
@@ -77,3 +77,34 @@ participants:
 
     Throughout BIDS you can indicate missing values with `n/a` (for "not
     available").
+
+samples:
+  name: Sample Information
+  description: |
+    The purpose of this file is to describe properties of samples, indicated by the `sample` entity.
+    This file is REQUIRED if `sample-<label>` is present in any file name within the dataset.
+    If this file exists, it MUST contain the three following columns:
+
+    -   `sample_id`: MUST consist of `sample-<label>` values identifying one row
+        for each sample
+
+    -   `participant_id`: MUST consist of `sub-<label>`
+
+    -   `sample_type`: MUST consist of sample type values, either `cell line`, `in vitro differentiated cells`,
+        `primary cell`, `cell-free sample`, `cloning host`, `tissue`, `whole organisms`, `organoid` or
+        `technical sample` from [ENCODE Biosample Type](https://www.encodeproject.org/profiles/biosample_type)
+
+    Other optional columns MAY be used to describe the samples.
+    Each sample MUST be described by one and only one row.
+
+    Commonly used *optional* columns in `samples.tsv` files are `pathology` and
+    `derived_from`. We RECOMMEND to make use of these columns, and in case that
+    you do use them, we RECOMMEND to use the following values for them:
+
+    -   `pathology`: string value describing the pathology of the sample or type of control.
+        When different from `healthy`, pathology SHOULD be specified in `samples.tsv`.
+        The pathology MAY instead be specified in
+        [Sessions files](../03-modality-agnostic-files.md#sessions-file) in case it changes over time.
+
+    -   `derived_from`: `sample-<label>` key/value pair from which a sample is derived from,
+        for example a slice of tissue (`sample-02`) derived from a block of tissue (`sample-01`)
diff --git a/src/schema/rules/datatypes/micr.yaml b/src/schema/rules/datatypes/micr.yaml
new file mode 100644
index 0000000000..3af2fb86d3
--- /dev/null
+++ b/src/schema/rules/datatypes/micr.yaml
@@ -0,0 +1,46 @@
+---
+# Microscopy
+- suffixes:
+  - TEM
+  - SEM
+  - uCT
+  - BF
+  - DF
+  - PC
+  - DIC
+  - FLUO
+  - CONF
+  - PLI
+  - CARS
+  - 2PE
+  - MPE
+  - SR
+  - NLO
+  - OCT
+  - SPIM
+  extensions:
+  - .ome.tif
+  - .ome.btf
+  - .png
+  - .tif
+  - .json
+  entities:
+    subject: required
+    session: optional
+    sample: required
+    acquisition: optional
+    stain: optional
+    run: optional
+    chunk: optional
+
+- suffixes:
+  - photo
+  extensions:
+  - .jpg
+  - .png
+  - .tif
+  entities:
+    subject: required
+    session: optional
+    sample: required
+    acquisition: optional
diff --git a/src/schema/rules/entities.yaml b/src/schema/rules/entities.yaml
index 648f99cfd9..1e145edee6 100644
--- a/src/schema/rules/entities.yaml
+++ b/src/schema/rules/entities.yaml
@@ -8,6 +8,7 @@
 - acquisition
 - ceagent
 - tracer
+- stain
 - reconstruction
 - direction
 - run
@@ -22,6 +23,7 @@
 - hemisphere
 - space
 - split
+- chunk
 - resolution
 - density
 - label
diff --git a/src/schema/rules/modalities.yaml b/src/schema/rules/modalities.yaml
index 9127db93e7..04b24489d7 100644
--- a/src/schema/rules/modalities.yaml
+++ b/src/schema/rules/modalities.yaml
@@ -22,3 +22,6 @@ beh:
 pet:
   datatypes:
   - pet
+micr:
+  datatypes:
+  - micr
diff --git a/tools/schemacode/schemacode/render.py b/tools/schemacode/schemacode/render.py
index db802d8db9..56480f351a 100644
--- a/tools/schemacode/schemacode/render.py
+++ b/tools/schemacode/schemacode/render.py
@@ -149,7 +149,7 @@ def _add_entity(filename_template, entity_pattern, requirement_level):
     return filename_template
 
 
-def make_filename_template(schema, **kwargs):
+def make_filename_template(schema, n_dupes_to_combine=6, **kwargs):
     """Create codeblocks containing example filename patterns for a given datatype.
 
     Parameters
@@ -157,6 +157,9 @@ def make_filename_template(schema, **kwargs):
     schema : dict
         The schema object, which is a dictionary with nested dictionaries and
         lists stored within it.
+    n_dupes_to_combine : int
+        The minimum number of suffixes/extensions to combine in the template as
+        <suffix>/<extension>.
     kwargs : dict
         Keyword arguments used to filter the schema.
         Example kwargs that may be used include: "suffixes", "datatypes",
@@ -220,7 +223,7 @@ def make_filename_template(schema, **kwargs):
 
             # In cases of large numbers of suffixes,
             # we use the "suffix" variable and expect a table later in the spec
-            if len(group["suffixes"]) > 5:
+            if len(group["suffixes"]) >= n_dupes_to_combine:
                 suffix = "_<suffix>"
                 string += suffix
                 strings = [string]
@@ -232,7 +235,7 @@ def make_filename_template(schema, **kwargs):
             extensions = group["extensions"]
             extensions = [ext if ext != "*" else ".<extension>" for ext in extensions]
             extensions = utils.combine_extensions(extensions)
-            if len(extensions) > 5:
+            if len(extensions) >= n_dupes_to_combine:
                 # Combine exts when there are many, but keep JSON separate
                 if ".json" in extensions:
                     extensions = [".<extension>", ".json"]
diff --git a/tools/schemacode/schemacode/utils.py b/tools/schemacode/schemacode/utils.py
index 3b25b2cd61..7505b2e000 100644
--- a/tools/schemacode/schemacode/utils.py
+++ b/tools/schemacode/schemacode/utils.py
@@ -20,29 +20,35 @@ def get_schema_path():
 def combine_extensions(lst):
     """Combine extensions with their compressed versions in a list.
 
-    This is a basic solution to combining extensions with their
-    compressed versions in a list. Something more robust could
-    be written in the future.
+    Valid combinations are hardcoded in the function,
+    since some extensions look like compressed versions of one another, but are not.
 
     Parameters
     ----------
     lst : list of str
+        Raw list of extensions.
+
+    Returns
+    -------
+    new_lst : list of str
+        List of extensions, with compressed and uncompressed versions of the same extension
+        combined.
     """
+    COMPRESSION_EXTENSIONS = [".gz"]
+
     new_lst = []
-    # First, sort by length
-    lst = sorted(lst, key=len)
+    items_to_remove = []
     for item in lst:
-        temp_lst = new_lst[:]
-
-        item_found = False
-        for j, new_item in enumerate(temp_lst):
-            if new_item in item:
-                temp_item = new_item + "[" + item.replace(new_item, "", 1) + "]"
-                new_lst[j] = temp_item
-                item_found = True
-
-        if not item_found:
-            new_lst.append(item)
+        for ext in COMPRESSION_EXTENSIONS:
+            if item.endswith(ext) and item.replace(ext, "") in lst:
+                temp_item = item.replace(ext, "") + "[" + ext + "]"
+                new_lst.append(temp_item)
+                items_to_remove.append(item)
+                items_to_remove.append(item.replace(ext, ""))
+                continue
+
+    items_to_add = [item for item in lst if item not in items_to_remove]
+    new_lst += items_to_add
 
     return new_lst